Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 102

1.

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.

2.

PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data.

Shao W, Kearney MF, Boltz VF, Spindler JE, Mellors JW, Maldarelli F, Coffin JM.

J Virol Methods. 2014 Jul;203:73-80. doi: 10.1016/j.jviromet.2014.03.008. Epub 2014 Mar 26.

3.

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
4.

RecDraw: a software package for the representation of HIV-1 recombinant structures.

Kijak GH, Tovanabutra S, Beyrer C, Sanders-Buell EE, Arroyo MA, Robb ML, Michael NL, McCutchan FE, Kim JH.

AIDS Res Hum Retroviruses. 2010 Dec;26(12):1317-21. doi: 10.1089/aid.2010.0127. Epub 2010 Oct 21.

5.

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.

6.

An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing.

Simen BB, Braverman MS, Abbate I, Aerssens J, Bidet Y, Bouchez O, Gabriel C, Izopet J, Kessler HH, Stelzl E, Di Giallonardo F, Schlapbach R, Radonic A, Paredes R, Recordon-Pinson P, Sakwa J, St John EP, Schmitz-Agheguian GG, Metzner KJ, Däumer MP; 454 HIV Alphastudy Group.

J Virol Methods. 2014 Aug;204:31-7. doi: 10.1016/j.jviromet.2014.04.007. Epub 2014 Apr 13.

PMID:
24731928
7.

CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.

Chung WC, Chen CC, Ho JM, Lin CY, Hsu WL, Wang YC, Lee DT, Lai F, Huang CW, Chang YJ.

PLoS One. 2014 Jun 4;9(6):e98146. doi: 10.1371/journal.pone.0098146. eCollection 2014.

8.

HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model.

Prabhakaran S, Rey M, Zagordi O, Beerenwinkel N, Roth V.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):182-91. doi: 10.1109/TCBB.2013.145.

PMID:
26355517
9.

ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.

Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N.

BMC Bioinformatics. 2011 Apr 26;12:119. doi: 10.1186/1471-2105-12-119.

10.

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.

Yuan T, Huang X, Dittmar RL, Du M, Kohli M, Boardman L, Thibodeau SN, Wang L.

BMC Genomics. 2014 Mar 5;15:176. doi: 10.1186/1471-2164-15-176.

11.

[Application of Next-generation Sequencing Techniques in the Dynamics of HIV-1 Quasispecies].

Zhang J, Xing H.

Bing Du Xue Bao. 2015 Sep;31(5):573-8. Review. Chinese.

PMID:
26738298
12.

Oasis: online analysis of small RNA deep sequencing data.

Capece V, Garcia Vizcaino JC, Vidal R, Rahman RU, Pena Centeno T, Shomroni O, Suberviola I, Fischer A, Bonn S.

Bioinformatics. 2015 Jul 1;31(13):2205-7. doi: 10.1093/bioinformatics/btv113. Epub 2015 Feb 19.

13.

SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects.

Dereeper A, Nicolas S, Le Cunff L, Bacilieri R, Doligez A, Peros JP, Ruiz M, This P.

BMC Bioinformatics. 2011 May 5;12:134. doi: 10.1186/1471-2105-12-134.

14.

Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes.

Gall A, Ferns B, Morris C, Watson S, Cotten M, Robinson M, Berry N, Pillay D, Kellam P.

J Clin Microbiol. 2012 Dec;50(12):3838-44. doi: 10.1128/JCM.01516-12. Epub 2012 Sep 19.

15.

High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems.

Yin L, Liu L, Sun Y, Hou W, Lowe AC, Gardner BP, Salemi M, Williams WB, Farmerie WG, Sleasman JW, Goodenow MM.

Retrovirology. 2012 Dec 17;9:108. doi: 10.1186/1742-4690-9-108.

16.

Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.

Wang B, Cunningham JM, Yang XH.

Bioinformatics. 2015 Sep 15;31(18):3043-5. doi: 10.1093/bioinformatics/btv289. Epub 2015 May 15.

17.

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.

18.

HIV-1 quasispecies delineation by tag linkage deep sequencing.

Wu NC, De La Cruz J, Al-Mawsawi LQ, Olson CA, Qi H, Luan HH, Nguyen N, Du Y, Le S, Wu TT, Li X, Lewis MJ, Yang OO, Sun R.

PLoS One. 2014 May 19;9(5):e97505. doi: 10.1371/journal.pone.0097505. eCollection 2014.

19.

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
20.

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.

Supplemental Content

Support Center