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Items: 1 to 20 of 93

1.

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.

2.

V-Phaser 2: variant inference for viral populations.

Yang X, Charlebois P, Macalalad A, Henn MR, Zody MC.

BMC Genomics. 2013 Oct 3;14:674. doi: 10.1186/1471-2164-14-674.

3.

ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering.

Verbist B, Clement L, Reumers J, Thys K, Vapirev A, Talloen W, Wetzels Y, Meys J, Aerssens J, Bijnens L, Thas O.

BMC Bioinformatics. 2015 Feb 22;16:59. doi: 10.1186/s12859-015-0458-7.

4.

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.

5.

Quantification of rare allelic variants from pooled genomic DNA.

Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD.

Nat Methods. 2009 Apr;6(4):263-5. doi: 10.1038/nmeth.1307. Epub 2009 Mar 1.

6.

De novo sequencing and variant calling with nanopores using PoreSeq.

Szalay T, Golovchenko JA.

Nat Biotechnol. 2015 Oct;33(10):1087-91. doi: 10.1038/nbt.3360. Epub 2015 Sep 9.

7.

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles.

Van der Borght K, Thys K, Wetzels Y, Clement L, Verbist B, Reumers J, van Vlijmen H, Aerssens J.

BMC Bioinformatics. 2015 Nov 10;16:379. doi: 10.1186/s12859-015-0812-9.

8.

Detection of rare genomic variants from pooled sequencing using SPLINTER.

Vallania F, Ramos E, Cresci S, Mitra RD, Druley TE.

J Vis Exp. 2012 Jun 23;(64). pii: 3943. doi: 10.3791/3943.

9.

Accurate viral population assembly from ultra-deep sequencing data.

Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E.

Bioinformatics. 2014 Jun 15;30(12):i329-37. doi: 10.1093/bioinformatics/btu295.

10.

Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

Ramos E, Levinson BT, Chasnoff S, Hughes A, Young AL, Thornton K, Li A, Vallania FL, Province M, Druley TE.

BMC Genomics. 2012 Dec 6;13:683. doi: 10.1186/1471-2164-13-683.

11.

Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data.

Zhang F, Flaherty P.

BMC Bioinformatics. 2017 Jan 19;18(1):45. doi: 10.1186/s12859-016-1451-5.

12.

Quality score based identification and correction of pyrosequencing errors.

Iyer S, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI.

PLoS One. 2013 Sep 5;8(9):e73015. doi: 10.1371/journal.pone.0073015. eCollection 2013.

13.

Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants.

Price EP, Inman-Bamber J, Thiruvenkataswamy V, Huygens F, Giffard PM.

BMC Bioinformatics. 2007 Aug 1;8:278.

14.
15.

Targeted capture and massively parallel sequencing of 12 human exomes.

Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, Bamshad M, Nickerson DA, Shendure J.

Nature. 2009 Sep 10;461(7261):272-6. doi: 10.1038/nature08250. Epub 2009 Aug 16.

16.

Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling.

McCrone JT, Lauring AS.

J Virol. 2016 Jul 11;90(15):6884-95. doi: 10.1128/JVI.00667-16. Print 2016 Aug 1.

17.

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM.

Retrovirology. 2013 Feb 13;10:18. doi: 10.1186/1742-4690-10-18.

18.

Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection.

Iyer S, Casey E, Bouzek H, Kim M, Deng W, Larsen BB, Zhao H, Bumgarner RE, Rolland M, Mullins JI.

PLoS One. 2015 Aug 28;10(8):e0135903. doi: 10.1371/journal.pone.0135903. eCollection 2015.

19.

VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering.

Verbist BM, Thys K, Reumers J, Wetzels Y, Van der Borght K, Talloen W, Aerssens J, Clement L, Thas O.

Bioinformatics. 2015 Jan 1;31(1):94-101. doi: 10.1093/bioinformatics/btu587. Epub 2014 Aug 31.

PMID:
25178459
20.

Performance of LigAmp assay for sensitive detection of drug-resistant hepatitis B virus minor variants in comparison with standard nucleotide sequencing.

Ismail AM, Sachithanandham J, Eapen CE, Kannangai R, Abraham P.

Mol Diagn Ther. 2014 Dec;18(6):655-63. doi: 10.1007/s40291-014-0119-y.

PMID:
25208639

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