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Items: 1 to 20 of 96

1.

Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs.

Chen-Harris H, Borucki MK, Torres C, Slezak TR, Allen JE.

BMC Genomics. 2013 Feb 12;14:96. doi: 10.1186/1471-2164-14-96.

2.

Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data.

Orton RJ, Wright CF, Morelli MJ, King DJ, Paton DJ, King DP, Haydon DT.

BMC Genomics. 2015 Mar 24;16:229. doi: 10.1186/s12864-015-1456-x.

3.

Viral population analysis and minority-variant detection using short read next-generation sequencing.

Watson SJ, Welkers MR, Depledge DP, Coulter E, Breuer JM, de Jong MD, Kellam P.

Philos Trans R Soc Lond B Biol Sci. 2013 Feb 4;368(1614):20120205. doi: 10.1098/rstb.2012.0205.

4.

Ultra-deep sequencing for the analysis of viral populations.

Beerenwinkel N, Zagordi O.

Curr Opin Virol. 2011 Nov;1(5):413-8. doi: 10.1016/j.coviro.2011.07.008. Review.

PMID:
22440844
5.

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.

6.

Estimation of sequencing error rates in short reads.

Wang XV, Blades N, Ding J, Sultana R, Parmigiani G.

BMC Bioinformatics. 2012 Jul 30;13:185. doi: 10.1186/1471-2105-13-185.

7.

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.

8.

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology.

Cheng DT, Mitchell TN, Zehir A, Shah RH, Benayed R, Syed A, Chandramohan R, Liu ZY, Won HH, Scott SN, Brannon AR, O'Reilly C, Sadowska J, Casanova J, Yannes A, Hechtman JF, Yao J, Song W, Ross DS, Oultache A, Dogan S, Borsu L, Hameed M, Nafa K, Arcila ME, Ladanyi M, Berger MF.

J Mol Diagn. 2015 May;17(3):251-64. doi: 10.1016/j.jmoldx.2014.12.006.

PMID:
25801821
9.

From deep sequencing to viral tagging: recent advances in viral metagenomics.

Willner D, Hugenholtz P.

Bioessays. 2013 May;35(5):436-42. doi: 10.1002/bies.201200174. Review.

10.

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.

11.

mirTrios: an integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing.

Li J, Jiang Y, Wang T, Chen H, Xie Q, Shao Q, Ran X, Xia K, Sun ZS, Wu J.

J Med Genet. 2015 Apr;52(4):275-81. doi: 10.1136/jmedgenet-2014-102656.

PMID:
25596308
12.

Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum.

Isakov O, Bordería AV, Golan D, Hamenahem A, Celniker G, Yoffe L, Blanc H, Vignuzzi M, Shomron N.

Bioinformatics. 2015 Jul 1;31(13):2141-50. doi: 10.1093/bioinformatics/btv101.

13.

Repeat-aware modeling and correction of short read errors.

Yang X, Aluru S, Dorman KS.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S52. doi: 10.1186/1471-2105-12-S1-S52.

14.

Detection of FLT3 internal tandem duplication in targeted, short-read-length, next-generation sequencing data.

Spencer DH, Abel HJ, Lockwood CM, Payton JE, Szankasi P, Kelley TW, Kulkarni S, Pfeifer JD, Duncavage EJ.

J Mol Diagn. 2013 Jan;15(1):81-93. doi: 10.1016/j.jmoldx.2012.08.001.

15.

Genomic variations in plasma cell free DNA differentiate early stage lung cancers from normal controls.

Xia S, Huang CC, Le M, Dittmar R, Du M, Yuan T, Guo Y, Wang Y, Wang X, Tsai S, Suster S, Mackinnon AC, Wang L.

Lung Cancer. 2015 Oct;90(1):78-84. doi: 10.1016/j.lungcan.2015.07.002.

PMID:
26233568
16.

Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias.

McElroy K, Zagordi O, Bull R, Luciani F, Beerenwinkel N.

BMC Genomics. 2013 Jul 24;14:501. doi: 10.1186/1471-2164-14-501.

17.

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.

PMID:
24731928
18.

Targeted single molecule mutation detection with massively parallel sequencing.

Gregory MT, Bertout JA, Ericson NG, Taylor SD, Mukherjee R, Robins HS, Drescher CW, Bielas JH.

Nucleic Acids Res. 2016 Feb 18;44(3):e22. doi: 10.1093/nar/gkv915.

19.

Next-generation sequencing is highly sensitive for the detection of beta-catenin mutations in desmoid-type fibromatoses.

Aitken SJ, Presneau N, Kalimuthu S, Dileo P, Berisha F, Tirabosco R, Amary MF, Flanagan AM.

Virchows Arch. 2015 Aug;467(2):203-10. doi: 10.1007/s00428-015-1765-0.

PMID:
25838078
20.

Routine Clinical Mutation Profiling of Non-Small Cell Lung Cancer Using Next-Generation Sequencing.

Deeb KK, Hohman CM, Risch NF, Metzger DJ, Starostik P.

Arch Pathol Lab Med. 2015 Jul;139(7):913-21. doi: 10.5858/arpa.2014-0095-OA.

PMID:
26125431

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