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Integrating Deep Learning and Synthetic Biology: A Co-Design Approach for Enhancing Gene Expression via N-terminal Coding Sequences (2402.13297v1)
Published 20 Feb 2024 in q-bio.QM and cs.AI
Abstract: N-terminal coding sequence (NCS) influences gene expression by impacting the translation initiation rate. The NCS optimization problem is to find an NCS that maximizes gene expression. The problem is important in genetic engineering. However, current methods for NCS optimization such as rational design and statistics-guided approaches are labor-intensive yield only relatively small improvements. This paper introduces a deep learning/synthetic biology co-designed few-shot training workflow for NCS optimization. Our method utilizes k-nearest encoding followed by word2vec to encode the NCS, then performs feature extraction using attention mechanisms, before constructing a time-series network for predicting gene expression intensity, and finally a direct search algorithm identifies the optimal NCS with limited training data. We took green fluorescent protein (GFP) expressed by Bacillus subtilis as a reporting protein of NCSs, and employed the fluorescence enhancement factor as the metric of NCS optimization. Within just six iterative experiments, our model generated an NCS (MLD62) that increased average GFP expression by 5.41-fold, outperforming the state-of-the-art NCS designs. Extending our findings beyond GFP, we showed that our engineered NCS (MLD62) can effectively boost the production of N-acetylneuraminic acid by enhancing the expression of the crucial rate-limiting GNA1 gene, demonstrating its practical utility. We have open-sourced our NCS expression database and experimental procedures for public use.
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[2020] Ding, N., Yuan, Z., Zhang, X., Chen, J., Zhou, S., Deng, Y.: Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor. Nucleic Acids Research 48(18), 10602–10613 (2020) Lv et al. [2023] Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Bosch, B., DeJesus, M.A., Poulton, N.C., Zhang, W., Engelhart, C.A., Zaveri, A., Lavalette, S., Ruecker, N., Trujillo, C., Wallach, J.B., et al.: Genome-wide gene expression tuning reveals diverse vulnerabilities of m. tuberculosis. Cell 184(17), 4579–4592 (2021) Fu et al. [2022] Fu, G., Yue, J., Li, D., Li, Y., Lee, S.Y., Zhang, D.: An operator-based expression toolkit for bacillus subtilis enables fine-tuning of gene expression and biosynthetic pathway regulation. Proceedings of the National Academy of Sciences 119(11), 2119980119 (2022) Lu et al. [2019] Lu, Z., Yang, S., Yuan, X., Shi, Y., Ouyang, L., Jiang, S., Yi, L., Zhang, G.: Crispr-assisted multi-dimensional regulation for fine-tuning gene expression in bacillus subtilis. Nucleic acids research 47(7), 40–40 (2019) Ding et al. [2020] Ding, N., Yuan, Z., Zhang, X., Chen, J., Zhou, S., Deng, Y.: Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor. Nucleic Acids Research 48(18), 10602–10613 (2020) Lv et al. [2023] Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Fu, G., Yue, J., Li, D., Li, Y., Lee, S.Y., Zhang, D.: An operator-based expression toolkit for bacillus subtilis enables fine-tuning of gene expression and biosynthetic pathway regulation. Proceedings of the National Academy of Sciences 119(11), 2119980119 (2022) Lu et al. [2019] Lu, Z., Yang, S., Yuan, X., Shi, Y., Ouyang, L., Jiang, S., Yi, L., Zhang, G.: Crispr-assisted multi-dimensional regulation for fine-tuning gene expression in bacillus subtilis. Nucleic acids research 47(7), 40–40 (2019) Ding et al. [2020] Ding, N., Yuan, Z., Zhang, X., Chen, J., Zhou, S., Deng, Y.: Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor. Nucleic Acids Research 48(18), 10602–10613 (2020) Lv et al. [2023] Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Lu, Z., Yang, S., Yuan, X., Shi, Y., Ouyang, L., Jiang, S., Yi, L., Zhang, G.: Crispr-assisted multi-dimensional regulation for fine-tuning gene expression in bacillus subtilis. Nucleic acids research 47(7), 40–40 (2019) Ding et al. [2020] Ding, N., Yuan, Z., Zhang, X., Chen, J., Zhou, S., Deng, Y.: Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor. Nucleic Acids Research 48(18), 10602–10613 (2020) Lv et al. [2023] Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Ding, N., Yuan, Z., Zhang, X., Chen, J., Zhou, S., Deng, Y.: Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor. Nucleic Acids Research 48(18), 10602–10613 (2020) Lv et al. [2023] Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. 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[2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. 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ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. 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[2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. 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The American Statistician 48(2), 88–91 (1994) Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
- Bosch, B., DeJesus, M.A., Poulton, N.C., Zhang, W., Engelhart, C.A., Zaveri, A., Lavalette, S., Ruecker, N., Trujillo, C., Wallach, J.B., et al.: Genome-wide gene expression tuning reveals diverse vulnerabilities of m. tuberculosis. Cell 184(17), 4579–4592 (2021) Fu et al. [2022] Fu, G., Yue, J., Li, D., Li, Y., Lee, S.Y., Zhang, D.: An operator-based expression toolkit for bacillus subtilis enables fine-tuning of gene expression and biosynthetic pathway regulation. Proceedings of the National Academy of Sciences 119(11), 2119980119 (2022) Lu et al. [2019] Lu, Z., Yang, S., Yuan, X., Shi, Y., Ouyang, L., Jiang, S., Yi, L., Zhang, G.: Crispr-assisted multi-dimensional regulation for fine-tuning gene expression in bacillus subtilis. Nucleic acids research 47(7), 40–40 (2019) Ding et al. [2020] Ding, N., Yuan, Z., Zhang, X., Chen, J., Zhou, S., Deng, Y.: Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor. 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[2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Fu, G., Yue, J., Li, D., Li, Y., Lee, S.Y., Zhang, D.: An operator-based expression toolkit for bacillus subtilis enables fine-tuning of gene expression and biosynthetic pathway regulation. Proceedings of the National Academy of Sciences 119(11), 2119980119 (2022) Lu et al. [2019] Lu, Z., Yang, S., Yuan, X., Shi, Y., Ouyang, L., Jiang, S., Yi, L., Zhang, G.: Crispr-assisted multi-dimensional regulation for fine-tuning gene expression in bacillus subtilis. Nucleic acids research 47(7), 40–40 (2019) Ding et al. [2020] Ding, N., Yuan, Z., Zhang, X., Chen, J., Zhou, S., Deng, Y.: Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor. Nucleic Acids Research 48(18), 10602–10613 (2020) Lv et al. [2023] Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Lu, Z., Yang, S., Yuan, X., Shi, Y., Ouyang, L., Jiang, S., Yi, L., Zhang, G.: Crispr-assisted multi-dimensional regulation for fine-tuning gene expression in bacillus subtilis. Nucleic acids research 47(7), 40–40 (2019) Ding et al. [2020] Ding, N., Yuan, Z., Zhang, X., Chen, J., Zhou, S., Deng, Y.: Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor. Nucleic Acids Research 48(18), 10602–10613 (2020) Lv et al. [2023] Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. 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Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. 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[2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. 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[2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. 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The American Statistician 48(2), 88–91 (1994) Ding, N., Yuan, Z., Zhang, X., Chen, J., Zhou, S., Deng, Y.: Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor. Nucleic Acids Research 48(18), 10602–10613 (2020) Lv et al. [2023] Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. 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[2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
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[2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Ding, N., Yuan, Z., Zhang, X., Chen, J., Zhou, S., Deng, Y.: Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor. Nucleic Acids Research 48(18), 10602–10613 (2020) Lv et al. [2023] Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Lv, X., Li, Y., Xiu, X., Liao, C., Xu, Y., Liu, Y., Li, J., Du, G., Liu, L.: Crispr genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnology Advances, 108261 (2023) Yang et al. [2017] Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. 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[2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. 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[2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. 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[2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. 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[2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. 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[2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
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[2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Yang, S., Du, G., Chen, J., Kang, Z.: Characterization and application of endogenous phase-dependent promoters in bacillus subtilis. Applied microbiology and biotechnology 101, 4151–4161 (2017) Tian et al. [2019] Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. 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Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. 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[2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. 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ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. 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[2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. 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[2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. 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The American Statistician 48(2), 88–91 (1994) Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. 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The American Statistician 48(2), 88–91 (1994) Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
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[2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
- Tian, R., Liu, Y., Chen, J., Li, J., Liu, L., Du, G., Chen, J.: Synthetic n-terminal coding sequences for fine-tuning gene expression and metabolic engineering in bacillus subtilis. Metabolic engineering 55, 131–141 (2019) Fredrick and Ibba [2010] Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Fredrick, K., Ibba, M.: How the sequence of a gene can tune its translation. Cell 141(2), 227–229 (2010) Tian et al. [2020] Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Tian, R., Liu, Y., Cao, Y., Zhang, Z., Li, J., Liu, L., Du, G., Chen, J.: Titrating bacterial growth and chemical biosynthesis for efficient n-acetylglucosamine and n-acetylneuraminic acid bioproduction. Nature Communications 11(1), 5078 (2020) Zhao et al. [2021] Zhao, H., Ding, W., Zang, J., Yang, Y., Liu, C., Hu, L., Chen, Y., Liu, G., Fang, Y., Yuan, Y., et al.: Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction. Nature Communications 12(1), 7039 (2021) Stork et al. [2021] Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. 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[2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. 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[2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. 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The American Statistician 48(2), 88–91 (1994) Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. 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ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. 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The American Statistician 48(2), 88–91 (1994) Stork, D.A., Squyres, G.R., Kuru, E., Gromek, K.A., Rittichier, J., Jog, A., Burton, B.M., Church, G.M., Garner, E.C., Kunjapur, A.M.: Designing efficient genetic code expansion in bacillus subtilis to gain biological insights. Nature Communications 12(1), 5429 (2021) Cambray et al. [2018] Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. 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The American Statistician 48(2), 88–91 (1994) Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. 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[2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. 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The American Statistician 48(2), 88–91 (1994) Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
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The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. 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Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
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The American Statistician 48(2), 88–91 (1994) Cambray, G., Guimaraes, J.C., Arkin, A.P.: Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in escherichia coli. Nature biotechnology 36(10), 1005–1015 (2018) Goodman et al. [2013] Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. [2017] Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Goodman, D.B., Church, G.M., Kosuri, S.: Causes and effects of n-terminal codon bias in bacterial genes. Science 342(6157), 475–479 (2013) Kudla et al. [2009] Kudla, G., Murray, A.W., Tollervey, D., Plotkin, J.B.: Coding-sequence determinants of gene expression in escherichia coli. science 324(5924), 255–258 (2009) Espah Borujeni et al. 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The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. 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Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
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Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. 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[2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., Salis, H.M.: Precise quantification of translation inhibition by mrna structures that overlap with the ribosomal footprint in n-terminal coding sequences. Nucleic acids research 45(9), 5437–5448 (2017) Wang et al. [2022] Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. 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The American Statistician 48(2), 88–91 (1994) Wang, C., Zhang, W., Tian, R., Zhang, J., Zhang, L., Deng, Z., Lv, X., Li, J., Liu, L., Du, G., et al.: Model-driven design of synthetic n-terminal coding sequences for regulating gene expression in yeast and bacteria. Biotechnology Journal 17(5), 2100655 (2022) Rong [2014] Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. 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Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. 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The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. 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[2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. 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Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
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[2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Rong, X.: word2vec parameter learning explained. arXiv preprint arXiv:1411.2738 (2014) Vaswani et al. [2017] Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
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- Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A.N., Kaiser, Ł., Polosukhin, I.: Attention is all you need. Advances in neural information processing systems 30 (2017) Graves and Graves [2012] Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
- Graves, A., Graves, A.: Long short-term memory. Supervised sequence labelling with recurrent neural networks, 37–45 (2012) Liu et al. [2020] Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
- Liu, J., Wu, X., Yao, M., Xiao, W., Zha, J.: Chassis engineering for microbial production of chemicals: from natural microbes to synthetic organisms. Current Opinion in Biotechnology 66, 105–112 (2020) Gu et al. [2018] Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
- Gu, Y., Xu, X., Wu, Y., Niu, T., Liu, Y., Li, J., Du, G., Liu, L.: Advances and prospects of bacillus subtilis cellular factories: from rational design to industrial applications. Metabolic engineering 50, 109–121 (2018) Xu et al. [2021] Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
- Xu, K., Tong, Y., Li, Y., Tao, J., Li, J., Zhou, J., Liu, S.: Rational design of the n-terminal coding sequence for regulating enzyme expression in bacillus subtilis. ACS Synthetic Biology 10(2), 265–276 (2021) Pukelsheim [1994] Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994) Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
- Pukelsheim, F.: The three sigma rule. The American Statistician 48(2), 88–91 (1994)
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