Literature DB >> 27197692

Microbiome Data Science: Understanding Our Microbial Planet.

Nikos C Kyrpides1, Emiley A Eloe-Fadrosh2, Natalia N Ivanova2.   

Abstract

Microbiology is experiencing a revolution brought on by recent developments in sequencing technology. The unprecedented volume of microbiome data being generated poses significant challenges that are currently hindering progress in the field. Here, we outline the major bottlenecks and propose a vision to advance microbiome research as a data-driven science.
Copyright © 2016 Elsevier Ltd. All rights reserved.

Keywords:  data integration; data interoperability; data science; data standards; metagenomics; microbiome

Mesh:

Year:  2016        PMID: 27197692     DOI: 10.1016/j.tim.2016.02.011

Source DB:  PubMed          Journal:  Trends Microbiol        ISSN: 0966-842X            Impact factor:   17.079


  17 in total

1.  Uncovering Earth's virome.

Authors:  David Paez-Espino; Emiley A Eloe-Fadrosh; Georgios A Pavlopoulos; Alex D Thomas; Marcel Huntemann; Natalia Mikhailova; Edward Rubin; Natalia N Ivanova; Nikos C Kyrpides
Journal:  Nature       Date:  2016-08-17       Impact factor: 49.962

2.  Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing.

Authors:  Zhigang Li; Florian P Breitwieser; Jennifer Lu; Albert S Jun; Laura Asnaghi; Steven L Salzberg; Charles G Eberhart
Journal:  Invest Ophthalmol Vis Sci       Date:  2018-01-01       Impact factor: 4.799

Review 3.  Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.

Authors:  Anja Spang; Tara A Mahendrarajah; Pierre Offre; Courtney W Stairs
Journal:  Genome Biol Evol       Date:  2022-05-31       Impact factor: 4.065

4.  IMG/M: integrated genome and metagenome comparative data analysis system.

Authors:  I-Min A Chen; Victor M Markowitz; Ken Chu; Krishna Palaniappan; Ernest Szeto; Manoj Pillay; Anna Ratner; Jinghua Huang; Evan Andersen; Marcel Huntemann; Neha Varghese; Michalis Hadjithomas; Kristin Tennessen; Torben Nielsen; Natalia N Ivanova; Nikos C Kyrpides
Journal:  Nucleic Acids Res       Date:  2016-10-13       Impact factor: 16.971

5.  Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities.

Authors:  Gongchao Jing; Zheng Sun; Honglei Wang; Yanhai Gong; Shi Huang; Kang Ning; Jian Xu; Xiaoquan Su
Journal:  Sci Rep       Date:  2017-01-12       Impact factor: 4.379

6.  Let microorganisms do the talking, let us talk more about microorganisms.

Authors:  Corrado Nai; Boris Magrini; Julia Offe
Journal:  Fungal Biol Biotechnol       Date:  2016-07-21

7.  HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks.

Authors:  Ariful Azad; Georgios A Pavlopoulos; Christos A Ouzounis; Nikos C Kyrpides; Aydin Buluç
Journal:  Nucleic Acids Res       Date:  2018-04-06       Impact factor: 16.971

8.  Identifying and Predicting Novelty in Microbiome Studies.

Authors:  Xiaoquan Su; Gongchao Jing; Daniel McDonald; Honglei Wang; Zengbin Wang; Antonio Gonzalez; Zheng Sun; Shi Huang; Jose Navas; Rob Knight; Jian Xu
Journal:  MBio       Date:  2018-11-13       Impact factor: 7.867

9.  Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications.

Authors:  Keith A Jolley; James E Bray; Martin C J Maiden
Journal:  Wellcome Open Res       Date:  2018-09-24

10.  Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection.

Authors:  Rekha Seshadri; Sinead C Leahy; Graeme T Attwood; Koon Hoong Teh; Suzanne C Lambie; Adrian L Cookson; Emiley A Eloe-Fadrosh; Georgios A Pavlopoulos; Michalis Hadjithomas; Neha J Varghese; David Paez-Espino; Rechelle Perry; Gemma Henderson; Christopher J Creevey; Nicolas Terrapon; Pascal Lapebie; Elodie Drula; Vincent Lombard; Edward Rubin; Nikos C Kyrpides; Bernard Henrissat; Tanja Woyke; Natalia N Ivanova; William J Kelly
Journal:  Nat Biotechnol       Date:  2018-03-19       Impact factor: 54.908

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