메뉴 건너뛰기




Volumn 64, Issue , 2020, Pages 1-9

Machine learning applications in systems metabolic engineering

Author keywords

[No Author keywords available]

Indexed keywords

BIG DATA; MACHINE LEARNING; METABOLISM; STRAIN;

EID: 85072703976     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2019.08.010     Document Type: Review
Times cited : (129)

References (70)
  • 1
    • 85022334903 scopus 로고    scopus 로고
    • Systems metabolic engineering as an enabling technology in accomplishing sustainable development goals
    • Yang, D., Cho, J.S., Choi, K.R., Kim, H.U., Lee, S.Y., Systems metabolic engineering as an enabling technology in accomplishing sustainable development goals. Microb Biotechnol 10 (2017), 1254–1258.
    • (2017) Microb Biotechnol , vol.10 , pp. 1254-1258
    • Yang, D.1    Cho, J.S.2    Choi, K.R.3    Kim, H.U.4    Lee, S.Y.5
  • 2
    • 84943604629 scopus 로고    scopus 로고
    • Systems strategies for developing industrial microbial strains
    • Lee, S.Y., Kim, H.U., Systems strategies for developing industrial microbial strains. Nat Biotechnol 33 (2015), 1061–1072.
    • (2015) Nat Biotechnol , vol.33 , pp. 1061-1072
    • Lee, S.Y.1    Kim, H.U.2
  • 3
    • 85061013548 scopus 로고    scopus 로고
    • Systems metabolic engineering strategies: integrating systems and synthetic biology with metabolic engineering
    • This paper reviews the state-of-the-art methods and strategies in systems metabolic engineering, which cover the project design, selection of host strains, metabolic pathway reconstruction, tolerance enhancement, metabolic flux optimization, fermentation, recovery, purification, and scale-up.
    • Choi, K.R., Jang, W.D., Yang, D., Cho, J.S., Park, D., Lee, S.Y., Systems metabolic engineering strategies: integrating systems and synthetic biology with metabolic engineering. Trends Biotechnol 37 (2019), 817–837 This paper reviews the state-of-the-art methods and strategies in systems metabolic engineering, which cover the project design, selection of host strains, metabolic pathway reconstruction, tolerance enhancement, metabolic flux optimization, fermentation, recovery, purification, and scale-up.
    • (2019) Trends Biotechnol , vol.37 , pp. 817-837
    • Choi, K.R.1    Jang, W.D.2    Yang, D.3    Cho, J.S.4    Park, D.5    Lee, S.Y.6
  • 5
    • 85064803940 scopus 로고    scopus 로고
    • From genotype to phenotype: augmenting deep learning with networks and systems biology
    • Gazestani, V.H., Lewis, N.E., From genotype to phenotype: augmenting deep learning with networks and systems biology. Curr Opin Syst Biol 15 (2019), 68–73.
    • (2019) Curr Opin Syst Biol , vol.15 , pp. 68-73
    • Gazestani, V.H.1    Lewis, N.E.2
  • 6
    • 85065410633 scopus 로고    scopus 로고
    • Systems metabolic engineering meets machine learning: a new era for data-driven metabolic engineering
    • Presnell, K.V., Alper, H.S., Systems metabolic engineering meets machine learning: a new era for data-driven metabolic engineering. Biotechnol J, 2019, e1800416.
    • (2019) Biotechnol J
    • Presnell, K.V.1    Alper, H.S.2
  • 8
    • 84979984875 scopus 로고    scopus 로고
    • Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites
    • Kim, H.U., Charusanti, P., Lee, S.Y., Weber, T., Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites. Nat Prod Rep 33 (2016), 933–941.
    • (2016) Nat Prod Rep , vol.33 , pp. 933-941
    • Kim, H.U.1    Charusanti, P.2    Lee, S.Y.3    Weber, T.4
  • 9
    • 85064489973 scopus 로고    scopus 로고
    • DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns
    • Clauwaert, J., Menschaert, G., Waegeman, W., DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns. Nucleic Acids Res, 47, 2019, e36.
    • (2019) Nucleic Acids Res , vol.47
    • Clauwaert, J.1    Menschaert, G.2    Waegeman, W.3
  • 10
    • 85072699177 scopus 로고    scopus 로고
    • Genome functional annotation across species using deep convolutional neural networks
    • 330308
    • Khodabandelou, G., Routhier, E., Mozziconacci, J., Genome functional annotation across species using deep convolutional neural networks. bioRxiv, 2019 330308.
    • (2019) bioRxiv
    • Khodabandelou, G.1    Routhier, E.2    Mozziconacci, J.3
  • 11
    • 85068580079 scopus 로고    scopus 로고
    • Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers
    • DeepEC allows high-quality and high-throughput prediction of enzyme commission (EC) numbers using a protein sequence as an input, which is critical for understanding enzyme functions and metabolism.
    • Ryu, J.Y., Kim, H.U., Lee, S.Y., Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers. Proc Natl Acad Sci U S A 116 (2019), 13996–14001 DeepEC allows high-quality and high-throughput prediction of enzyme commission (EC) numbers using a protein sequence as an input, which is critical for understanding enzyme functions and metabolism.
    • (2019) Proc Natl Acad Sci U S A , vol.116 , pp. 13996-14001
    • Ryu, J.Y.1    Kim, H.U.2    Lee, S.Y.3
  • 13
    • 85034608709 scopus 로고    scopus 로고
    • Recent development of computational resources for new antibiotics discovery
    • Kim, H.U., Blin, K., Lee, S.Y., Weber, T., Recent development of computational resources for new antibiotics discovery. Curr Opin Microbiol 39 (2017), 113–120.
    • (2017) Curr Opin Microbiol , vol.39 , pp. 113-120
    • Kim, H.U.1    Blin, K.2    Lee, S.Y.3    Weber, T.4
  • 15
    • 85023161576 scopus 로고    scopus 로고
    • PRISM 3: expanded prediction of natural product chemical structures from microbial genomes
    • Skinnider, M.A., Merwin, N.J., Johnston, C.W., Magarvey, N.A., PRISM 3: expanded prediction of natural product chemical structures from microbial genomes. Nucleic Acids Res 45 (2017), W49–W54.
    • (2017) Nucleic Acids Res , vol.45 , pp. W49-W54
    • Skinnider, M.A.1    Merwin, N.J.2    Johnston, C.W.3    Magarvey, N.A.4
  • 17
    • 85067169925 scopus 로고    scopus 로고
    • Retrosynthetic design of metabolic pathways to chemicals not found in nature
    • Lin, G.-M., Warden-Rothman, R., Voigt, C.A., Retrosynthetic design of metabolic pathways to chemicals not found in nature. Curr Opin Syst Biol 14 (2019), 82–107.
    • (2019) Curr Opin Syst Biol , vol.14 , pp. 82-107
    • Lin, G.-M.1    Warden-Rothman, R.2    Voigt, C.A.3
  • 18
    • 85044660186 scopus 로고    scopus 로고
    • Planning chemical syntheses with deep neural networks and symbolic AI
    • This study explores the power of Monte Carlo tree search (MCTS) combined with three different neural networks to design retrosynthetic routes of various target chemicals. Double-blind AB test performed in this study shows that MCTS-driven routes are considered to be as reasonable as those reported in literature.
    • Segler, M.H.S., Preuss, M., Waller, M.P., Planning chemical syntheses with deep neural networks and symbolic AI. Nature 555 (2018), 604–610 This study explores the power of Monte Carlo tree search (MCTS) combined with three different neural networks to design retrosynthetic routes of various target chemicals. Double-blind AB test performed in this study shows that MCTS-driven routes are considered to be as reasonable as those reported in literature.
    • (2018) Nature , vol.555 , pp. 604-610
    • Segler, M.H.S.1    Preuss, M.2    Waller, M.P.3
  • 19
    • 84883001788 scopus 로고    scopus 로고
    • Production of bulk chemicals via novel metabolic pathways in microorganisms
    • Shin, J.H., Kim, H.U., Kim, D.I., Lee, S.Y., Production of bulk chemicals via novel metabolic pathways in microorganisms. Biotechnol Adv 31 (2013), 925–935.
    • (2013) Biotechnol Adv , vol.31 , pp. 925-935
    • Shin, J.H.1    Kim, H.U.2    Kim, D.I.3    Lee, S.Y.4
  • 20
    • 84936966835 scopus 로고    scopus 로고
    • Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways
    • Hadadi, N., Hatzimanikatis, V., Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. Curr Opin Chem Biol 28 (2015), 99–104.
    • (2015) Curr Opin Chem Biol , vol.28 , pp. 99-104
    • Hadadi, N.1    Hatzimanikatis, V.2
  • 24
    • 84975246102 scopus 로고    scopus 로고
    • Semisupervised Gaussian process for automated enzyme search
    • Mellor, J., Grigoras, I., Carbonell, P., Faulon, J.L., Semisupervised Gaussian process for automated enzyme search. ACS Synth Biol 5 (2016), 518–528.
    • (2016) ACS Synth Biol , vol.5 , pp. 518-528
    • Mellor, J.1    Grigoras, I.2    Carbonell, P.3    Faulon, J.L.4
  • 26
    • 85065511410 scopus 로고    scopus 로고
    • Machine learning-assisted directed protein evolution with combinatorial libraries
    • Machine learning-assisted directed evolution was shown to reach protein variants having the highest fitness more efficiently than representative existing directed evolution approaches, ‘single mutation walk’ and ‘recombining mutations in best variants’. Application of the machine learning-assisted approach was also successfully applied to evolving an enzyme for the selective synthesis of enantiomeric products.
    • Wu, Z., Kan, S.B.J., Lewis, R.D., Wittmann, B.J., Arnold, F.H., Machine learning-assisted directed protein evolution with combinatorial libraries. Proc Natl Acad Sci U S A 116 (2019), 8852–8858 Machine learning-assisted directed evolution was shown to reach protein variants having the highest fitness more efficiently than representative existing directed evolution approaches, ‘single mutation walk’ and ‘recombining mutations in best variants’. Application of the machine learning-assisted approach was also successfully applied to evolving an enzyme for the selective synthesis of enantiomeric products.
    • (2019) Proc Natl Acad Sci U S A , vol.116 , pp. 8852-8858
    • Wu, Z.1    Kan, S.B.J.2    Lewis, R.D.3    Wittmann, B.J.4    Arnold, F.H.5
  • 27
    • 77952753917 scopus 로고    scopus 로고
    • Machine learning methods for protein structure prediction
    • Cheng, J., Tegge, A.N., Baldi, P., Machine learning methods for protein structure prediction. IEEE Rev Biomed Eng 1 (2008), 41–49.
    • (2008) IEEE Rev Biomed Eng , vol.1 , pp. 41-49
    • Cheng, J.1    Tegge, A.N.2    Baldi, P.3
  • 28
    • 85064397545 scopus 로고    scopus 로고
    • End-to-end differentiable learning of protein structure
    • e293
    • AlQuraishi, M., End-to-end differentiable learning of protein structure. Cell Syst 8 (2019), 292–301 e293.
    • (2019) Cell Syst , vol.8 , pp. 292-301
    • AlQuraishi, M.1
  • 29
    • 85069435877 scopus 로고    scopus 로고
    • Machine-learning-guided directed evolution for protein engineering
    • Yang, K.K., Wu, Z., Arnold, F.H., Machine-learning-guided directed evolution for protein engineering. Nat Methods 16 (2019), 687–694.
    • (2019) Nat Methods , vol.16 , pp. 687-694
    • Yang, K.K.1    Wu, Z.2    Arnold, F.H.3
  • 31
    • 84875670972 scopus 로고    scopus 로고
    • Quantitative design of regulatory elements based on high-precision strength prediction using artificial neural network
    • Meng, H., Wang, J., Xiong, Z., Xu, F., Zhao, G., Wang, Y., Quantitative design of regulatory elements based on high-precision strength prediction using artificial neural network. PLoS One, 8, 2013, e60288.
    • (2013) PLoS One , vol.8
    • Meng, H.1    Wang, J.2    Xiong, Z.3    Xu, F.4    Zhao, G.5    Wang, Y.6
  • 35
    • 85019592417 scopus 로고    scopus 로고
    • sgRNA Scorer 2.0: a species-independent model to predict CRISPR/Cas9 activity
    • Chari, R., Yeo, N.C., Chavez, A., Church, G.M., sgRNA Scorer 2.0: a species-independent model to predict CRISPR/Cas9 activity. ACS Synth Biol 6 (2017), 902–904.
    • (2017) ACS Synth Biol , vol.6 , pp. 902-904
    • Chari, R.1    Yeo, N.C.2    Chavez, A.3    Church, G.M.4
  • 37
    • 85045642536 scopus 로고    scopus 로고
    • MiYA, an efficient machine-learning workflow in conjunction with the YeastFab assembly strategy for combinatorial optimization of heterologous metabolic pathways in Saccharomyces cerevisiae
    • A Machine-learning workflow in conjunction with YeastFab Assembly strategy (MiYA) was developed to accelerate the optimization procedure of heterologous biosynthetic pathways in Saccharomyces cerevisiae. The MiYA was validated by experimentally producing β-carotene and violacein using S. cerevisiae, which require the expression of heterologous genes.
    • Zhou, Y., Li, G., Dong, J., Xing, X.H., Dai, J., Zhang, C., MiYA, an efficient machine-learning workflow in conjunction with the YeastFab assembly strategy for combinatorial optimization of heterologous metabolic pathways in Saccharomyces cerevisiae. Metab Eng 47 (2018), 294–302 A Machine-learning workflow in conjunction with YeastFab Assembly strategy (MiYA) was developed to accelerate the optimization procedure of heterologous biosynthetic pathways in Saccharomyces cerevisiae. The MiYA was validated by experimentally producing β-carotene and violacein using S. cerevisiae, which require the expression of heterologous genes.
    • (2018) Metab Eng , vol.47 , pp. 294-302
    • Zhou, Y.1    Li, G.2    Dong, J.3    Xing, X.H.4    Dai, J.5    Zhang, C.6
  • 39
    • 84930227327 scopus 로고    scopus 로고
    • Using genome-scale models to predict biological capabilities
    • O'Brien, E.J., Monk, J.M., Palsson, B.O., Using genome-scale models to predict biological capabilities. Cell 161 (2015), 971–987.
    • (2015) Cell , vol.161 , pp. 971-987
    • O'Brien, E.J.1    Monk, J.M.2    Palsson, B.O.3
  • 43
    • 84864584520 scopus 로고    scopus 로고
    • Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters
    • Adadi, R., Volkmer, B., Milo, R., Heinemann, M., Shlomi, T., Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters. PLoS Comput Biol, 8, 2012, e1002575.
    • (2012) PLoS Comput Biol , vol.8
    • Adadi, R.1    Volkmer, B.2    Milo, R.3    Heinemann, M.4    Shlomi, T.5
  • 45
    • 85052702486 scopus 로고    scopus 로고
    • A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data
    • Costello, Z., Martin, H.G., A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data. NPJ Syst Biol Appl, 4, 2018, 19.
    • (2018) NPJ Syst Biol Appl , vol.4 , pp. 19
    • Costello, Z.1    Martin, H.G.2
  • 46
    • 85044948558 scopus 로고    scopus 로고
    • Using deep learning to model the hierarchical structure and function of a cell
    • A deep neural network model, called DCell, was developed to structurally mimic biological hierarchy of Saccharomyces cerevisiae in terms of the Gene Ontology. DCell accurately simulates the S. cerevisiae phenotype, and also allows examining molecular mechanisms behind genotype–phenotype associations through the DCell's model structure.
    • Ma, J., Yu, M.K., Fong, S., Ono, K., Sage, E., Demchak, B., Sharan, R., Ideker, T., Using deep learning to model the hierarchical structure and function of a cell. Nat Methods 15 (2018), 290–298 A deep neural network model, called DCell, was developed to structurally mimic biological hierarchy of Saccharomyces cerevisiae in terms of the Gene Ontology. DCell accurately simulates the S. cerevisiae phenotype, and also allows examining molecular mechanisms behind genotype–phenotype associations through the DCell's model structure.
    • (2018) Nat Methods , vol.15 , pp. 290-298
    • Ma, J.1    Yu, M.K.2    Fong, S.3    Ono, K.4    Sage, E.5    Demchak, B.6    Sharan, R.7    Ideker, T.8
  • 49
    • 85010817822 scopus 로고    scopus 로고
    • Artificial neural network – genetic algorithm to optimize wheat germ fermentation condition: application to the production of two anti-tumor benzoquinones
    • Zheng, Z.Y., Guo, X.N., Zhu, K.X., Peng, W., Zhou, H.M., Artificial neural network – genetic algorithm to optimize wheat germ fermentation condition: application to the production of two anti-tumor benzoquinones. Food Chem 227 (2017), 264–270.
    • (2017) Food Chem , vol.227 , pp. 264-270
    • Zheng, Z.Y.1    Guo, X.N.2    Zhu, K.X.3    Peng, W.4    Zhou, H.M.5
  • 50
    • 85007199207 scopus 로고    scopus 로고
    • Optimization of bioethanol production from sorghum grains using artificial neural networks integrated with ant colony
    • Sebayang, A.H., Masjuki, H.H., Ong, H.C., Dharma, S., Silitonga, A.S., Kusumo, F., Milano, J., Optimization of bioethanol production from sorghum grains using artificial neural networks integrated with ant colony. Ind Crops Prod 97 (2017), 146–155.
    • (2017) Ind Crops Prod , vol.97 , pp. 146-155
    • Sebayang, A.H.1    Masjuki, H.H.2    Ong, H.C.3    Dharma, S.4    Silitonga, A.S.5    Kusumo, F.6    Milano, J.7
  • 51
    • 85010781177 scopus 로고    scopus 로고
    • Artificial neural network and regression coupled genetic algorithm to optimize parameters for enhanced xylitol production by Debaryomyces nepalensis in bioreactor
    • Pappu, S.M.J., Gummadi, S.N., Artificial neural network and regression coupled genetic algorithm to optimize parameters for enhanced xylitol production by Debaryomyces nepalensis in bioreactor. Biochem Eng J 120 (2017), 136–145.
    • (2017) Biochem Eng J , vol.120 , pp. 136-145
    • Pappu, S.M.J.1    Gummadi, S.N.2
  • 53
    • 85066975467 scopus 로고    scopus 로고
    • Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima
    • A set of linear and nonlinear regression models are examined to select the one that best performs for predicting the optimal growth temperature (OGT) of microorganisms and optimal catalytic temperature of enzymes. Support vector regression and random forest performed the best for each case, respectively.
    • Li, G., Rabe, K.S., Nielsen, J., Engqvist, M.K.M., Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima. ACS Synth Biol 8 (2019), 1411–1420 A set of linear and nonlinear regression models are examined to select the one that best performs for predicting the optimal growth temperature (OGT) of microorganisms and optimal catalytic temperature of enzymes. Support vector regression and random forest performed the best for each case, respectively.
    • (2019) ACS Synth Biol , vol.8 , pp. 1411-1420
    • Li, G.1    Rabe, K.S.2    Nielsen, J.3    Engqvist, M.K.M.4
  • 54
    • 85067668950 scopus 로고    scopus 로고
    • Predicting the optimal growth temperatures of prokaryotes using only genome derived features
    • Sauer, D.B., Wang, D.N., Predicting the optimal growth temperatures of prokaryotes using only genome derived features. Bioinformatics 35 (2019), 3224–3231.
    • (2019) Bioinformatics , vol.35 , pp. 3224-3231
    • Sauer, D.B.1    Wang, D.N.2
  • 56
    • 85020710659 scopus 로고    scopus 로고
    • Engineering biological systems using automated biofoundries
    • Chao, R., Mishra, S., Si, T., Zhao, H., Engineering biological systems using automated biofoundries. Metab Eng 42 (2017), 98–108.
    • (2017) Metab Eng , vol.42 , pp. 98-108
    • Chao, R.1    Mishra, S.2    Si, T.3    Zhao, H.4
  • 61
    • 85072703706 scopus 로고    scopus 로고
    • Methods and systems for engineering collagen. PCT patent 2019, WO2019103981A1.
    • Persikov AV, Ouzounov N, Lorestani A: Methods and systems for engineering collagen. PCT patent 2019, WO2019103981A1.
    • Persikov, A.V.1    Ouzounov, N.2    Lorestani, A.3
  • 62
    • 85072695504 scopus 로고    scopus 로고
    • Multifactorial process optimisation method and system. US patent 2017, US20170016079A1.
    • Gershater MC, Ward SM, Sadowski MI, Grant CR: Multifactorial process optimisation method and system. US patent 2017, US20170016079A1.
    • Gershater, M.C.1    Ward, S.M.2    Sadowski, M.I.3    Grant, C.R.4
  • 63
    • 85054892364 scopus 로고    scopus 로고
    • Efficient flexible backbone protein-protein docking for challenging targets
    • Marze, N.A., Roy Burman, S.S., Sheffler, W., Gray, J.J., Efficient flexible backbone protein-protein docking for challenging targets. Bioinformatics 34 (2018), 3461–3469.
    • (2018) Bioinformatics , vol.34 , pp. 3461-3469
    • Marze, N.A.1    Roy Burman, S.S.2    Sheffler, W.3    Gray, J.J.4
  • 64
    • 85072690809 scopus 로고    scopus 로고
    • Knight Jr TF, Rettberg RD: Methods and systems for cell state quantification. US patent 2016, US9506167B2.
    • Shetty R, Knight Jr TF, Rettberg RD: Methods and systems for cell state quantification. US patent 2016, US9506167B2.
    • Shetty, R.1
  • 68
    • 85072690788 scopus 로고    scopus 로고
    • Von Maltzahn GA, Berendes R, Jeck EM, Knight BL, Raymond RA, Trivisvavet P, Wong JYH, Rajdev NH, Meunier M-CJ: Machine learning in agricultural planting, growing, and harvesting contexts. US patent 2019, US20190050948A1.
    • Perry DP, Von Maltzahn GA, Berendes R, Jeck EM, Knight BL, Raymond RA, Trivisvavet P, Wong JYH, Rajdev NH, Meunier M-CJ: Machine learning in agricultural planting, growing, and harvesting contexts. US patent 2019, US20190050948A1.
    • Perry, D.P.1
  • 69
    • 85072714882 scopus 로고    scopus 로고
    • Enhanced nucleic acid constructs for eukaryotic gene expression. US patent 2017, US9534234B2.
    • Minshull J, Welch M, Govindrajan S, Caves K: Enhanced nucleic acid constructs for eukaryotic gene expression. US patent 2017, US9534234B2.
    • Minshull, J.1    Welch, M.2    Govindrajan, S.3    Caves, K.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.