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Items: 1 to 20 of 81

1.

SEK: sparsity exploiting k-mer-based estimation of bacterial community composition.

Chatterjee S, Koslicki D, Dong S, Innocenti N, Cheng L, Lan Y, Vehkaperä M, Skoglund M, Rasmussen LK, Aurell E, Corander J.

Bioinformatics. 2014 Sep 1;30(17):2423-31. doi: 10.1093/bioinformatics/btu320. Epub 2014 May 7.

PMID:
24812337
2.

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition.

Koslicki D, Chatterjee S, Shahrivar D, Walker AW, Francis SC, Fraser LJ, Vehkaperä M, Lan Y, Corander J.

PLoS One. 2015 Oct 23;10(10):e0140644. doi: 10.1371/journal.pone.0140644. eCollection 2015.

3.

Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing.

Koslicki D, Foucart S, Rosen G.

Bioinformatics. 2013 Sep 1;29(17):2096-102. doi: 10.1093/bioinformatics/btt336. Epub 2013 Jun 20.

PMID:
23786768
4.

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.

PMID:
24369151
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.

Ensemble analysis of adaptive compressed genome sequencing strategies.

Taghavi Z.

BMC Bioinformatics. 2014;15 Suppl 9:S13. doi: 10.1186/1471-2105-15-S9-S13. Epub 2014 Sep 10.

7.

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads.

Mysara M, Leys N, Raes J, Monsieurs P.

BMC Bioinformatics. 2015 Mar 15;16:88. doi: 10.1186/s12859-015-0520-5.

8.

Genometa--a fast and accurate classifier for short metagenomic shotgun reads.

Davenport CF, Neugebauer J, Beckmann N, Friedrich B, Kameri B, Kokott S, Paetow M, Siekmann B, Wieding-Drewes M, Wienhöfer M, Wolf S, Tümmler B, Ahlers V, Sprengel F.

PLoS One. 2012;7(8):e41224. doi: 10.1371/journal.pone.0041224. Epub 2012 Aug 21.

9.

Bacterial community reconstruction using compressed sensing.

Amir A, Zuk O.

J Comput Biol. 2011 Nov;18(11):1723-41. doi: 10.1089/cmb.2011.0189. Epub 2011 Oct 14.

PMID:
21999287
10.

Reference databases for taxonomic assignment in metagenomics.

Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G.

Brief Bioinform. 2012 Nov;13(6):682-95. doi: 10.1093/bib/bbs036. Epub 2012 Jul 10. Review.

PMID:
22786784
11.

WGSQuikr: fast whole-genome shotgun metagenomic classification.

Koslicki D, Foucart S, Rosen G.

PLoS One. 2014 Mar 13;9(3):e91784. doi: 10.1371/journal.pone.0091784. eCollection 2014.

12.

Accurate taxonomic assignment of short pyrosequencing reads.

Clemente JC, Jansson J, Valiente G.

Pac Symp Biocomput. 2010:3-9.

13.

Flexible taxonomic assignment of ambiguous sequencing reads.

Clemente JC, Jansson J, Valiente G.

BMC Bioinformatics. 2011 Jan 7;12:8. doi: 10.1186/1471-2105-12-8.

14.

Mixture models for analysis of the taxonomic composition of metagenomes.

Meinicke P, Asshauer KP, Lingner T.

Bioinformatics. 2011 Jun 15;27(12):1618-24. doi: 10.1093/bioinformatics/btr266. Epub 2011 May 5.

15.

Further steps in TANGO: improved taxonomic assignment in metagenomics.

Alonso-Alemany D, Barré A, Beretta S, Bonizzoni P, Nikolski M, Valiente G.

Bioinformatics. 2014 Jan 1;30(1):17-23. doi: 10.1093/bioinformatics/btt256. Epub 2013 May 3.

PMID:
23645816
16.

High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.

Amir A, Zeisel A, Zuk O, Elgart M, Stern S, Shamir O, Turnbaugh PJ, Soen Y, Shental N.

Nucleic Acids Res. 2013 Dec;41(22):e205. doi: 10.1093/nar/gkt1070. Epub 2013 Nov 7.

17.

A de novo metagenomic assembly program for shotgun DNA reads.

Lai B, Ding R, Li Y, Duan L, Zhu H.

Bioinformatics. 2012 Jun 1;28(11):1455-62. doi: 10.1093/bioinformatics/bts162. Epub 2012 Apr 11.

PMID:
22495746
18.

Computational challenges of sequence classification in microbiomic data.

Ribeca P, Valiente G.

Brief Bioinform. 2011 Nov;12(6):614-25. doi: 10.1093/bib/bbr019. Epub 2011 Apr 18.

PMID:
21504986
19.

Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform.

Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, Allcock R, O'Donnell A.

J Microbiol Methods. 2012 Oct;91(1):80-8. doi: 10.1016/j.mimet.2012.07.008. Epub 2012 Jul 29.

PMID:
22849830
20.

CCLasso: correlation inference for compositional data through Lasso.

Fang H, Huang C, Zhao H, Deng M.

Bioinformatics. 2015 Oct 1;31(19):3172-80. doi: 10.1093/bioinformatics/btv349. Epub 2015 Jun 4.

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