Literature DB >> 30080835

Reply to "Challenges in modeling the human gut microbiome".

Stefanía Magnúsdóttir1, Almut Heinken1, Ronan M T Fleming2, Ines Thiele1.   

Abstract

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Year:  2018        PMID： 30080835     DOI： 10.1038/nbt.4212

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  25 in total

1.  A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks.

Authors:  S Schuster; D A Fell; T Dandekar
Journal:  Nat Biotechnol       Date:  2000-03       Impact factor: 54.908

2.  Energy balance for analysis of complex metabolic networks.

Authors:  Daniel A Beard; Shou-dan Liang; Hong Qian
Journal:  Biophys J       Date:  2002-07       Impact factor: 4.033

3.  Comparison of network-based pathway analysis methods.

Authors:  Jason A Papin; Joerg Stelling; Nathan D Price; Steffen Klamt; Stefan Schuster; Bernhard O Palsson
Journal:  Trends Biotechnol       Date:  2004-08       Impact factor: 19.536

4.  von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.

Authors:  Ronan M T Fleming; Ines Thiele
Journal:  Bioinformatics       Date:  2010-11-28       Impact factor: 6.937

Review 5.  The acetate switch.

Authors:  Alan J Wolfe
Journal:  Microbiol Mol Biol Rev       Date:  2005-03       Impact factor: 11.056

6.  Optimizing genome-scale network reconstructions.

Authors:  Jonathan Monk; Juan Nogales; Bernhard O Palsson
Journal:  Nat Biotechnol       Date:  2014-05       Impact factor: 54.908

7.  Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.

Authors:  Nathan E Lewis; Kim K Hixson; Tom M Conrad; Joshua A Lerman; Pep Charusanti; Ashoka D Polpitiya; Joshua N Adkins; Gunnar Schramm; Samuel O Purvine; Daniel Lopez-Ferrer; Karl K Weitz; Roland Eils; Rainer König; Richard D Smith; Bernhard Ø Palsson
Journal:  Mol Syst Biol       Date:  2010-07       Impact factor: 11.429

8.  Integration of expression data in genome-scale metabolic network reconstructions.

Authors:  Anna S Blazier; Jason A Papin
Journal:  Front Physiol       Date:  2012-08-06       Impact factor: 4.566

Review 9.  Applications of genome-scale metabolic reconstructions.

Authors:  Matthew A Oberhardt; Bernhard Ø Palsson; Jason A Papin
Journal:  Mol Syst Biol       Date:  2009-11-03       Impact factor: 11.429

10.  fastGapFill: efficient gap filling in metabolic networks.

Authors:  Ines Thiele; Nikos Vlassis; Ronan M T Fleming
Journal:  Bioinformatics       Date:  2014-05-07       Impact factor: 6.937
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  4 in total

Review 1.  Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes.

Authors:  Patrick A Leggieri; Yiyi Liu; Madeline Hayes; Bryce Connors; Susanna Seppälä; Michelle A O'Malley; Ophelia S Venturelli
Journal:  Annu Rev Biomed Eng       Date:  2021-03-29       Impact factor: 9.590

2.  Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.

Authors:  Almut Heinken; Dmitry A Ravcheev; Federico Baldini; Laurent Heirendt; Ronan M T Fleming; Ines Thiele
Journal:  Microbiome       Date:  2019-05-15       Impact factor: 14.650

Review 3.  Current status and applications of genome-scale metabolic models.

Authors:  Changdai Gu; Gi Bae Kim; Won Jun Kim; Hyun Uk Kim; Sang Yup Lee
Journal:  Genome Biol       Date:  2019-06-13       Impact factor: 13.583

Review 4.  Understanding the host-microbe interactions using metabolic modeling.

Authors:  Jack Jansma; Sahar El Aidy
Journal:  Microbiome       Date:  2021-01-20       Impact factor: 14.650
  4 in total

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