Machine learning for metabolic engineering: A review.

Metabolic Engineering
Christopher E LawsonHector Garcia Martin

Abstract

Machine learning provides researchers a unique opportunity to make metabolic engineering more predictable. In this review, we offer an introduction to this discipline in terms that are relatable to metabolic engineers, as well as providing in-depth illustrative examples leveraging omics data and improving production. We also include practical advice for the practitioner in terms of data management, algorithm libraries, computational resources, and important non-technical issues. A variety of applications ranging from pathway construction and optimization, to genetic editing optimization, cell factory testing, and production scale-up are discussed. Moreover, the promising relationship between machine learning and mechanistic models is thoroughly reviewed. Finally, the future perspectives and most promising directions for this combination of disciplines are examined.

References

Sep 8, 1998·Microbiology and Molecular Biology Reviews : MMBR·K Kovárová-Kovar, T Egli
Dec 11, 1999·Nucleic Acids Research·A Bairoch, R Apweiler
Sep 12, 2003·Biotechnology and Bioengineering·Matthew C ColemanDavid E Block
Nov 7, 2003·Nucleic Acids Research·Clotilde Claudel-RenardDaniel Kahn
Jul 9, 2005·Biotechnology and Bioengineering·Joseph J Heijnen
Jul 13, 2006·Annual Review of Biomedical Engineering·Paul Sajda
Jan 30, 2007·Ecology Letters·Alan HastingsWilliam G Wilson
Feb 27, 2007·Nature Biotechnology·Richard J FoxGjalt W Huisman
Oct 4, 2007·Statistical Applications in Genetics and Molecular Biology·Mark J van der LaanAlan E Hubbard
Nov 4, 2008·Trends in Biotechnology·Salim CharaniyaGeorge Karypis
Oct 6, 2009·Nature Biotechnology·Howard M SalisChristopher A Voigt
Jan 9, 2010·Nature Protocols·Ines Thiele, Bernhard Ø Palsson
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Virgil A Rhodius, Vivek K Mutalik
Jun 17, 2010·Bioinformatics·Pablo Carbonell, Jean-Loup Faulon
Oct 12, 2010·Science·Parayil Kumaran AjikumarGregory Stephanopoulos
Oct 19, 2010·Archives of Toxicology·Mamas MamasRoyston Goodacre
Nov 13, 2010·Nucleic Acids Research·Dennis A BensonEric W Sayers
Mar 23, 2011·Critical Reviews in Biochemistry and Molecular Biology·Ahmet Ay, David N Arnosti
May 20, 2011·Nucleic Acids Research·Robert D FinnSean R Eddy
May 31, 2011·Nature Genetics·Balázs SzappanosBalázs Papp
Sep 29, 2011·Metabolic Engineering·C Eric Hodgman, Michael C Jewett
Nov 22, 2011·Nucleic Acids Research·David R KelleySteven L Salzberg
Apr 10, 2012·Nature Biotechnology·Deepak ReyonJ Keith Joung
Jul 5, 2012·Nature Communications·Joshua A LermanBernhard O Palsson
Jul 24, 2012·Cell·Jonathan R KarrMarkus W Covert
Aug 17, 2012·Nature·Pamela P Peralta-YahyaJay D Keasling
Aug 28, 2012·Bioinformatics·Narendra Kumar, Jeffrey Skolnick
Nov 3, 2012·Current Topics in Medicinal Chemistry·Rosanna G AldersonNeetika Nath
Jan 2, 2013·Proceedings of the National Academy of Sciences of the United States of America·Philip A RomeroFrances H Arnold
Jan 24, 2013·Molecular Systems Biology·Kevin M Esvelt, Harris H Wang
Feb 20, 2013·Trends in Biotechnology·Timothy S Gardner
Mar 26, 2013·Journal of Chemical Information and Modeling·Robert P Sheridan
Apr 2, 2013·Annual Review of Chemical and Biomolecular Engineering·Benjamin M WoolstonGregory Stephanopoulos
Jul 23, 2013·Nature Biotechnology·Patrick D HsuFeng Zhang
Feb 1, 2014·Nature Methods·Florian HeigwerMichael Boutros
Apr 2, 2014·Nature Reviews. Microbiology·Chris J Paddon, Jay D Keasling
Jan 1, 2012·Computational and Structural Biotechnology Journal·Michalis KoutinasAthanasios Mantalaris
Apr 15, 2014·Nature Biotechnology·Juan A VizcaínoHenning Hermjakob
Oct 14, 2014·Cell·Luke A GilbertJonathan S Weissman
Oct 29, 2014·Nucleic Acids Research·UNKNOWN UniProt Consortium

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Citations

Jun 9, 2021·Biochemical Society Transactions·Christopher J RobinsonNigel S Scrutton
Jun 27, 2021·Nature Reviews. Microbiology·Jay KeaslingEric Sundstrom
Jul 2, 2021·Materials Today. Bio·O Burgos-MoralesW Weber
Jul 8, 2021·Natural Product Reports·Mauro A RinaldiNigel S Scrutton
Jul 10, 2021·Current Opinion in Biotechnology·Andrew J BorchertGregg T Beckham
Sep 1, 2021·MSystems·Christopher E Lawson
Sep 25, 2021·Microbial Cell Factories·Kaushik RajRadhakrishnan Mahadevan
Oct 16, 2021·Chemical Society Reviews·Sijie ZhouYing-Jin Yuan
Aug 20, 2021·Frontiers in Bioengineering and Biotechnology·Kunal DuttaIbrahim Khalifa

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