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Items: 1 to 20 of 336

1.

Short clones or long clones? A simulation study on the use of paired reads in metagenomics.

Mitra S, Schubach M, Huson DH.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S12. doi: 10.1186/1471-2105-11-S1-S12.

2.

Unlocking short read sequencing for metagenomics.

Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW.

PLoS One. 2010 Jul 28;5(7):e11840. doi: 10.1371/journal.pone.0011840.

3.

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.

Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J.

BMC Bioinformatics. 2009 Dec 18;10:430. doi: 10.1186/1471-2105-10-430.

4.

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

Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC.

Bioinformatics. 2010 Feb 1;26(3):295-301. doi: 10.1093/bioinformatics/btp687. Epub 2009 Dec 14.

5.

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG.

Mitra S, Rupek P, Richter DC, Urich T, Gilbert JA, Meyer F, Wilke A, Huson DH.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S21. doi: 10.1186/1471-2105-12-S1-S21.

6.

Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology.

Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD.

BMC Genomics. 2006 Oct 24;7:272.

7.

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

Brown BL, Watson M, Minot SS, Rivera MC, Franklin RB.

Gigascience. 2017 Mar 1;6(3):1-10. doi: 10.1093/gigascience/gix007.

8.

MEGAN analysis of metagenomic data.

Huson DH, Auch AF, Qi J, Schuster SC.

Genome Res. 2007 Mar;17(3):377-86. Epub 2007 Jan 25.

9.

MetaSim: a sequencing simulator for genomics and metagenomics.

Richter DC, Ott F, Auch AF, Schmid R, Huson DH.

PLoS One. 2008 Oct 8;3(10):e3373. doi: 10.1371/journal.pone.0003373.

10.

A better sequence-read simulator program for metagenomics.

Johnson S, Trost B, Long JR, Pittet V, Kusalik A.

BMC Bioinformatics. 2014;15 Suppl 9:S14. doi: 10.1186/1471-2105-15-S9-S14. Epub 2014 Sep 10.

11.

Metagenomics: read length matters.

Wommack KE, Bhavsar J, Ravel J.

Appl Environ Microbiol. 2008 Mar;74(5):1453-63. doi: 10.1128/AEM.02181-07. Epub 2008 Jan 11.

12.

GemSIM: general, error-model based simulator of next-generation sequencing data.

McElroy KE, Luciani F, Thomas T.

BMC Genomics. 2012 Feb 15;13:74. doi: 10.1186/1471-2164-13-74.

13.

Assessment of metagenomic assembly using simulated next generation sequencing data.

Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P.

PLoS One. 2012;7(2):e31386. doi: 10.1371/journal.pone.0031386. Epub 2012 Feb 23. Erratum in: PLoS One. 2014;9(11):e114063.

14.

Analysis of 16S rRNA environmental sequences using MEGAN.

Mitra S, Stärk M, Huson DH.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S17. doi: 10.1186/1471-2164-12-S3-S17. Epub 2011 Nov 30.

15.

A pilot study for channel catfish whole genome sequencing and de novo assembly.

Jiang Y, Lu J, Peatman E, Kucuktas H, Liu S, Wang S, Sun F, Liu Z.

BMC Genomics. 2011 Dec 22;12:629. doi: 10.1186/1471-2164-12-629.

16.

SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences.

Monzoorul Haque M, Ghosh TS, Komanduri D, Mande SS.

Bioinformatics. 2009 Jul 15;25(14):1722-30. doi: 10.1093/bioinformatics/btp317. Epub 2009 May 13.

PMID:
19439565
17.

Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

Huson DH, Tappu R, Bazinet AL, Xie C, Cummings MP, Nieselt K, Williams R.

Microbiome. 2017 Jan 25;5(1):11. doi: 10.1186/s40168-017-0233-2.

18.

MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing.

Pan W, Chen B, Xu Y.

Interdiscip Sci. 2015 Dec;7(4):405-13. doi: 10.1007/s12539-015-0281-x. Epub 2015 Aug 21.

PMID:
26293485
19.

Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing.

Mitra S, Förster-Fromme K, Damms-Machado A, Scheurenbrand T, Biskup S, Huson DH, Bischoff SC.

BMC Genomics. 2013;14 Suppl 5:S16. doi: 10.1186/1471-2164-14-S5-S16. Epub 2013 Oct 16.

20.

MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.

Reddy RM, Mohammed MH, Mande SS.

Genomics. 2014 Feb-Mar;103(2-3):161-8. doi: 10.1016/j.ygeno.2014.02.007. Epub 2014 Mar 5.

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