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Items: 1 to 20 of 72

1.

Complete genome sequence of the giant Pseudomonas phage Lu11.

Adriaenssens EM, Mattheus W, Cornelissen A, Shaburova O, Krylov VN, Kropinski AM, Lavigne R.

J Virol. 2012 Jun;86(11):6369-70. doi: 10.1128/JVI.00641-12.

2.

Performance comparison of benchtop high-throughput sequencing platforms.

Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ.

Nat Biotechnol. 2012 May;30(5):434-9. doi: 10.1038/nbt.2198. Erratum in: Nat Biotechnol. 2012 Jun;30(6):562.

PMID:
22522955
3.

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A, Robertson DL.

BMC Bioinformatics. 2012 Mar 23;13:47. doi: 10.1186/1471-2105-13-47.

4.

Insights into hominid evolution from the gorilla genome sequence.

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R.

Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842.

5.

Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting.

Matsushita H, Vesely MD, Koboldt DC, Rickert CG, Uppaluri R, Magrini VJ, Arthur CD, White JM, Chen YS, Shea LK, Hundal J, Wendl MC, Demeter R, Wylie T, Allison JP, Smyth MJ, Old LJ, Mardis ER, Schreiber RD.

Nature. 2012 Feb 8;482(7385):400-4. doi: 10.1038/nature10755.

6.

Ultra-deep sequencing of HIV-1 reverse transcriptase before start of an NNRTI-based regimen in treatment-naive patients.

Messiaen P, Verhofstede C, Vandenbroucke I, Dinakis S, Van Eygen V, Thys K, Winters B, Aerssens J, Vogelaers D, Stuyver LJ, Vandekerckhove L.

Virology. 2012 Apr 25;426(1):7-11. doi: 10.1016/j.virol.2012.01.002. Epub 2012 Feb 4.

7.

Cancer genomics: technology, discovery, and translation.

Tran B, Dancey JE, Kamel-Reid S, McPherson JD, Bedard PL, Brown AM, Zhang T, Shaw P, Onetto N, Stein L, Hudson TJ, Neel BG, Siu LL.

J Clin Oncol. 2012 Feb 20;30(6):647-60. doi: 10.1200/JCO.2011.39.2316. Epub 2012 Jan 23. Review. Erratum in: J Clin Oncol. 2012 Apr 1;30(10):1149.

PMID:
22271477
8.

Discordance in HIV-1 co-receptor use prediction by different genotypic algorithms and phenotype assay: intermediate profile in relation to concordant predictions.

Trabaud MA, Icard V, Scholtes C, Perpoint T, Koffi J, Cotte L, Makhloufi D, Tardy JC, André P.

J Med Virol. 2012 Mar;84(3):402-13. doi: 10.1002/jmv.23209.

PMID:
22246825
9.

Study of genotypic and phenotypic HIV-1 dynamics of integrase mutations during raltegravir treatment: a refined analysis by ultra-deep 454 pyrosequencing.

Armenia D, Vandenbroucke I, Fabeni L, Van Marck H, Cento V, D'Arrigo R, Van Wesenbeeck L, Scopelliti F, Micheli V, Bruzzone B, Lo Caputo S, Aerssens J, Rizzardini G, Tozzi V, Narciso P, Antinori A, Stuyver L, Perno CF, Ceccherini-Silberstein F.

J Infect Dis. 2012 Feb 15;205(4):557-67. doi: 10.1093/infdis/jir821. Epub 2012 Jan 11.

10.

Correlation of the virological response to short-term maraviroc monotherapy with standard and deep-sequencing-based genotypic tropism prediction methods.

Gonzalez-Serna A, McGovern RA, Harrigan PR, Vidal F, Poon AF, Ferrando-Martinez S, Abad MA, Genebat M, Leal M, Ruiz-Mateos E.

Antimicrob Agents Chemother. 2012 Mar;56(3):1202-7. doi: 10.1128/AAC.05857-11. Epub 2011 Dec 5.

11.

Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR.

Howden BP, McEvoy CR, Allen DL, Chua K, Gao W, Harrison PF, Bell J, Coombs G, Bennett-Wood V, Porter JL, Robins-Browne R, Davies JK, Seemann T, Stinear TP.

PLoS Pathog. 2011 Nov;7(11):e1002359. doi: 10.1371/journal.ppat.1002359. Epub 2011 Nov 10.

12.

Deep molecular characterization of HIV-1 dynamics under suppressive HAART.

Buzón MJ, Codoñer FM, Frost SD, Pou C, Puertas MC, Massanella M, Dalmau J, Llibre JM, Stevenson M, Blanco J, Clotet B, Paredes R, Martinez-Picado J.

PLoS Pathog. 2011 Oct;7(10):e1002314. doi: 10.1371/journal.ppat.1002314. Epub 2011 Oct 27.

13.

Deep V3 sequencing for HIV type 1 tropism in treatment-naive patients: a reanalysis of the MERIT trial of maraviroc.

Swenson LC, Mo T, Dong WW, Zhong X, Woods CK, Thielen A, Jensen MA, Knapp DJ, Chapman D, Portsmouth S, Lewis M, James I, Heera J, Valdez H, Harrigan PR.

Clin Infect Dis. 2011 Oct;53(7):732-42. doi: 10.1093/cid/cir493.

PMID:
21890778
14.

Switching between raltegravir resistance pathways analyzed by deep sequencing.

Mukherjee R, Jensen ST, Male F, Bittinger K, Hodinka RL, Miller MD, Bushman FD.

AIDS. 2011 Oct 23;25(16):1951-9. doi: 10.1097/QAD.0b013e32834b34de.

15.

Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.

Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Møller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK.

N Engl J Med. 2011 Aug 25;365(8):709-17. doi: 10.1056/NEJMoa1106920. Epub 2011 Jul 27.

16.

An integrated semiconductor device enabling non-optical genome sequencing.

Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, Sabina J, Feierstein E, Schorn M, Alanjary M, Dimalanta E, Dressman D, Kasinskas R, Sokolsky T, Fidanza JA, Namsaraev E, McKernan KJ, Williams A, Roth GT, Bustillo J.

Nature. 2011 Jul 20;475(7356):348-52. doi: 10.1038/nature10242.

PMID:
21776081
17.

High concordance between the position-specific scoring matrix and geno2pheno algorithms for genotypic interpretation of HIV-1 tropism: V3 length as the major cause of disagreement.

Seclén E, Soriano V, González MM, Gómez S, Thielen A, Poveda E.

J Clin Microbiol. 2011 Sep;49(9):3380-2. doi: 10.1128/JCM.00908-11. Epub 2011 Jul 6.

18.

Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing.

Bunnik EM, Swenson LC, Edo-Matas D, Huang W, Dong W, Frantzell A, Petropoulos CJ, Coakley E, Schuitemaker H, Harrigan PR, van 't Wout AB.

PLoS Pathog. 2011 Jun;7(6):e1002106. doi: 10.1371/journal.ppat.1002106. Epub 2011 Jun 23.

19.

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).

Miller W, Hayes VM, Ratan A, Petersen DC, Wittekindt NE, Miller J, Walenz B, Knight J, Qi J, Zhao F, Wang Q, Bedoya-Reina OC, Katiyar N, Tomsho LP, Kasson LM, Hardie RA, Woodbridge P, Tindall EA, Bertelsen MF, Dixon D, Pyecroft S, Helgen KM, Lesk AM, Pringle TH, Patterson N, Zhang Y, Kreiss A, Woods GM, Jones ME, Schuster SC.

Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12348-53. doi: 10.1073/pnas.1102838108. Epub 2011 Jun 27. Erratum in: Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18625.

20.

Improved V3 genotyping with duplicate PCR amplification for determining HIV-1 tropism.

Raymond S, Recordon-Pinson P, Saliou A, Delobel P, Nicot F, Descamps D, Marcelin AG, Flandre P, Calvez V, Masquelier B, Izopet J; ANRS AC11 Resistance Study Group..

J Antimicrob Chemother. 2011 Sep;66(9):1972-5. doi: 10.1093/jac/dkr224. Epub 2011 Jun 14.

PMID:
21676905

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