Literature DB >> 21358620

Taxonomic metagenome sequence assignment with structured output models.

Kaustubh R Patil, Peter Haider, Phillip B Pope, Peter J Turnbaugh, Mark Morrison, Tobias Scheffer, Alice C McHardy.   

Abstract

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Year:  2011        PMID： 21358620      PMCID： PMC3131843          DOI： 10.1038/nmeth0311-191

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  5 in total

1.  MEGAN analysis of metagenomic data.

Authors:  Daniel H Huson; Alexander F Auch; Ji Qi; Stephan C Schuster
Journal:  Genome Res       Date:  2007-01-25       Impact factor: 9.043

Review 2.  What's in the mix: phylogenetic classification of metagenome sequence samples.

Authors:  Alice C McHardy; Isidore Rigoutsos
Journal:  Curr Opin Microbiol       Date:  2007-10-22       Impact factor: 7.934

Review 3.  A bioinformatician's guide to metagenomics.

Authors:  Victor Kunin; Alex Copeland; Alla Lapidus; Konstantinos Mavromatis; Philip Hugenholtz
Journal:  Microbiol Mol Biol Rev       Date:  2008-12       Impact factor: 11.056

4.  Accurate phylogenetic classification of variable-length DNA fragments.

Authors:  Alice Carolyn McHardy; Héctor García Martín; Aristotelis Tsirigos; Philip Hugenholtz; Isidore Rigoutsos
Journal:  Nat Methods       Date:  2006-12-10       Impact factor: 28.547

5.  Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.

Authors:  Arthur Brady; Steven L Salzberg
Journal:  Nat Methods       Date:  2009-08-02       Impact factor: 28.547
  5 in total
  64 in total

1.  Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics.

Authors:  Masaru K Nobu; Jeremy A Dodsworth; Senthil K Murugapiran; Christian Rinke; Esther A Gies; Gordon Webster; Patrick Schwientek; Peter Kille; R John Parkes; Henrik Sass; Bo B Jørgensen; Andrew J Weightman; Wen-Tso Liu; Steven J Hallam; George Tsiamis; Tanja Woyke; Brian P Hedlund
Journal:  ISME J       Date:  2015-06-19       Impact factor: 10.302

2.  TIPP: taxonomic identification and phylogenetic profiling.

Authors:  Nam-Phuong Nguyen; Siavash Mirarab; Bo Liu; Mihai Pop; Tandy Warnow
Journal:  Bioinformatics       Date:  2014-10-29       Impact factor: 6.937

3.  Low-Density Locality-Sensitive Hashing Boosts Metagenomic Binning.

Authors:  Yunan Luo; Jianyang Zeng; Bonnie Berger; Jian Peng
Journal:  Res Comput Mol Biol       Date:  2016-04

Review 4.  Microbial genome-enabled insights into plant-microorganism interactions.

Authors:  David S Guttman; Alice C McHardy; Paul Schulze-Lefert
Journal:  Nat Rev Genet       Date:  2014-09-30       Impact factor: 53.242

5.  Analysis of the bovine rumen microbiome reveals a diversity of Sus-like polysaccharide utilization loci from the bacterial phylum Bacteroidetes.

Authors:  Carly P Rosewarne; Phillip B Pope; Jane L Cheung; Mark Morrison
Journal:  J Ind Microbiol Biotechnol       Date:  2014-01-22       Impact factor: 3.346

Review 6.  Metabolic network modeling of microbial communities.

Authors:  Matthew B Biggs; Gregory L Medlock; Glynis L Kolling; Jason A Papin
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2015-06-24

Review 7.  The role of the intestinal microbiota in type 1 diabetes mellitus.

Authors:  Mikael Knip; Heli Siljander
Journal:  Nat Rev Endocrinol       Date:  2016-01-04       Impact factor: 43.330

8.  Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.

Authors:  J A Frank; Y Pan; A Tooming-Klunderud; V G H Eijsink; A C McHardy; A J Nederbragt; P B Pope
Journal:  Sci Rep       Date:  2016-05-09       Impact factor: 4.379

9.  Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.

Authors:  Migun Shakya; Christopher Quince; James H Campbell; Zamin K Yang; Christopher W Schadt; Mircea Podar
Journal:  Environ Microbiol       Date:  2013-02-06       Impact factor: 5.491

10.  MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Authors:  Todd J Treangen; Sergey Koren; Daniel D Sommer; Bo Liu; Irina Astrovskaya; Brian Ondov; Aaron E Darling; Adam M Phillippy; Mihai Pop
Journal:  Genome Biol       Date:  2013-01-15       Impact factor: 13.583
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