Literature DB >> 30080831

Challenges in modeling the human gut microbiome.

Parizad Babaei1, Saeed Shoaie2, Boyang Ji1, Jens Nielsen1,3.   

Abstract

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Year:  2018        PMID： 30080831     DOI： 10.1038/nbt.4213

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


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  14 in total

Review 1.  Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota.

Authors:  Michael Graham Espey
Journal:  Free Radic Biol Med       Date:  2012-11-02       Impact factor: 7.376

2.  Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota.

Authors:  Lindsey Albenberg; Tatiana V Esipova; Colleen P Judge; Kyle Bittinger; Jun Chen; Alice Laughlin; Stephanie Grunberg; Robert N Baldassano; James D Lewis; Hongzhe Li; Stephen R Thom; Frederic D Bushman; Sergei A Vinogradov; Gary D Wu
Journal:  Gastroenterology       Date:  2014-07-18       Impact factor: 22.682

3.  A metagenome-wide association study of gut microbiota in type 2 diabetes.

Authors:  Junjie Qin; Yingrui Li; Zhiming Cai; Shenghui Li; Jianfeng Zhu; Fan Zhang; Suisha Liang; Wenwei Zhang; Yuanlin Guan; Dongqian Shen; Yangqing Peng; Dongya Zhang; Zhuye Jie; Wenxian Wu; Youwen Qin; Wenbin Xue; Junhua Li; Lingchuan Han; Donghui Lu; Peixian Wu; Yali Dai; Xiaojuan Sun; Zesong Li; Aifa Tang; Shilong Zhong; Xiaoping Li; Weineng Chen; Ran Xu; Mingbang Wang; Qiang Feng; Meihua Gong; Jing Yu; Yanyan Zhang; Ming Zhang; Torben Hansen; Gaston Sanchez; Jeroen Raes; Gwen Falony; Shujiro Okuda; Mathieu Almeida; Emmanuelle LeChatelier; Pierre Renault; Nicolas Pons; Jean-Michel Batto; Zhaoxi Zhang; Hua Chen; Ruifu Yang; Weimou Zheng; Songgang Li; Huanming Yang; Jian Wang; S Dusko Ehrlich; Rasmus Nielsen; Oluf Pedersen; Karsten Kristiansen; Jun Wang
Journal:  Nature       Date:  2012-09-26       Impact factor: 49.962

4.  Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics.

Authors:  William R Harcombe; William J Riehl; Ilija Dukovski; Brian R Granger; Alex Betts; Alex H Lang; Gracia Bonilla; Amrita Kar; Nicholas Leiby; Pankaj Mehta; Christopher J Marx; Daniel Segrè
Journal:  Cell Rep       Date:  2014-05-01       Impact factor: 9.423

5.  Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome.

Authors:  Saeed Shoaie; Pouyan Ghaffari; Petia Kovatcheva-Datchary; Adil Mardinoglu; Partho Sen; Estelle Pujos-Guillot; Tomas de Wouters; Catherine Juste; Salwa Rizkalla; Julien Chilloux; Lesley Hoyles; Jeremy K Nicholson; Joel Dore; Marc E Dumas; Karine Clement; Fredrik Bäckhed; Jens Nielsen
Journal:  Cell Metab       Date:  2015-08-04       Impact factor: 27.287

6.  F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks.

Authors:  Abdelhalim Larhlimi; Laszlo David; Joachim Selbig; Alexander Bockmayr
Journal:  BMC Bioinformatics       Date:  2012-04-23       Impact factor: 3.169

7.  OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities.

Authors:  Ali R Zomorrodi; Costas D Maranas
Journal:  PLoS Comput Biol       Date:  2012-02-02       Impact factor: 4.475

8.  BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.

Authors:  Zachary A King; Justin Lu; Andreas Dräger; Philip Miller; Stephen Federowicz; Joshua A Lerman; Ali Ebrahim; Bernhard O Palsson; Nathan E Lewis
Journal:  Nucleic Acids Res       Date:  2015-10-17       Impact factor: 16.971

9.  The gut microbiota modulates host amino acid and glutathione metabolism in mice.

Authors:  Adil Mardinoglu; Saeed Shoaie; Mattias Bergentall; Pouyan Ghaffari; Cheng Zhang; Erik Larsson; Fredrik Bäckhed; Jens Nielsen
Journal:  Mol Syst Biol       Date:  2015-10-16       Impact factor: 11.429

10.  Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

Authors:  Kristoffer Forslund; Falk Hildebrand; Trine Nielsen; Gwen Falony; Emmanuelle Le Chatelier; Shinichi Sunagawa; Edi Prifti; Sara Vieira-Silva; Valborg Gudmundsdottir; Helle K Pedersen; Manimozhiyan Arumugam; Karsten Kristiansen; Anita Yvonne Voigt; Henrik Vestergaard; Rajna Hercog; Paul Igor Costea; Jens Roat Kultima; Junhua Li; Torben Jørgensen; Florence Levenez; Joël Dore; H Bjørn Nielsen; Søren Brunak; Jeroen Raes; Torben Hansen; Jun Wang; S Dusko Ehrlich; Peer Bork; Oluf Pedersen
Journal:  Nature       Date:  2015-12-02       Impact factor: 49.962
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  7 in total

1.  Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling.

Authors:  Manish Kumar; Boyang Ji; Parizad Babaei; Promi Das; Dimitra Lappa; Girija Ramakrishnan; Todd E Fox; Rashidul Haque; William A Petri; Fredrik Bäckhed; Jens Nielsen
Journal:  Metab Eng       Date:  2018-07-31       Impact factor: 9.783

Review 2.  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

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.  Bringing microbiome-drug interaction research into the clinic.

Authors:  Leah Guthrie; Libusha Kelly
Journal:  EBioMedicine       Date:  2019-05-28       Impact factor: 8.143

5.  BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.

Authors:  Charles J Norsigian; Neha Pusarla; John Luke McConn; James T Yurkovich; Andreas Dräger; Bernhard O Palsson; Zachary King
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

Review 6.  Understanding the host-microbe interactions using metabolic modeling.

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

7.  High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure.

Authors:  Juan P Molina Ortiz; Mark Norman Read; Dale David McClure; Andrew Holmes; Fariba Dehghani; Erin Rose Shanahan
Journal:  Gut Microbes       Date:  2022 Jan-Dec
  7 in total

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