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Items: 20

1.

A flexible approach for highly multiplexed candidate gene targeted resequencing.

Natsoulis G, Bell JM, Xu H, Buenrostro JD, Ordonez H, Grimes S, Newburger D, Jensen M, Zahn JM, Zhang N, Ji HP.

PLoS One. 2011;6(6):e21088. doi: 10.1371/journal.pone.0021088. Epub 2011 Jun 30.

2.

Statistical analysis strategies for association studies involving rare variants.

Bansal V, Libiger O, Torkamani A, Schork NJ.

Nat Rev Genet. 2010 Nov;11(11):773-85. doi: 10.1038/nrg2867. Epub 2010 Oct 13. Review.

3.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD; MAQC Consortium..

Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665. Epub 2010 Jul 30.

4.

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.

5.

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.

6.

A statistical method for the detection of variants from next-generation resequencing of DNA pools.

Bansal V.

Bioinformatics. 2010 Jun 15;26(12):i318-24. doi: 10.1093/bioinformatics/btq214. Erratum in: Bioinformatics. 2016 Oct 15;32(20):3213.

7.

Characterization of quasispecies of pandemic 2009 influenza A virus (A/H1N1/2009) by de novo sequencing using a next-generation DNA sequencer.

Kuroda M, Katano H, Nakajima N, Tobiume M, Ainai A, Sekizuka T, Hasegawa H, Tashiro M, Sasaki Y, Arakawa Y, Hata S, Watanabe M, Sata T.

PLoS One. 2010 Apr 23;5(4):e10256. doi: 10.1371/journal.pone.0010256.

8.

VarScan: variant detection in massively parallel sequencing of individual and pooled samples.

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L.

Bioinformatics. 2009 Sep 1;25(17):2283-5. doi: 10.1093/bioinformatics/btp373. Epub 2009 Jun 19.

9.

The Sequence Alignment/Map format and SAMtools.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup..

Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8.

10.

Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo.

Tsibris AM, Korber B, Arnaout R, Russ C, Lo CC, Leitner T, Gaschen B, Theiler J, Paredes R, Su Z, Hughes MD, Gulick RM, Greaves W, Coakley E, Flexner C, Nusbaum C, Kuritzkes DR.

PLoS One. 2009 May 25;4(5):e5683. doi: 10.1371/journal.pone.0005683.

11.

Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes.

Nejentsev S, Walker N, Riches D, Egholm M, Todd JA.

Science. 2009 Apr 17;324(5925):387-9. doi: 10.1126/science.1167728. Epub 2009 Mar 5.

12.

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.

13.

Next-generation DNA sequencing.

Shendure J, Ji H.

Nat Biotechnol. 2008 Oct;26(10):1135-45. doi: 10.1038/nbt1486.

PMID:
18846087
14.

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.

Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

Nucleic Acids Res. 2008 Sep;36(16):e105. doi: 10.1093/nar/gkn425. Epub 2008 Jul 26.

15.

High-resolution melting analysis for rapid detection of KRAS, BRAF, and PIK3CA gene mutations in colorectal cancer.

Simi L, Pratesi N, Vignoli M, Sestini R, Cianchi F, Valanzano R, Nobili S, Mini E, Pazzagli M, Orlando C.

Am J Clin Pathol. 2008 Aug;130(2):247-53. doi: 10.1309/LWDY1AXHXUULNVHQ.

PMID:
18628094
16.

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance.

Wang C, Mitsuya Y, Gharizadeh B, Ronaghi M, Shafer RW.

Genome Res. 2007 Aug;17(8):1195-201. Epub 2007 Jun 28.

17.

Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing.

Thomas RK, Nickerson E, Simons JF, Jänne PA, Tengs T, Yuza Y, Garraway LA, LaFramboise T, Lee JC, Shah K, O'Neill K, Sasaki H, Lindeman N, Wong KK, Borras AM, Gutmann EJ, Dragnev KH, DeBiasi R, Chen TH, Glatt KA, Greulich H, Desany B, Lubeski CK, Brockman W, Alvarez P, Hutchison SK, Leamon JH, Ronan MT, Turenchalk GS, Egholm M, Sellers WR, Rothberg JM, Meyerson M.

Nat Med. 2006 Jul;12(7):852-5. Epub 2006 Jun 25. Erratum in: Nat Med. 2006 Oct;12(10):1220.

PMID:
16799556
18.

Denaturing high-performance liquid chromatography: A review.

Xiao W, Oefner PJ.

Hum Mutat. 2001 Jun;17(6):439-74. Review.

PMID:
11385705
19.

Assessing the accuracy of prediction algorithms for classification: an overview.

Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H.

Bioinformatics. 2000 May;16(5):412-24. Review.

PMID:
10871264

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