Literature DB >> 24824669

Estimating coverage in metagenomic data sets and why it matters.

Luis M Rodriguez-R1, Konstantinos T Konstantinidis1.   

Abstract

Mesh：

Year:  2014        PMID： 24824669      PMCID： PMC4992084          DOI： 10.1038/ismej.2014.76

Source DB:  PubMed          Journal:  ISME J        ISSN： 1751-7362            Impact factor:   10.302


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  10 in total

Review 1.  Bacterial species may exist, metagenomics reveal.

Authors:  Alejandro Caro-Quintero; Konstantinos T Konstantinidis
Journal:  Environ Microbiol       Date:  2011-12-12       Impact factor: 5.491

2.  Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets.

Authors:  Luis M Rodriguez-R; Konstantinos T Konstantinidis
Journal:  Bioinformatics       Date:  2013-10-11       Impact factor: 6.937

3.  Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities.

Authors:  Patrick D Schloss; Sarah L Westcott; Thomas Ryabin; Justine R Hall; Martin Hartmann; Emily B Hollister; Ryan A Lesniewski; Brian B Oakley; Donovan H Parks; Courtney J Robinson; Jason W Sahl; Blaz Stres; Gerhard G Thallinger; David J Van Horn; Carolyn F Weber
Journal:  Appl Environ Microbiol       Date:  2009-10-02       Impact factor: 4.792

4.  Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

Authors:  Noah Fierer; Jonathan W Leff; Byron J Adams; Uffe N Nielsen; Scott Thomas Bates; Christian L Lauber; Sarah Owens; Jack A Gilbert; Diana H Wall; J Gregory Caporaso
Journal:  Proc Natl Acad Sci U S A       Date:  2012-12-10       Impact factor: 11.205

5.  Genomic mapping by fingerprinting random clones: a mathematical analysis.

Authors:  E S Lander; M S Waterman
Journal:  Genomics       Date:  1988-04       Impact factor: 5.736

6.  Occupancy modeling, maximum contig size probabilities and designing metagenomics experiments.

Authors:  Stephen A Stanhope
Journal:  PLoS One       Date:  2010-07-29       Impact factor: 3.240

7.  Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem.

Authors:  Michael C Wendl; Karthik Kota; George M Weinstock; Makedonka Mitreva
Journal:  J Math Biol       Date:  2012-09-11       Impact factor: 2.259

8.  Predicting the molecular complexity of sequencing libraries.

Authors:  Timothy Daley; Andrew D Smith
Journal:  Nat Methods       Date:  2013-02-24       Impact factor: 28.547

9.  Differential expression analysis for sequence count data.

Authors:  Simon Anders; Wolfgang Huber
Journal:  Genome Biol       Date:  2010-10-27       Impact factor: 13.583

10.  Estimating DNA coverage and abundance in metagenomes using a gamma approximation.

Authors:  Sean D Hooper; Daniel Dalevi; Amrita Pati; Konstantinos Mavromatis; Natalia N Ivanova; Nikos C Kyrpides
Journal:  Bioinformatics       Date:  2009-12-14       Impact factor: 6.937
  10 in total
  46 in total

1.  Widely Used Benzalkonium Chloride Disinfectants Can Promote Antibiotic Resistance.

Authors:  Minjae Kim; Michael R Weigand; Seungdae Oh; Janet K Hatt; Raj Krishnan; Ulas Tezel; Spyros G Pavlostathis; Konstantinos T Konstantinidis
Journal:  Appl Environ Microbiol       Date:  2018-08-17       Impact factor: 4.792

2.  Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths.

Authors:  Eric R Johnston; Janet K Hatt; Zhili He; Liyou Wu; Xue Guo; Yiqi Luo; Edward A G Schuur; James M Tiedje; Jizhong Zhou; Konstantinos T Konstantinidis
Journal:  Proc Natl Acad Sci U S A       Date:  2019-07-08       Impact factor: 11.205

3.  Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe.

Authors:  Ximei Zhang; Eric R Johnston; Linghao Li; Konstantinos T Konstantinidis; Xingguo Han
Journal:  ISME J       Date:  2016-12-20       Impact factor: 10.302

4.  Partial recovery of microbiomes after antibiotic treatment.

Authors:  Frédéric Raymond; Maxime Déraspe; Maurice Boissinot; Michel G Bergeron; Jacques Corbeil
Journal:  Gut Microbes       Date:  2016-08-05

5.  Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.

Authors:  Alejandro Palomo; S Jane Fowler; Arda Gülay; Simon Rasmussen; Thomas Sicheritz-Ponten; Barth F Smets
Journal:  ISME J       Date:  2016-04-29       Impact factor: 10.302

6.  Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill.

Authors:  Luis M Rodriguez-R; Will A Overholt; Christopher Hagan; Markus Huettel; Joel E Kostka; Konstantinos T Konstantinidis
Journal:  ISME J       Date:  2015-02-17       Impact factor: 10.302

7.  Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods.

Authors:  Andrew D Huang; Chengwei Luo; Angela Pena-Gonzalez; Michael R Weigand; Cheryl L Tarr; Konstantinos T Konstantinidis
Journal:  Appl Environ Microbiol       Date:  2017-01-17       Impact factor: 4.792

8.  Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal.

Authors:  Norihisa Matsuura; Yalkhin Masakke; Smruthi Karthikeyan; Sui Kanazawa; Ryo Honda; Ryoko Yamamoto-Ikemoto; Konstantinos T Konstantinidis
Journal:  Appl Microbiol Biotechnol       Date:  2021-02-08       Impact factor: 4.813

9.  Structure and variation of root-associated microbiomes of potato grown in alfisol.

Authors:  Ayslu Mardanova; Marat Lutfullin; Guzel Hadieva; Yaw Akosah; Daria Pudova; Daniil Kabanov; Elena Shagimardanova; Petr Vankov; Semyon Vologin; Natalia Gogoleva; Zenon Stasevski; Margarita Sharipova
Journal:  World J Microbiol Biotechnol       Date:  2019-11-14       Impact factor: 3.312

10.  Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.

Authors:  Yuanqi Wang; Janet K Hatt; Despina Tsementzi; Luis M Rodriguez-R; Carlos A Ruiz-Pérez; Michael R Weigand; Heidi Kizer; Gina Maresca; Raj Krishnan; Rachel Poretsky; Jim C Spain; Konstantinos T Konstantinidis
Journal:  Appl Environ Microbiol       Date:  2017-03-31       Impact factor: 4.792
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