The biomass objective function
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TLDR
Fundamental issues associated with its formulation and use are reviewed and use to compute optimal growth states are reviewed.About:
This article is published in Current Opinion in Microbiology.The article was published on 2010-04-27 and is currently open access. It has received 565 citations till now. The article focuses on the topics: Flux balance analysis.read more
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A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011
Jeffrey D. Orth,Tom M Conrad,Jessica Na,Joshua A. Lerman,Hojung Nam,Adam M. Feist,Bernhard O. Palsson +6 more
TL;DR: The initial genome‐scale reconstruction of the metabolic network of Escherichia coli K‐12 MG1655 was assembled in 2000 and an update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites.
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Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
TL;DR: This work describes a phylogeny of COBRA methods that has rapidly evolved from the few early methods, such as flux balance analysis and elementary flux mode analysis, into a repertoire of more than 100 methods, including antibiotic discovery, metabolic engineering and modelling of microbial community behaviour.
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Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0
Laurent Heirendt,Sylvain Arreckx,Thomas Pfau,Sebastián N. Mendoza,Anne Richelle,Almut Heinken,Hulda S. Haraldsdóttir,Jacek Wachowiak,Sarah M. Keating,Vanja Vlasov,Stefania Magnusdottir,Chiam Yu Ng,German Preciat,Alise Žagare,Siu Hung Joshua Chan,Maike K. Aurich,Catherine M. Clancy,Jennifer Modamio,John T. Sauls,Alberto Noronha,Aarash Bordbar,Benjamin Cousins,Diana C. El Assal,Luis Vitores Valcárcel,Iñigo Apaolaza,Susan Ghaderi,Masoud Ahookhosh,Marouen Ben Guebila,Andrejs Kostromins,Nicolas Sompairac,Hoai M. Le,Ding Ma,Yuekai Sun,Lin Wang,James T. Yurkovich,Miguel A.P. Oliveira,Phan Tu Vuong,Lemmer P. El Assal,Inna Kuperstein,Andrei Zinovyev,H. Scott Hinton,William A. Bryant,Francisco J. Aragón Artacho,Francisco J. Planes,Egils Stalidzans,Alejandro Maass,Santosh Vempala,Michael Hucka,Michael A. Saunders,Costas D. Maranas,Nathan E. Lewis,Thomas Sauter,Bernhard O. Palsson,Bernhard O. Palsson,Ines Thiele,Ronan M. T. Fleming,Ronan M. T. Fleming +56 more
TL;DR: This protocol provides an overview of all new features of the COBRA Toolbox and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios.
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A brief history of synthetic biology
TL;DR: This Timeline article charts the technological and cultural lifetime of synthetic biology, with an emphasis on key breakthroughs and future challenges.
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Using Genome-scale Models to Predict Biological Capabilities.
TL;DR: This Primer will get you started in constraint-based reconstruction and analysis at the genome scale for metabolic engineering, antibiotic design, and organismal and enzyme evolution.
References
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Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Tomoya Baba,Takeshi Ara,Miki Hasegawa,Yuki Takai,Yoshiko Okumura,Miki Baba,Kirill A. Datsenko,Masaru Tomita,Barry L. Wanner,Hirotada Mori,Hirotada Mori +10 more
TL;DR: These mutants—the ‘Keio collection’—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome‐wide testing of mutational effects in a common strain background, E. coli K‐12 BW25113.
Journal ArticleDOI
KEGG for linking genomes to life and the environment
Minoru Kanehisa,Michihiro Araki,Susumu Goto,Masahiro Hattori,Mika Hirakawa,Masumi Itoh,Toshiaki Katayama,Shuichi Kawashima,Shujiro Okuda,Toshiaki Tokimatsu,Yoshihiro Yamanishi +10 more
TL;DR: KEGG PATHWAY is now supplemented with a new global map of metabolic pathways, which is essentially a combined map of about 120 existing pathway maps, and the KEGG resource is being expanded to suit the needs for practical applications.
Journal ArticleDOI
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi,Richard Billington,Luciana Ferrer,Hartmut Foerster,Carol A. Fulcher,Ingrid M. Keseler,Anamika Kothari,Markus Krummenacker,Mario Latendresse,Lukas A. Mueller,Quang Ong,Suzanne M. Paley,Pallavi Subhraveti,Daniel Weaver,Peter D. Karp +14 more
TL;DR: The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.
Journal ArticleDOI
A protocol for generating a high-quality genome-scale metabolic reconstruction.
TL;DR: This protocol provides a helpful manual for all stages of the reconstruction process and presents a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction.
Journal ArticleDOI
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
Adam M. Feist,Christopher S. Henry,Jennifer L. Reed,Markus Krummenacker,Andrew R. Joyce,Peter D. Karp,Linda J. Broadbelt,Vassily Hatzimanikatis,Bernhard O. Palsson +8 more
TL;DR: An updated genome‐scale reconstruction of the metabolic network in Escherichia coli K‐12 MG1655 with increased scope and computational capability is presented, expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism.