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Results: 1 to 20 of 101

1.

Metagenomic biomarker discovery and explanation.

Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C.

Genome Biol. 2011 Jun 24;12(6):R60. doi: 10.1186/gb-2011-12-6-r60.

PMID:
21702898
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.

Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M.

BMC Genomics. 2011;12 Suppl 2:S4. doi: 10.1186/1471-2164-12-S2-S4. Epub 2011 Jul 27.

PMID:
21989143
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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

Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C.

Nat Methods. 2012 Jun 10;9(8):811-4. doi: 10.1038/nmeth.2066.

PMID:
22688413
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions.

Wang TY, Su CH, Tsai HK.

Bioinformatics. 2011 Dec 15;27(24):3341-7. doi: 10.1093/bioinformatics/btr583. Epub 2011 Oct 20.

PMID:
22016405
[PubMed - indexed for MEDLINE]
Free Article
5.

Bambus 2: scaffolding metagenomes.

Koren S, Treangen TJ, Pop M.

Bioinformatics. 2011 Nov 1;27(21):2964-71. doi: 10.1093/bioinformatics/btr520. Epub 2011 Sep 16.

PMID:
21926123
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.

Jiao D, Ye Y, Tang H.

PLoS Comput Biol. 2013;9(3):e1002981. doi: 10.1371/journal.pcbi.1002981. Epub 2013 Mar 21.

PMID:
23555216
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Identifying biologically relevant differences between metagenomic communities.

Parks DH, Beiko RG.

Bioinformatics. 2010 Mar 15;26(6):715-21. doi: 10.1093/bioinformatics/btq041. Epub 2010 Feb 3.

PMID:
20130030
[PubMed - indexed for MEDLINE]
Free Article
8.

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.

Nijkamp JF, Pop M, Reinders MJ, de Ridder D.

Bioinformatics. 2013 Nov 15;29(22):2826-34. doi: 10.1093/bioinformatics/btt502. Epub 2013 Sep 20.

PMID:
24058058
[PubMed - indexed for MEDLINE]
9.

cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data.

Zhou F, Xu Y.

Bioinformatics. 2010 Aug 15;26(16):2051-2. doi: 10.1093/bioinformatics/btq299. Epub 2010 Jun 10.

PMID:
20538725
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

[A review on the bioinformatics pipelines for metagenomic research].

Ye DD, Fan MM, Guan Q, Chen HJ, Ma ZS.

Dongwuxue Yanjiu. 2012 Dec;33(6):574-85. doi: 10.3724/SP.J.1141.2012.06574. Review. Chinese.

PMID:
23266976
[PubMed - indexed for MEDLINE]
Free Article
11.

SitePainter: a tool for exploring biogeographical patterns.

Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R.

Bioinformatics. 2012 Feb 1;28(3):436-8. doi: 10.1093/bioinformatics/btr685. Epub 2011 Dec 9.

PMID:
22171330
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Adapting functional genomic tools to metagenomic analyses: investigating the role of gut bacteria in relation to obesity.

Liu Y, Zhang C, Zhao L, Nardini C.

Brief Funct Genomics. 2010 Dec;9(5-6):355-61. doi: 10.1093/bfgp/elq011. Epub 2010 May 6.

PMID:
21266343
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes.

Kristiansson E, Hugenholtz P, Dalevi D.

Bioinformatics. 2009 Oct 15;25(20):2737-8. doi: 10.1093/bioinformatics/btp508. Epub 2009 Aug 20.

PMID:
19696045
[PubMed - indexed for MEDLINE]
Free Article
14.

CoMet--a web server for comparative functional profiling of metagenomes.

Lingner T, Asshauer KP, Schreiber F, Meinicke P.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W518-23. doi: 10.1093/nar/gkr388. Epub 2011 May 26.

PMID:
21622656
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Sparse distance-based learning for simultaneous multiclass classification and feature selection of metagenomic data.

Liu Z, Hsiao W, Cantarel BL, Drábek EF, Fraser-Liggett C.

Bioinformatics. 2011 Dec 1;27(23):3242-9. doi: 10.1093/bioinformatics/btr547. Epub 2011 Oct 7.

PMID:
21984758
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Ocean viruses: rigorously evaluating the metagenomic sample-to-sequence pipeline.

Duhaime MB, Sullivan MB.

Virology. 2012 Dec 20;434(2):181-6. doi: 10.1016/j.virol.2012.09.036. Epub 2012 Oct 16. Review.

PMID:
23084423
[PubMed - indexed for MEDLINE]
Free Article
17.

MetaBinG: using GPUs to accelerate metagenomic sequence classification.

Jia P, Xuan L, Liu L, Wei C.

PLoS One. 2011;6(11):e25353. doi: 10.1371/journal.pone.0025353. Epub 2011 Nov 23.

PMID:
22132069
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Metagenomics and antibiotics.

Garmendia L, Hernandez A, Sanchez MB, Martinez JL.

Clin Microbiol Infect. 2012 Jul;18 Suppl 4:27-31. doi: 10.1111/j.1469-0691.2012.03868.x. Review.

PMID:
22647044
[PubMed - indexed for MEDLINE]
19.

Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics.

Shah N, Tang H, Doak TG, Ye Y.

Pac Symp Biocomput. 2011:165-76.

PMID:
21121044
[PubMed - indexed for MEDLINE]
Free Article
20.

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.

Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL.

Nucleic Acids Res. 2012 Jan;40(1):e9. doi: 10.1093/nar/gkr1067. Epub 2011 Nov 18.

PMID:
22102569
[PubMed - indexed for MEDLINE]
Free PMC Article

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