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For: Wang L, Dash S, Ng CY, Maranas CD. A review of computational tools for design and reconstruction of metabolic pathways. Synth Syst Biotechnol 2017;2:243-252. [PMID: 29552648 PMCID: PMC5851934 DOI: 10.1016/j.synbio.2017.11.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 11/28/2022]  Open
Number Cited by Other Article(s)
1
Sveshnikova A, Oftadeh O, Hatzimanikatis V. Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking. Nat Commun 2025;16:4839. [PMID: 40413182 PMCID: PMC12103536 DOI: 10.1038/s41467-025-59827-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 05/06/2025] [Indexed: 05/27/2025]  Open
2
Chen A, Peng X, Shen T, Zheng L, Wu D, Wang S. Discovery, design, and engineering of enzymes based on molecular retrobiosynthesis. MLIFE 2025;4:107-125. [PMID: 40313979 PMCID: PMC12042125 DOI: 10.1002/mlf2.70009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2024] [Revised: 02/06/2025] [Accepted: 02/13/2025] [Indexed: 05/03/2025]
3
Basnet BB, Zhou ZY, Wei B, Wang H. Advances in AI-based strategies and tools to facilitate natural product and drug development. Crit Rev Biotechnol 2025:1-32. [PMID: 40159111 DOI: 10.1080/07388551.2025.2478094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2024] [Revised: 02/11/2025] [Accepted: 02/16/2025] [Indexed: 04/02/2025]
4
De Florio M, Zou Z, Schiavazzi DE, Karniadakis GE. Quantification of total uncertainty in the physics-informed reconstruction of CVSim-6 physiology. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2025;383:20240221. [PMID: 40078150 DOI: 10.1098/rsta.2024.0221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 10/23/2024] [Accepted: 11/11/2024] [Indexed: 03/14/2025]
5
Yook S, Alper HS. Recent advances in genetic engineering and chemical production in yeast species. FEMS Yeast Res 2025;25:foaf009. [PMID: 40082732 PMCID: PMC11963765 DOI: 10.1093/femsyr/foaf009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 03/07/2025] [Accepted: 03/11/2025] [Indexed: 03/16/2025]  Open
6
Scott H, Segrè D. Metabolic Flux Modeling in Marine Ecosystems. ANNUAL REVIEW OF MARINE SCIENCE 2025;17:593-620. [PMID: 39259978 DOI: 10.1146/annurev-marine-032123-033718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
7
Guo F, Liu K, Qiao Y, Zheng Y, Liu C, Wu Y, Zhang Z, Jiang W, Jiang Y, Xin F, Jiang M, Zhang W. Evolutionary engineering of Saccharomyces cerevisiae: Crafting a synthetic methylotroph via self-reprogramming. SCIENCE ADVANCES 2024;10:eadq3484. [PMID: 39705340 DOI: 10.1126/sciadv.adq3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 11/18/2024] [Indexed: 12/22/2024]
8
Hosoda S, Iwata H, Miura T, Tanabe M, Okada T, Mochizuki A, Sato M. BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks. BMC Bioinformatics 2024;25:297. [PMID: 39256657 PMCID: PMC11389226 DOI: 10.1186/s12859-024-05921-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 09/04/2024] [Indexed: 09/12/2024]  Open
9
Huang Y, Ma T, Wan Z, Zhong C, Wang J. AFP: Finding pathways accounting for stoichiometry along with atom group tracking in metabolic network. J Biotechnol 2024;392:139-151. [PMID: 39009230 DOI: 10.1016/j.jbiotec.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 04/29/2024] [Accepted: 07/08/2024] [Indexed: 07/17/2024]
10
De Florio M, Zou Z, Schiavazzi DE, Karniadakis GE. Quantification of total uncertainty in the physics-informed reconstruction of CVSim-6 physiology. ARXIV 2024:arXiv:2408.07201v1. [PMID: 39184536 PMCID: PMC11343238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
11
Ferreira S, Balola A, Sveshnikova A, Hatzimanikatis V, Vilaça P, Maia P, Carreira R, Stoney R, Carbonell P, Souza CS, Correia J, Lousa D, Soares CM, Rocha I. Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli. Front Bioeng Biotechnol 2024;12:1360740. [PMID: 38978715 PMCID: PMC11228882 DOI: 10.3389/fbioe.2024.1360740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 06/03/2024] [Indexed: 07/10/2024]  Open
12
Siddharth T, Lewis NE. Predicting pathways for old and new metabolites through clustering. J Theor Biol 2024;578:111684. [PMID: 38048983 PMCID: PMC11139542 DOI: 10.1016/j.jtbi.2023.111684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/17/2023] [Accepted: 11/29/2023] [Indexed: 12/06/2023]
13
Meng W, Pan H, Sha Y, Zhai X, Xing A, Lingampelly SS, Sripathi SR, Wang Y, Li K. Metabolic Connectome and Its Role in the Prediction, Diagnosis, and Treatment of Complex Diseases. Metabolites 2024;14:93. [PMID: 38392985 PMCID: PMC10890086 DOI: 10.3390/metabo14020093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/17/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024]  Open
14
Kumari P, Deepa N, Trivedi PK, Singh BK, Srivastava V, Singh A. Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites. Microb Cell Fact 2023;22:226. [PMID: 37925404 PMCID: PMC10625306 DOI: 10.1186/s12934-023-02234-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023]  Open
15
Qiu S, Yang A, Zeng H. Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook. PLoS Comput Biol 2023;19:e1011391. [PMID: 37619239 PMCID: PMC10449171 DOI: 10.1371/journal.pcbi.1011391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]  Open
16
Upadhyay V, Boorla VS, Maranas CD. Rank-ordering of known enzymes as starting points for re-engineering novel substrate activity using a convolutional neural network. Metab Eng 2023;78:171-182. [PMID: 37301359 DOI: 10.1016/j.ymben.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/19/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
17
Gurdo N, Volke DC, McCloskey D, Nikel PI. Automating the design-build-test-learn cycle towards next-generation bacterial cell factories. N Biotechnol 2023;74:1-15. [PMID: 36736693 DOI: 10.1016/j.nbt.2023.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/15/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023]
18
Tan Z, Li J, Hou J, Gonzalez R. Designing artificial pathways for improving chemical production. Biotechnol Adv 2023;64:108119. [PMID: 36764336 DOI: 10.1016/j.biotechadv.2023.108119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
19
Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
20
Yu T, Boob AG, Volk MJ, Liu X, Cui H, Zhao H. Machine learning-enabled retrobiosynthesis of molecules. Nat Catal 2023. [DOI: 10.1038/s41929-022-00909-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
21
Qin Y, Li Q, Fan L, Ning X, Wei X, You C. Biomanufacturing by In Vitro Biotransformation (ivBT) Using Purified Cascade Multi-enzymes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023;186:1-27. [PMID: 37455283 DOI: 10.1007/10_2023_231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
22
Shrivastava A, Pal M, Sharma RK. Pichia as Yeast Cell Factory for Production of Industrially Important Bio-Products: Current Trends, Challenges, and Future Prospects. JOURNAL OF BIORESOURCES AND BIOPRODUCTS 2023. [DOI: 10.1016/j.jobab.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
23
Sieow BFL, De Sotto R, Seet ZRD, Hwang IY, Chang MW. Synthetic Biology Meets Machine Learning. Methods Mol Biol 2023;2553:21-39. [PMID: 36227537 DOI: 10.1007/978-1-0716-2617-7_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
24
From degrader to producer: reversing the gallic acid metabolism of Pseudomonas putida KT2440. Int Microbiol 2022;26:243-255. [PMID: 36357545 PMCID: PMC9649394 DOI: 10.1007/s10123-022-00282-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/18/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022]
25
Xu Z, Mahadevan R. Efficient Enumeration of Branched Novel Biochemical Pathways Using a Probabilistic Technique. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.1c02211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Kellman BP, Richelle A, Yang JY, Chapla D, Chiang AWT, Najera JA, Liang C, Fürst A, Bao B, Koga N, Mohammad MA, Bruntse AB, Haymond MW, Moremen KW, Bode L, Lewis NE. Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration. Nat Commun 2022;13:2455. [PMID: 35508452 PMCID: PMC9068700 DOI: 10.1038/s41467-022-29867-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/04/2022] [Indexed: 12/18/2022]  Open
27
Kovács SC, Szappanos B, Tengölics R, Notebaart RA, Papp B. Underground metabolism as a rich reservoir for pathway engineering. Bioinformatics 2022;38:3070-3077. [PMID: 35441658 PMCID: PMC9154287 DOI: 10.1093/bioinformatics/btac282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022]  Open
28
PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search. PLoS One 2022;17:e0266783. [PMID: 35404943 PMCID: PMC9000129 DOI: 10.1371/journal.pone.0266783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/26/2022] [Indexed: 11/30/2022]  Open
29
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. Nat Commun 2022;13:1560. [PMID: 35322036 PMCID: PMC8943196 DOI: 10.1038/s41467-022-29238-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/07/2022] [Indexed: 12/23/2022]  Open
30
Khana DB, Callaghan MM, Amador-Noguez D. Novel computational and experimental approaches for investigating the thermodynamics of metabolic networks. Curr Opin Microbiol 2021;66:21-31. [PMID: 34974376 DOI: 10.1016/j.mib.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022]
31
Sleight TW, Sexton CN, Mpourmpakis G, Gilbertson LM, Ng CA. A Classification Model to Identify Direct-Acting Mutagenic Polycyclic Aromatic Hydrocarbon Transformation Products. Chem Res Toxicol 2021;34:2273-2286. [PMID: 34662518 DOI: 10.1021/acs.chemrestox.1c00187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
32
Wang L, Upadhyay V, Maranas CD. dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. PLoS Comput Biol 2021;17:e1009448. [PMID: 34570771 PMCID: PMC8496854 DOI: 10.1371/journal.pcbi.1009448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 10/07/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022]  Open
33
Nakazawa S, Imaichi O, Kogure T, Kubota T, Toyoda K, Suda M, Inui M, Ito K, Shirai T, Araki M. History-Driven Genetic Modification Design Technique Using a Domain-Specific Lexical Model for the Acceleration of DBTL Cycles for Microbial Cell Factories. ACS Synth Biol 2021;10:2308-2317. [PMID: 34351735 DOI: 10.1021/acssynbio.1c00234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
34
Recent advances in biocatalysis of nitrogen-containing heterocycles. Biotechnol Adv 2021;54:107813. [PMID: 34450199 DOI: 10.1016/j.biotechadv.2021.107813] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/27/2021] [Accepted: 08/08/2021] [Indexed: 12/20/2022]
35
Hafner J, Mohammadi‐Peyhani H, Hatzimanikatis V. Pathway Design. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
36
Khattab AR, Farag MA. Marine and terrestrial endophytic fungi: a mine of bioactive xanthone compounds, recent progress, limitations, and novel applications. Crit Rev Biotechnol 2021;42:403-430. [PMID: 34266351 DOI: 10.1080/07388551.2021.1940087] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
37
Shah HA, Liu J, Yang Z, Feng J. Review of Machine Learning Methods for the Prediction and Reconstruction of Metabolic Pathways. Front Mol Biosci 2021;8:634141. [PMID: 34222327 PMCID: PMC8247443 DOI: 10.3389/fmolb.2021.634141] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/01/2021] [Indexed: 11/13/2022]  Open
38
Dixon TA, Williams TC, Pretorius IS. Bioinformational trends in grape and wine biotechnology. Trends Biotechnol 2021;40:124-135. [PMID: 34108075 DOI: 10.1016/j.tibtech.2021.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 02/08/2023]
39
Wang L, Maranas CD. Computationally Prospecting Potential Pathways from Lignin Monomers and Dimers toward Aromatic Compounds. ACS Synth Biol 2021;10:1064-1076. [PMID: 33877818 DOI: 10.1021/acssynbio.0c00598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
40
Hafner J, Hatzimanikatis V. Finding metabolic pathways in large networks through atom-conserving substrate-product pairs. Bioinformatics 2021;37:3560-3568. [PMID: 34003971 PMCID: PMC8545321 DOI: 10.1093/bioinformatics/btab368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 11/29/2022]  Open
41
Constraint-based metabolic control analysis for rational strain engineering. Metab Eng 2021;66:191-203. [PMID: 33895366 DOI: 10.1016/j.ymben.2021.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/10/2021] [Accepted: 03/02/2021] [Indexed: 11/20/2022]
42
Bourgade B, Minton NP, Islam MA. Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms. FEMS Microbiol Rev 2021;45:fuab008. [PMID: 33595667 PMCID: PMC8351756 DOI: 10.1093/femsre/fuab008] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022]  Open
43
Tiwari P, Khare T, Shriram V, Bae H, Kumar V. Plant synthetic biology for producing potent phyto-antimicrobials to combat antimicrobial resistance. Biotechnol Adv 2021;48:107729. [PMID: 33705914 DOI: 10.1016/j.biotechadv.2021.107729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/22/2021] [Accepted: 03/04/2021] [Indexed: 12/14/2022]
44
Fuji T, Nakazawa S, Ito K. Feasible-metabolic-pathway-exploration technique using chemical latent space. Bioinformatics 2021;36:i770-i778. [PMID: 33381845 PMCID: PMC8454040 DOI: 10.1093/bioinformatics/btaa809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
45
Bernstein DB, Sulheim S, Almaas E, Segrè D. Addressing uncertainty in genome-scale metabolic model reconstruction and analysis. Genome Biol 2021;22:64. [PMID: 33602294 PMCID: PMC7890832 DOI: 10.1186/s13059-021-02289-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023]  Open
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Lipid Traffic Analysis reveals the impact of high paternal carbohydrate intake on offsprings' lipid metabolism. Commun Biol 2021;4:163. [PMID: 33547386 PMCID: PMC7864968 DOI: 10.1038/s42003-021-01686-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/08/2021] [Indexed: 12/12/2022]  Open
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Kim Y, Ryu JY, Kim HU, Jang WD, Lee SY. A deep learning approach to evaluate the feasibility of enzymatic reactions generated by retrobiosynthesis. Biotechnol J 2021;16:e2000605. [PMID: 33386776 DOI: 10.1002/biot.202000605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/30/2020] [Indexed: 12/29/2022]
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Otero-Muras I, Carbonell P. Automated engineering of synthetic metabolic pathways for efficient biomanufacturing. Metab Eng 2020;63:61-80. [PMID: 33316374 DOI: 10.1016/j.ymben.2020.11.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/15/2020] [Accepted: 11/20/2020] [Indexed: 12/19/2022]
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Suthers PF, Foster CJ, Sarkar D, Wang L, Maranas CD. Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms. Metab Eng 2020;63:13-33. [PMID: 33310118 DOI: 10.1016/j.ymben.2020.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/13/2020] [Accepted: 11/27/2020] [Indexed: 12/16/2022]
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Desmet S, Brouckaert M, Boerjan W, Morreel K. Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. Comput Struct Biotechnol J 2020;19:72-85. [PMID: 33384856 PMCID: PMC7753198 DOI: 10.1016/j.csbj.2020.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023]  Open
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