Literature DB >> 34719002

A Beginner's Guide to the COBRA Toolbox.

Ali Navid1.   

Abstract

COBRA toolbox is one of the most popular tools for systems biology analyses using genome-scale metabolic reconstructions. The toolbox permits the use of many constraint-based analytical methods for examining characteristics of metabolism in the biosystems ranging in complexity from single cells to microbial communities and ultimately multicellular organisms. The toolbox has a number of different variants that can be used depending on a user's choice of programming language. Here, I provide a basic tutorial for beginners that plan to use the original MATLAB version of the toolbox.
© 2022. Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Systems biology, Genome-scale models, Constraint-based analysis, FBA, Metabolic networks, COBRA toolbox

Mesh：

Year:  2022        PMID： 34719002     DOI： 10.1007/978-1-0716-1585-0_15

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  41 in total

1.  Applications of system-level models of metabolism for analysis of bacterial physiology and identification of new drug targets.

Authors:  Ali Navid
Journal:  Brief Funct Genomics       Date:  2011-11       Impact factor: 4.241

2.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.

Authors:  Scott A Becker; Adam M Feist; Monica L Mo; Gregory Hannum; Bernhard Ø Palsson; Markus J Herrgard
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

3.  Metabolic engineering of Synechocystis sp. PCC 6803 for enhanced ethanol production based on flux balance analysis.

Authors:  Katsunori Yoshikawa; Yoshihiro Toya; Hiroshi Shimizu
Journal:  Bioprocess Biosyst Eng       Date:  2017-03-03       Impact factor: 3.210

4.  A metabolic network-based approach for developing feeding strategies for CHO cells to increase monoclonal antibody production.

Authors:  Hamideh Fouladiha; Sayed-Amir Marashi; Fatemeh Torkashvand; Fereidoun Mahboudi; Nathan E Lewis; Behrouz Vaziri
Journal:  Bioprocess Biosyst Eng       Date:  2020-03-24       Impact factor: 3.210

5.  Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization.

Authors:  Anthony P Burgard; Priti Pharkya; Costas D Maranas
Journal:  Biotechnol Bioeng       Date:  2003-12-20       Impact factor: 4.530

Review 6.  Reconstructing organisms in silico: genome-scale models and their emerging applications.

Authors:  Xin Fang; Colton J Lloyd; Bernhard O Palsson
Journal:  Nat Rev Microbiol       Date:  2020-09-21       Impact factor: 60.633

7.  Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction.

Authors:  Sidhartha Chaudhury; Mohamed Diwan M Abdulhameed; Narender Singh; Gregory J Tawa; Patrik M D'haeseleer; Adam T Zemla; Ali Navid; Carol E Zhou; Matthew C Franklin; Jonah Cheung; Michael J Rudolph; James Love; John F Graf; David A Rozak; Jennifer L Dankmeyer; Kei Amemiya; Simon Daefler; Anders Wallqvist
Journal:  PLoS One       Date:  2013-05-21       Impact factor: 3.240

8.  Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001.

Authors:  Ali Navid; Eivind Almaas
Journal:  Mol Biosyst       Date:  2009-01-26

9.  Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation.

Authors:  Jin Hwan Park; Kwang Ho Lee; Tae Yong Kim; Sang Yup Lee
Journal:  Proc Natl Acad Sci U S A       Date:  2007-04-26       Impact factor: 11.205

10.  Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Authors:  Laurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N Mendoza; Anne Richelle; Almut Heinken; Hulda S Haraldsdóttir; Jacek Wachowiak; Sarah M Keating; Vanja Vlasov; Stefania Magnusdóttir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu H J Chan; Maike K Aurich; Catherine M Clancy; Jennifer Modamio; John T Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C El Assal; Luis V Valcarcel; 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 T 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 Ø Palsson; Ines Thiele; Ronan M T Fleming
Journal:  Nat Protoc       Date:  2019-03       Impact factor: 13.491
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