Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 28

References for PMC Articles for PubMed (Select 22438797)

1.

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, Günthard 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.

2.

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.

Prosperi MC, Salemi M.

Bioinformatics. 2012 Jan 1;28(1):132-3. doi: 10.1093/bioinformatics/btr627. Epub 2011 Nov 15.

3.

Inferring viral quasispecies spectra from 454 pyrosequencing reads.

Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A.

BMC Bioinformatics. 2011;12 Suppl 6:S1. doi: 10.1186/1471-2105-12-S6-S1. Epub 2011 Jul 28.

4.

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.

5.

A framework for variation discovery and genotyping using next-generation DNA sequencing data.

DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ.

Nat Genet. 2011 May;43(5):491-8. doi: 10.1038/ng.806. Epub 2011 Apr 10.

6.

Removing noise from pyrosequenced amplicons.

Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ.

BMC Bioinformatics. 2011 Jan 28;12:38. doi: 10.1186/1471-2105-12-38.

7.

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.

8.

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies.

Zagordi O, Klein R, Däumer M, Beerenwinkel N.

Nucleic Acids Res. 2010 Nov;38(21):7400-9. doi: 10.1093/nar/gkq655. Epub 2010 Jul 29.

9.

Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.

Hedskog C, Mild M, Jernberg J, Sherwood E, Bratt G, Leitner T, Lundeberg J, Andersson B, Albert J.

PLoS One. 2010 Jul 7;5(7):e11345. doi: 10.1371/journal.pone.0011345.

10.

Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction.

Zagordi O, Geyrhofer L, Roth V, Beerenwinkel N.

J Comput Biol. 2010 Mar;17(3):417-28. doi: 10.1089/cmb.2009.0164.

PMID:
20377454
11.

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.

Bioinformatics. 2010 Mar 15;26(6):730-6. doi: 10.1093/bioinformatics/btq040. Epub 2010 Feb 3.

12.

Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design.

Boltz VF, Maldarelli F, Martinson N, Morris L, McIntyre JA, Gray G, Hopley MJ, Kimura T, Mayers DL, Robinson P, Mellors JW, Coffin JM, Palmer SE.

J Virol Methods. 2010 Mar;164(1-2):122-6. doi: 10.1016/j.jviromet.2009.11.025. Epub 2009 Dec 3.

PMID:
19948190
13.

SNP detection for massively parallel whole-genome resequencing.

Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J.

Genome Res. 2009 Jun;19(6):1124-32. doi: 10.1101/gr.088013.108. Epub 2009 May 6.

14.

Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations.

Rozera G, Abbate I, Bruselles A, Vlassi C, D'Offizi G, Narciso P, Chillemi G, Prosperi M, Ippolito G, Capobianchi MR.

Retrovirology. 2009 Feb 12;6:15. doi: 10.1186/1742-4690-6-15.

15.

Accurate whole human genome sequencing using reversible terminator chemistry.

Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ.

Nature. 2008 Nov 6;456(7218):53-9. doi: 10.1038/nature07517.

16.

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.

Malhis N, Butterfield YS, Ester M, Jones SJ.

Bioinformatics. 2009 Jan 1;25(1):6-13. doi: 10.1093/bioinformatics/btn565. Epub 2008 Oct 30.

17.

Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Li H, Ruan J, Durbin R.

Genome Res. 2008 Nov;18(11):1851-8. doi: 10.1101/gr.078212.108. Epub 2008 Aug 19.

18.

Viral population estimation using pyrosequencing.

Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N.

PLoS Comput Biol. 2008 May 9;4(4):e1000074. doi: 10.1371/journal.pcbi.1000074.

19.

Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing.

Salazar-Gonzalez JF, Bailes E, Pham KT, Salazar MG, Guffey MB, Keele BF, Derdeyn CA, Farmer P, Hunter E, Allen S, Manigart O, Mulenga J, Anderson JA, Swanstrom R, Haynes BF, Athreya GS, Korber BT, Sharp PM, Shaw GM, Hahn BH.

J Virol. 2008 Apr;82(8):3952-70. doi: 10.1128/JVI.02660-07. Epub 2008 Feb 6.

20.

Quality scores and SNP detection in sequencing-by-synthesis systems.

Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB.

Genome Res. 2008 May;18(5):763-70. doi: 10.1101/gr.070227.107. Epub 2008 Jan 22.

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Write to the Help Desk