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Results: 1 to 20 of 106

Similar articles for PubMed (Select 23257116)

1.

Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes.

Schirmer M, Sloan WT, Quince C.

Brief Bioinform. 2014 May;15(3):431-42. doi: 10.1093/bib/bbs081. Epub 2012 Dec 19. Review.

PMID:
23257116
2.

ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing.

Jayasundara D, Saeed I, Maheswararajah S, Chang BC, Tang SL, Halgamuge SK.

Bioinformatics. 2015 Mar 15;31(6):886-96. doi: 10.1093/bioinformatics/btu754. Epub 2014 Nov 13.

PMID:
25398613
3.

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.

Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.

Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386. Epub 2013 Jul 3.

4.

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.

Giallonardo FD, Töpfer A, Rey M, Prabhakaran S, Duport Y, Leemann C, Schmutz S, Campbell NK, Joos B, Lecca MR, Patrignani A, Däumer M, Beisel C, Rusert P, Trkola A, Günthard HF, Roth V, Beerenwinkel N, Metzner KJ.

Nucleic Acids Res. 2014 Aug;42(14):e115. doi: 10.1093/nar/gku537. Epub 2014 Jun 27.

5.

Viral quasispecies assembly via maximal clique enumeration.

Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A, Beerenwinkel N.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003515. doi: 10.1371/journal.pcbi.1003515. eCollection 2014 Mar.

6.

Nautilus: a bioinformatics package for the analysis of HIV type 1 targeted deep sequencing data.

Kijak GH, Pham P, Sanders-Buell E, Harbolick EA, Eller LA, Robb ML, Michael NL, Kim JH, Tovanabutra S.

AIDS Res Hum Retroviruses. 2013 Oct;29(10):1361-4. doi: 10.1089/AID.2013.0175. Epub 2013 Aug 2.

7.

The linkage method: a novel approach for SNP detection and haplotype reconstruction from a single diploid individual using next-generation sequence data.

Sasaki E, Sugino RP, Innan H.

Mol Biol Evol. 2013 Sep;30(9):2187-96. doi: 10.1093/molbev/mst103. Epub 2013 May 31.

8.

HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data.

Berger E, Yorukoglu D, Peng J, Berger B.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003502. doi: 10.1371/journal.pcbi.1003502. eCollection 2014 Mar.

9.

Haplotype reconstruction from SNP alignment.

Li LM, Kim JH, Waterman MS.

J Comput Biol. 2004;11(2-3):505-16.

PMID:
15285905
10.
11.

HapCompass: a fast cycle basis algorithm for accurate haplotype assembly of sequence data.

Aguiar D, Istrail S.

J Comput Biol. 2012 Jun;19(6):577-90. doi: 10.1089/cmb.2012.0084.

12.

Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing.

Djari A, Esquerré D, Weiss B, Martins F, Meersseman C, Boussaha M, Klopp C, Rocha D.

BMC Genomics. 2013 May 7;14:307. doi: 10.1186/1471-2164-14-307.

13.

HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination.

Zhang K, Sun F, Zhao H.

Bioinformatics. 2005 Jan 1;21(1):90-103. Epub 2004 Jul 1.

14.

Haplotype reconstruction using perfect phylogeny and sequence data.

Efros A, Halperin E.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S3. doi: 10.1186/1471-2105-13-S6-S3.

15.
16.

Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination.

Di Giallonardo F, Zagordi O, Duport Y, Leemann C, Joos B, Künzli-Gontarczyk M, Bruggmann R, Beerenwinkel N, Günthard HF, Metzner KJ.

PLoS One. 2013 Sep 18;8(9):e74249. doi: 10.1371/journal.pone.0074249. eCollection 2013.

17.

Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows.

Skums P, Mancuso N, Artyomenko A, Tork B, Mandoiu I, Khudyakov Y, Zelikovsky A.

BMC Bioinformatics. 2013;14 Suppl 9:S2. doi: 10.1186/1471-2105-14-S9-S2. Epub 2013 Jun 28.

18.

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.

19.

Mutant-bin: unsupervised haplotype estimation of viral population diversity without reference genome.

Prabhakara S, Malhotra R, Acharya R, Poss M.

J Comput Biol. 2013 Jun;20(6):453-63. doi: 10.1089/cmb.2012.0174.

PMID:
23718149
20.

HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies.

Kim JH, Kim WC, Li LM, Park S.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W557-61. doi: 10.1093/nar/gkr354. Epub 2011 May 16.

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