Literature DB >> 26448087

Strain recovery from metagenomes.

C Titus Brown1.   

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Year:  2015        PMID： 26448087     DOI： 10.1038/nbt.3375

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


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  12 in total

1.  SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Authors:  Anton Bankevich; Sergey Nurk; Dmitry Antipov; Alexey A Gurevich; Mikhail Dvorkin; Alexander S Kulikov; Valery M Lesin; Sergey I Nikolenko; Son Pham; Andrey D Prjibelski; Alexey V Pyshkin; Alexander V Sirotkin; Nikolay Vyahhi; Glenn Tesler; Max A Alekseyev; Pavel A Pevzner
Journal:  J Comput Biol       Date:  2012-04-16       Impact factor: 1.479

2.  Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota.

Authors:  Vaughn Iverson; Robert M Morris; Christian D Frazar; Chris T Berthiaume; Rhonda L Morales; E Virginia Armbrust
Journal:  Science       Date:  2012-02-03       Impact factor: 47.728

3.  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

4.  Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning.

Authors:  Brian Cleary; Ilana Lauren Brito; Katherine Huang; Dirk Gevers; Terrance Shea; Sarah Young; Eric J Alm
Journal:  Nat Biotechnol       Date:  2015-09-14       Impact factor: 54.908

5.  Metagenomic microbial community profiling using unique clade-specific marker genes.

Authors:  Nicola Segata; Levi Waldron; Annalisa Ballarini; Vagheesh Narasimhan; Olivier Jousson; Curtis Huttenhower
Journal:  Nat Methods       Date:  2012-06-10       Impact factor: 28.547

6.  Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.

Authors:  Itai Sharon; Michael J Morowitz; Brian C Thomas; Elizabeth K Costello; David A Relman; Jillian F Banfield
Journal:  Genome Res       Date:  2012-08-30       Impact factor: 9.043

7.  Metabolic reconstruction for metagenomic data and its application to the human microbiome.

Authors:  Sahar Abubucker; Nicola Segata; Johannes Goll; Alyxandria M Schubert; Jacques Izard; Brandi L Cantarel; Beltran Rodriguez-Mueller; Jeremy Zucker; Mathangi Thiagarajan; Bernard Henrissat; Owen White; Scott T Kelley; Barbara Methé; Patrick D Schloss; Dirk Gevers; Makedonka Mitreva; Curtis Huttenhower
Journal:  PLoS Comput Biol       Date:  2012-06-13       Impact factor: 4.475

8.  Open science resources for the discovery and analysis of Tara Oceans data.

Authors:  Stéphane Pesant; Fabrice Not; Marc Picheral; Stefanie Kandels-Lewis; Noan Le Bescot; Gabriel Gorsky; Daniele Iudicone; Eric Karsenti; Sabrina Speich; Romain Troublé; Céline Dimier; Sarah Searson
Journal:  Sci Data       Date:  2015-05-26       Impact factor: 6.444

9.  Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.

Authors:  Andy Rimmer; Hang Phan; Iain Mathieson; Zamin Iqbal; Stephen R F Twigg; Andrew O M Wilkie; Gil McVean; Gerton Lunter
Journal:  Nat Genet       Date:  2014-07-13       Impact factor: 38.330

10.  GroopM: an automated tool for the recovery of population genomes from related metagenomes.

Authors:  Michael Imelfort; Donovan Parks; Ben J Woodcroft; Paul Dennis; Philip Hugenholtz; Gene W Tyson
Journal:  PeerJ       Date:  2014-09-30       Impact factor: 2.984
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  7 in total

1.  Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters.

Authors:  David M Needham; Rohan Sachdeva; Jed A Fuhrman
Journal:  ISME J       Date:  2017-04-11       Impact factor: 10.302

2.  Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets.

Authors:  Yi Yue; Hao Huang; Zhao Qi; Hui-Min Dou; Xin-Yi Liu; Tian-Fei Han; Yue Chen; Xiang-Jun Song; You-Hua Zhang; Jian Tu
Journal:  BMC Bioinformatics       Date:  2020-07-28       Impact factor: 3.169

3.  Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level.

Authors:  Michael Schmid; Jonathan Muri; Damianos Melidis; Adithi R Varadarajan; Vincent Somerville; Adrian Wicki; Aline Moser; Marc Bourqui; Claudia Wenzel; Elisabeth Eugster-Meier; Juerg E Frey; Stefan Irmler; Christian H Ahrens
Journal:  Front Microbiol       Date:  2018-01-30       Impact factor: 5.640

4.  Exploring neighborhoods in large metagenome assembly graphs using spacegraphcats reveals hidden sequence diversity.

Authors:  C Titus Brown; Dominik Moritz; Michael P O'Brien; Felix Reidl; Taylor Reiter; Blair D Sullivan
Journal:  Genome Biol       Date:  2020-07-06       Impact factor: 13.583

5.  Pseudomonas PB1-Like Phages: Whole Genomes from Metagenomes Offer Insight into an Abundant Group of Bacteriophages.

Authors:  Siobhan C Watkins; Emily Sible; Catherine Putonti
Journal:  Viruses       Date:  2018-06-16       Impact factor: 5.048

Review 6.  Recovering complete and draft population genomes from metagenome datasets.

Authors:  Naseer Sangwan; Fangfang Xia; Jack A Gilbert
Journal:  Microbiome       Date:  2016-03-08       Impact factor: 14.650

Review 7.  Single-cell metagenomics: challenges and applications.

Authors:  Yuan Xu; Fangqing Zhao
Journal:  Protein Cell       Date:  2018-04-25       Impact factor: 14.870
  7 in total

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