Literature DB >> 20491063

Network-based modeling of the human gut microbiome.

Ammar Naqvi1, Huzefa Rangwala, Ali Keshavarzian, Patrick Gillevet.   

Abstract

In this article, we used a network-based approach to characterize the microflora abundance in colonic mucosal samples and correlate potential interactions between the identified species with respect to the healthy and diseased states. We analyzed the modelled network by computing several local and global network statistics, identified recurring patterns or motifs, fit the network models to a family of well-studied graph models. This study has demonstrated, for the first time, an approach that differentiated the gut microbiota in alcoholic subjects and healthy subjects using topological network analysis of the gut microbiome.

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Year:  2010        PMID: 20491063      PMCID: PMC3681515          DOI: 10.1002/cbdv.200900324

Source DB:  PubMed          Journal:  Chem Biodivers        ISSN: 1612-1872            Impact factor:   2.408


  20 in total

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5.  The human microbiome project.

Authors:  Peter J Turnbaugh; Ruth E Ley; Micah Hamady; Claire M Fraser-Liggett; Rob Knight; Jeffrey I Gordon
Journal:  Nature       Date:  2007-10-18       Impact factor: 49.962

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Journal:  Anal Biochem       Date:  1996-11-01       Impact factor: 3.365

7.  Human colonic biota studied by ribosomal DNA sequence analysis.

Authors:  K H Wilson; R B Blitchington
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8.  The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis.

Authors:  J R Cole; B Chai; R J Farris; Q Wang; S A Kulam; D M McGarrell; G M Garrity; J M Tiedje
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

9.  GraphCrunch: a tool for large network analyses.

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10.  NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.

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Journal:  Nucleic Acids Res       Date:  2008-06-04       Impact factor: 16.971

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  19 in total

1.  Colonic microbiome is altered in alcoholism.

Authors:  Ece A Mutlu; Patrick M Gillevet; Huzefa Rangwala; Masoumeh Sikaroodi; Ammar Naqvi; Phillip A Engen; Mary Kwasny; Cynthia K Lau; Ali Keshavarzian
Journal:  Am J Physiol Gastrointest Liver Physiol       Date:  2012-01-12       Impact factor: 4.052

2.  Posttraumatic stress disorder is associated with altered gut microbiota that modulates cognitive performance in veterans with cirrhosis.

Authors:  Jasmohan S Bajaj; Masoumeh Sikaroodi; Andrew Fagan; Douglas Heuman; HoChong Gilles; Edith A Gavis; Michael Fuchs; Javier Gonzalez-Maeso; Shahzor Nizam; Patrick M Gillevet; James B Wade
Journal:  Am J Physiol Gastrointest Liver Physiol       Date:  2019-08-28       Impact factor: 4.052

3.  Systems biology analysis of omeprazole therapy in cirrhosis demonstrates significant shifts in gut microbiota composition and function.

Authors:  Jasmohan S Bajaj; I Jane Cox; Naga S Betrapally; Douglas M Heuman; Mitchell L Schubert; Maiyuran Ratneswaran; Phillip B Hylemon; Melanie B White; Kalyani Daita; Nicole A Noble; Masoumeh Sikaroodi; Roger Williams; Mary M E Crossey; Simon D Taylor-Robinson; Patrick M Gillevet
Journal:  Am J Physiol Gastrointest Liver Physiol       Date:  2014-09-25       Impact factor: 4.052

4.  Linkage of gut microbiome with cognition in hepatic encephalopathy.

Authors:  Jasmohan S Bajaj; Jason M Ridlon; Phillip B Hylemon; Leroy R Thacker; Douglas M Heuman; Sean Smith; Masoumeh Sikaroodi; Patrick M Gillevet
Journal:  Am J Physiol Gastrointest Liver Physiol       Date:  2011-09-22       Impact factor: 4.052

5.  Salivary microbiota reflects changes in gut microbiota in cirrhosis with hepatic encephalopathy.

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Journal:  Hepatology       Date:  2015-05-06       Impact factor: 17.425

6.  Reduced alcohol preference and intake after fecal transplant in patients with alcohol use disorder is transmissible to germ-free mice.

Authors:  Jennifer T Wolstenholme; Justin M Saunders; Maren Smith; Jason D Kang; Phillip B Hylemon; Javier González-Maeso; Andrew Fagan; Derrick Zhao; Masoumeh Sikaroodi; Jeremy Herzog; Amirhossein Shamsaddini; Marcela Peña-Rodríguez; Lianyong Su; Yun-Ling Tai; Jing Zheng; Po-Cheng Cheng; R Balfour Sartor; Patrick M Gillevet; Huiping Zhou; Jasmohan S Bajaj
Journal:  Nat Commun       Date:  2022-10-19       Impact factor: 17.694

7.  Gut microbiota drive the development of neuroinflammatory response in cirrhosis in mice.

Authors:  Dae Joong Kang; Naga S Betrapally; Siddhartha A Ghosh; R Balfour Sartor; Phillip B Hylemon; Patrick M Gillevet; Arun J Sanyal; Douglas M Heuman; Daniel Carl; Huiping Zhou; Runping Liu; Xiang Wang; Jing Yang; Chunhua Jiao; Jeremy Herzog; H Robert Lippman; Masoumeh Sikaroodi; Robert R Brown; Jasmohan S Bajaj
Journal:  Hepatology       Date:  2016-07-29       Impact factor: 17.425

8.  Randomised clinical trial: Lactobacillus GG modulates gut microbiome, metabolome and endotoxemia in patients with cirrhosis.

Authors:  J S Bajaj; D M Heuman; P B Hylemon; A J Sanyal; P Puri; R K Sterling; V Luketic; R T Stravitz; M S Siddiqui; M Fuchs; L R Thacker; J B Wade; K Daita; S Sistrun; M B White; N A Noble; C Thorpe; G Kakiyama; W M Pandak; M Sikaroodi; P M Gillevet
Journal:  Aliment Pharmacol Ther       Date:  2014-03-16       Impact factor: 8.171

9.  Microbial functional change is linked with clinical outcomes after capsular fecal transplant in cirrhosis.

Authors:  Jasmohan S Bajaj; Nita Salzman; Chathur Acharya; Hajime Takei; Genta Kakiyama; Andrew Fagan; Melanie B White; Edith A Gavis; Mary L Holtz; Michael Hayward; Hiroshi Nittono; Phillip B Hylemon; I Jane Cox; Roger Williams; Simon D Taylor-Robinson; Richard K Sterling; Scott C Matherly; Michael Fuchs; Hannah Lee; Puneet Puri; R Todd Stravitz; Arun J Sanyal; Lola Ajayi; Adrien Le Guennec; R Andrew Atkinson; Mohammad S Siddiqui; Velimir Luketic; William M Pandak; Masoumeh Sikaroodi; Patrick M Gillevet
Journal:  JCI Insight       Date:  2019-12-19

10.  Impaired Gut-Liver-Brain Axis in Patients with Cirrhosis.

Authors:  Vishwadeep Ahluwalia; Naga S Betrapally; Phillip B Hylemon; Melanie B White; Patrick M Gillevet; Ariel B Unser; Andrew Fagan; Kalyani Daita; Douglas M Heuman; Huiping Zhou; Masoumeh Sikaroodi; Jasmohan S Bajaj
Journal:  Sci Rep       Date:  2016-05-26       Impact factor: 4.379

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