Literature DB >> 26776218

COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES.

Casey S Greene1, James A Foster, Bruce A Stanton, Deborah A Hogan, Yana Bromberg.   

Abstract

Technological advances are making large-scale measurements of microbial communities commonplace. These newly acquired datasets are allowing researchers to ask and answer questions about the composition of microbial communities, the roles of members in these communities, and how genes and molecular pathways are regulated in individual community members and communities as a whole to effectively respond to diverse and changing environments. In addition to providing a more comprehensive survey of the microbial world, this new information allows for the development of computational approaches to model the processes underlying microbial systems. We anticipate that the field of computational microbiology will continue to grow rapidly in the coming years. In this manuscript we highlight both areas of particular interest in microbiology as well as computational approaches that begin to address these challenges.

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Year:  2016        PMID: 26776218      PMCID: PMC4832978     

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN: 2335-6928


  65 in total

1.  Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.

Authors:  Rachel Mackelprang; Mark P Waldrop; Kristen M DeAngelis; Maude M David; Krystle L Chavarria; Steven J Blazewicz; Edward M Rubin; Janet K Jansson
Journal:  Nature       Date:  2011-11-06       Impact factor: 49.962

2.  Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries.

Authors:  Wei Xie; Fengping Wang; Lei Guo; Zeling Chen; Stefan M Sievert; Jun Meng; Guangrui Huang; Yuxin Li; Qingyu Yan; Shan Wu; Xin Wang; Shangwu Chen; Guangyuan He; Xiang Xiao; Anlong Xu
Journal:  ISME J       Date:  2010-10-07       Impact factor: 10.302

3.  Asthma: Undoing millions of years of coevolution in early life?

Authors:  Maria Gloria Dominguez-Bello; Martin J Blaser
Journal:  Sci Transl Med       Date:  2015-09-30       Impact factor: 17.956

4.  Functional metagenomic profiling of nine biomes.

Authors:  Elizabeth A Dinsdale; Robert A Edwards; Dana Hall; Florent Angly; Mya Breitbart; Jennifer M Brulc; Mike Furlan; Christelle Desnues; Matthew Haynes; Linlin Li; Lauren McDaniel; Mary Ann Moran; Karen E Nelson; Christina Nilsson; Robert Olson; John Paul; Beltran Rodriguez Brito; Yijun Ruan; Brandon K Swan; Rick Stevens; David L Valentine; Rebecca Vega Thurber; Linda Wegley; Bryan A White; Forest Rohwer
Journal:  Nature       Date:  2008-03-12       Impact factor: 49.962

5.  Severity-related changes of bronchial microbiome in chronic obstructive pulmonary disease.

Authors:  Marian Garcia-Nuñez; Laura Millares; Xavier Pomares; Rafaela Ferrari; Vicente Pérez-Brocal; Miguel Gallego; Mateu Espasa; Andrés Moya; Eduard Monsó
Journal:  J Clin Microbiol       Date:  2014-09-24       Impact factor: 5.948

6.  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

7.  Human genetics shape the gut microbiome.

Authors:  Julia K Goodrich; Jillian L Waters; Angela C Poole; Jessica L Sutter; Omry Koren; Ran Blekhman; Michelle Beaumont; William Van Treuren; Rob Knight; Jordana T Bell; Timothy D Spector; Andrew G Clark; Ruth E Ley
Journal:  Cell       Date:  2014-11-06       Impact factor: 41.582

8.  Prevalence of streptococci and increased polymicrobial diversity associated with cystic fibrosis patient stability.

Authors:  L M Filkins; T H Hampton; A H Gifford; M J Gross; D A Hogan; M L Sogin; H G Morrison; B J Paster; G A O'Toole
Journal:  J Bacteriol       Date:  2012-06-29       Impact factor: 3.490

Review 9.  Role of the bitter taste receptor T2R38 in upper respiratory infection and chronic rhinosinusitis.

Authors:  Robert J Lee; Noam A Cohen
Journal:  Curr Opin Allergy Clin Immunol       Date:  2015-02

10.  Characterization of the diversity and temporal stability of bacterial communities in human milk.

Authors:  Katherine M Hunt; James A Foster; Larry J Forney; Ursel M E Schütte; Daniel L Beck; Zaid Abdo; Lawrence K Fox; Janet E Williams; Michelle K McGuire; Mark A McGuire
Journal:  PLoS One       Date:  2011-06-17       Impact factor: 3.240

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  3 in total

1.  Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks.

Authors:  Jie Tan; Georgia Doing; Kimberley A Lewis; Courtney E Price; Kathleen M Chen; Kyle C Cady; Barret Perchuk; Michael T Laub; Deborah A Hogan; Casey S Greene
Journal:  Cell Syst       Date:  2017-07-12       Impact factor: 10.304

2.  ADAGE signature analysis: differential expression analysis with data-defined gene sets.

Authors:  Jie Tan; Matthew Huyck; Dongbo Hu; René A Zelaya; Deborah A Hogan; Casey S Greene
Journal:  BMC Bioinformatics       Date:  2017-11-22       Impact factor: 3.169

3.  PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia.

Authors:  Kathleen M Chen; Jie Tan; Gregory P Way; Georgia Doing; Deborah A Hogan; Casey S Greene
Journal:  BioData Min       Date:  2018-07-03       Impact factor: 2.522

  3 in total

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