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Items: 1 to 20 of 35

1.

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.

Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM, Casali M, Pesko KN, Boutwell CL, DeVincenzo JP, Ebel GD, Allen TM, Zody MC, Henn MR, Levin JZ.

Nucleic Acids Res. 2013 Jan 7;41(1):e13. doi: 10.1093/nar/gks794. Epub 2012 Sep 8.

2.

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.

Namiki T, Hachiya T, Tanaka H, Sakakibara Y.

Nucleic Acids Res. 2012 Nov 1;40(20):e155. doi: 10.1093/nar/gks678. Epub 2012 Jul 19.

3.

Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity.

Parameswaran P, Charlebois P, Tellez Y, Nunez A, Ryan EM, Malboeuf CM, Levin JZ, Lennon NJ, Balmaseda A, Harris E, Henn MR.

J Virol. 2012 Aug;86(16):8546-58. doi: 10.1128/JVI.00736-12. Epub 2012 May 30.

4.

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.

Macalalad AR, Zody MC, Charlebois P, Lennon NJ, Newman RM, Malboeuf CM, Ryan EM, Boutwell CL, Power KA, Brackney DE, Pesko KN, Levin JZ, Ebel GD, Allen TM, Birren BW, Henn MR.

PLoS Comput Biol. 2012;8(3):e1002417. doi: 10.1371/journal.pcbi.1002417. Epub 2012 Mar 15.

5.

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.

Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, G√ľnthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM.

PLoS Pathog. 2012;8(3):e1002529. doi: 10.1371/journal.ppat.1002529. Epub 2012 Mar 8.

6.

Internally deleted WNV genomes isolated from exotic birds in New Mexico: function in cells, mosquitoes, and mice.

Pesko KN, Fitzpatrick KA, Ryan EM, Shi PY, Zhang B, Lennon NJ, Newman RM, Henn MR, Ebel GD.

Virology. 2012 May 25;427(1):10-7. doi: 10.1016/j.virol.2012.01.028. Epub 2012 Feb 23.

7.

Virus identification in unknown tropical febrile illness cases using deep sequencing.

Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, DeRisi JL.

PLoS Negl Trop Dis. 2012;6(2):e1485. doi: 10.1371/journal.pntd.0001485. Epub 2012 Feb 7.

8.

Analysis of hepatitis C virus intrahost diversity across the coding region by ultradeep pyrosequencing.

Lauck M, Alvarado-Mora MV, Becker EA, Bhattacharya D, Striker R, Hughes AL, Carrilho FJ, O'Connor DH, Pinho JR.

J Virol. 2012 Apr;86(7):3952-60. doi: 10.1128/JVI.06627-11. Epub 2012 Jan 25.

9.

De novo assembly and genotyping of variants using colored de Bruijn graphs.

Iqbal Z, Caccamo M, Turner I, Flicek P, McVean G.

Nat Genet. 2012 Jan 8;44(2):226-32. doi: 10.1038/ng.1028.

10.

High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections.

Thai KT, Henn MR, Zody MC, Tricou V, Nguyet NM, Charlebois P, Lennon NJ, Green L, de Vries PJ, Hien TT, Farrar J, van Doorn HR, de Jong MD, Birren BW, Holmes EC, Simmons CP.

J Virol. 2012 Jan;86(2):835-43. doi: 10.1128/JVI.05985-11. Epub 2011 Nov 16.

11.

Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes.

Herbeck JT, Rolland M, Liu Y, McLaughlin S, McNevin J, Zhao H, Wong K, Stoddard JN, Raugi D, Sorensen S, Genowati I, Birditt B, McKay A, Diem K, Maust BS, Deng W, Collier AC, Stekler JD, McElrath MJ, Mullins JI.

J Virol. 2011 Aug;85(15):7523-34. doi: 10.1128/JVI.02697-10. Epub 2011 May 18.

12.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.

13.

The evolutionary analysis of emerging low frequency HIV-1 CXCR4 using variants through time--an ultra-deep approach.

Archer J, Rambaut A, Taillon BE, Harrigan PR, Lewis M, Robertson DL.

PLoS Comput Biol. 2010 Dec 16;6(12):e1001022. doi: 10.1371/journal.pcbi.1001022.

14.

High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1513-8. doi: 10.1073/pnas.1017351108. Epub 2010 Dec 27.

15.

Development of a low bias method for characterizing viral populations using next generation sequencing technology.

Willerth SM, Pedro HA, Pachter L, Humeau LM, Arkin AP, Schaffer DV.

PLoS One. 2010 Oct 22;5(10):e13564. doi: 10.1371/journal.pone.0013564.

16.

Comprehensive comparative analysis of strand-specific RNA sequencing methods.

Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A.

Nat Methods. 2010 Sep;7(9):709-15. doi: 10.1038/nmeth.1491. Epub 2010 Aug 15.

17.

The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA.

Genome Res. 2010 Sep;20(9):1297-303. doi: 10.1101/gr.107524.110. Epub 2010 Jul 19.

18.

Efficient construction of an assembly string graph using the FM-index.

Simpson JT, Durbin R.

Bioinformatics. 2010 Jun 15;26(12):i367-73. doi: 10.1093/bioinformatics/btq217.

19.

A survey of sequence alignment algorithms for next-generation sequencing.

Li H, Homer N.

Brief Bioinform. 2010 Sep;11(5):473-83. doi: 10.1093/bib/bbq015. Epub 2010 May 11. Review.

20.

Intra- and interhost evolutionary dynamics of equine influenza virus.

Murcia PR, Baillie GJ, Daly J, Elton D, Jervis C, Mumford JA, Newton R, Parrish CR, Hoelzer K, Dougan G, Parkhill J, Lennard N, Ormond D, Moule S, Whitwham A, McCauley JW, McKinley TJ, Holmes EC, Grenfell BT, Wood JL.

J Virol. 2010 Jul;84(14):6943-54. doi: 10.1128/JVI.00112-10. Epub 2010 May 5.

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