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Items: 1 to 20 of 203

1.

metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.

Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ.

BMC Bioinformatics. 2013;14 Suppl 5:S2. doi: 10.1186/1471-2105-14-S5-S2. Epub 2013 Apr 10.

2.

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform.

Cox AJ, Bauer MJ, Jakobi T, Rosone G.

Bioinformatics. 2012 Jun 1;28(11):1415-9. doi: 10.1093/bioinformatics/bts173. Epub 2012 May 3.

3.

Adaptive reference-free compression of sequence quality scores.

Janin L, Rosone G, Cox AJ.

Bioinformatics. 2014 Jan 1;30(1):24-30. doi: 10.1093/bioinformatics/btt257. Epub 2013 May 9.

4.

CLAST: CUDA implemented large-scale alignment search tool.

Yano M, Mori H, Akiyama Y, Yamada T, Kurokawa K.

BMC Bioinformatics. 2014 Dec 11;15:406. doi: 10.1186/s12859-014-0406-y.

5.

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.

6.

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.

7.

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads.

Rosen GL, Reichenberger ER, Rosenfeld AM.

Bioinformatics. 2011 Jan 1;27(1):127-9. doi: 10.1093/bioinformatics/btq619. Epub 2010 Nov 8.

8.

High throughput sequencing methods for microbiome profiling: application to food animal systems.

Highlander SK.

Anim Health Res Rev. 2012 Jun;13(1):40-53. doi: 10.1017/S1466252312000126. Review.

PMID:
22853944
9.

Phylogeny-based classification of microbial communities.

Tanaseichuk O, Borneman J, Jiang T.

Bioinformatics. 2014 Feb 15;30(4):449-56. doi: 10.1093/bioinformatics/btt700. Epub 2013 Dec 24.

10.

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets.

Scheuch M, Höper D, Beer M.

BMC Bioinformatics. 2015 Mar 3;16:69. doi: 10.1186/s12859-015-0503-6.

11.

Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.

12.

Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis.

Danhorn T, Young CR, DeLong EF.

ISME J. 2012 Nov;6(11):2056-66. doi: 10.1038/ismej.2012.35. Epub 2012 Apr 26. Erratum in: ISME J. 2012 Nov;6(11):2152.

13.

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C.

Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.

14.

A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.

Zhang Y, Sun Y, Cole JR.

PLoS Comput Biol. 2014 Aug 14;10(8):e1003737. doi: 10.1371/journal.pcbi.1003737. eCollection 2014 Aug.

15.

Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches.

Logares R, Haverkamp TH, Kumar S, Lanzén A, Nederbragt AJ, Quince C, Kauserud H.

J Microbiol Methods. 2012 Oct;91(1):106-13. doi: 10.1016/j.mimet.2012.07.017. Epub 2012 Jul 28. Review.

PMID:
22849829
16.

Low sequencing efforts bias analyses of shared taxa in microbial communities.

Lemos LN, Fulthorpe RR, Roesch LF.

Folia Microbiol (Praha). 2012 Sep;57(5):409-13. doi: 10.1007/s12223-012-0155-0. Epub 2012 May 5.

PMID:
22562492
17.

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms.

Liu J, Wang H, Yang H, Zhang Y, Wang J, Zhao F, Qi J.

Nucleic Acids Res. 2013 Jan 7;41(1):e3. doi: 10.1093/nar/gks828. Epub 2012 Aug 31.

18.

BEETL-fastq: a searchable compressed archive for DNA reads.

Janin L, Schulz-Trieglaff O, Cox AJ.

Bioinformatics. 2014 Oct;30(19):2796-801. doi: 10.1093/bioinformatics/btu387. Epub 2014 Jun 20.

19.

A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.

Jiang H, An L, Lin SM, Feng G, Qiu Y.

PLoS One. 2012;7(10):e46450. doi: 10.1371/journal.pone.0046450. Epub 2012 Oct 1. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/c08da7e7-60fe-4f7d-a457-299bf9f24148.

20.

Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.

Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML.

ISME J. 2015 Mar 17;9(4):968-79. doi: 10.1038/ismej.2014.195.

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