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Items: 26

1.

Precision medicine screening using whole-genome sequencing and advanced imaging to identify disease risk in adults.

Perkins BA, Caskey CT, Brar P, Dec E, Karow DS, Kahn AM, Hou YC, Shah N, Boeldt D, Coughlin E, Hands G, Lavrenko V, Yu J, Procko A, Appis J, Dale AM, Guo L, Jönsson TJ, Wittmann BM, Bartha I, Ramakrishnan S, Bernal A, Brewer JB, Brewerton S, Biggs WH, Turpaz Y, Venter JC.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):3686-3691. doi: 10.1073/pnas.1706096114. Epub 2018 Mar 19.

2.

Identification of individuals by trait prediction using whole-genome sequencing data.

Lippert C, Sabatini R, Maher MC, Kang EY, Lee S, Arikan O, Harley A, Bernal A, Garst P, Lavrenko V, Yocum K, Wong T, Zhu M, Yang WY, Chang C, Lu T, Lee CWH, Hicks B, Ramakrishnan S, Tang H, Xie C, Piper J, Brewerton S, Turpaz Y, Telenti A, Roby RK, Och FJ, Venter JC.

Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):10166-10171. doi: 10.1073/pnas.1711125114. Epub 2017 Sep 5. Erratum in: Proc Natl Acad Sci U S A. 2017 Oct 2;:.

3.

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.

Xie C, Yeo ZX, Wong M, Piper J, Long T, Kirkness EF, Biggs WH, Bloom K, Spellman S, Vierra-Green C, Brady C, Scheuermann RH, Telenti A, Howard S, Brewerton S, Turpaz Y, Venter JC.

Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8059-8064. doi: 10.1073/pnas.1707945114. Epub 2017 Jul 3.

4.

The blood DNA virome in 8,000 humans.

Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A.

PLoS Pathog. 2017 Mar 22;13(3):e1006292. doi: 10.1371/journal.ppat.1006292. eCollection 2017 Mar.

5.

Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites.

Long T, Hicks M, Yu HC, Biggs WH, Kirkness EF, Menni C, Zierer J, Small KS, Mangino M, Messier H, Brewerton S, Turpaz Y, Perkins BA, Evans AM, Miller LA, Guo L, Caskey CT, Schork NJ, Garner C, Spector TD, Venter JC, Telenti A.

Nat Genet. 2017 Apr;49(4):568-578. doi: 10.1038/ng.3809. Epub 2017 Mar 6.

PMID:
28263315
6.

Deep sequencing of 10,000 human genomes.

Telenti A, Pierce LC, Biggs WH, di Iulio J, Wong EH, Fabani MM, Kirkness EF, Moustafa A, Shah N, Xie C, Brewerton SC, Bulsara N, Garner C, Metzker G, Sandoval E, Perkins BA, Och FJ, Turpaz Y, Venter JC.

Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):11901-11906. Epub 2016 Oct 4.

7.

Cistrome: an integrative platform for transcriptional regulation studies.

Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS.

Genome Biol. 2011 Aug 22;12(8):R83. doi: 10.1186/gb-2011-12-8-r83.

8.

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.

9.

A gene expression signature of CD34+ cells to predict major cytogenetic response in chronic-phase chronic myeloid leukemia patients treated with imatinib.

McWeeney SK, Pemberton LC, Loriaux MM, Vartanian K, Willis SG, Yochum G, Wilmot B, Turpaz Y, Pillai R, Druker BJ, Snead JL, MacPartlin M, O'Brien SG, Melo JV, Lange T, Harrington CA, Deininger MW.

Blood. 2010 Jan 14;115(2):315-25. doi: 10.1182/blood-2009-03-210732. Epub 2009 Oct 16.

10.

Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed-tissue RNA reference samples.

Pine PS, Boedigheimer M, Rosenzweig BA, Turpaz Y, He YD, Delenstarr G, Ganter B, Jarnagin K, Jones WD, Reid LH, Thompson KL.

Pharmacogenomics. 2008 Nov;9(11):1753-63. doi: 10.2217/14622416.9.11.1753.

11.
12.

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies.

Shi L, Jones WD, Jensen RV, Harris SC, Perkins RG, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H, Qian F, Amur S, Bao W, Barbacioru CC, Bertholet V, Cao XM, Chu TM, Collins PJ, Fan XH, Frueh FW, Fuscoe JC, Guo X, Han J, Herman D, Hong H, Kawasaki ES, Li QZ, Luo Y, Ma Y, Mei N, Peterson RL, Puri RK, Shippy R, Su Z, Sun YA, Sun H, Thorn B, Turpaz Y, Wang C, Wang SJ, Warrington JA, Willey JC, Wu J, Xie Q, Zhang L, Zhang L, Zhong S, Wolfinger RD, Tong W.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S10. doi: 10.1186/1471-2105-9-S9-S10.

13.

CYP4F2 genetic variant alters required warfarin dose.

Caldwell MD, Awad T, Johnson JA, Gage BF, Falkowski M, Gardina P, Hubbard J, Turpaz Y, Langaee TY, Eby C, King CR, Brower A, Schmelzer JR, Glurich I, Vidaillet HJ, Yale SH, Qi Zhang K, Berg RL, Burmester JK.

Blood. 2008 Apr 15;111(8):4106-12. doi: 10.1182/blood-2007-11-122010. Epub 2008 Feb 4.

14.

Massively parallel pathogen identification using high-density microarrays.

Berthet N, Dickinson P, Filliol I, Reinhardt AK, Batejat C, Vallaeys T, Kong KA, Davies C, Lee W, Zhang S, Turpaz Y, Heym B, Coralie G, Dacheux L, Burguière AM, Bourhy H, Old IG, Manuguerra JC, Cole ST, Kennedy GC.

Microb Biotechnol. 2008 Jan;1(1):79-86. doi: 10.1111/j.1751-7915.2007.00012.x.

15.

DNA copy number analysis in gastrointestinal stromal tumors using gene expression microarrays.

Antonescu CR, Wu K, Xing GL, Cao M, Turpaz Y, Leversha MA, Hubbell E, Maki RG, Miyada CG, Pillai R.

Cancer Inform. 2008;6:59-75. Epub 2008 Mar 27.

17.
18.

Identification of interspecies concordance of mechanisms of arsenic-induced bladder cancer.

Sen B, Wolf DC, Turpaz Y, Bugrim A, Retief J, Hester SD.

Toxicol In Vitro. 2007 Dec;21(8):1513-29. Epub 2007 Jul 21.

PMID:
17720352
19.

Candidate glioblastoma development gene identification using concordance between copy number abnormalities and gene expression level changes.

Lo KC, Rossi MR, LaDuca J, Hicks DG, Turpaz Y, Hawthorn L, Cowell JK.

Genes Chromosomes Cancer. 2007 Oct;46(10):875-94.

PMID:
17620294
20.

Overlay tool for aCGHViewer: an analysis module built for aCGHViewer used to perform comparisons of data derived from different microarray platforms.

Lo KC, Shankar G, Turpaz Y, Bailey D, Rossi MR, Burkhardt T, Liang P, Cowell JK.

Cancer Inform. 2007 Aug 8;3:307-19.

21.

Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array.

Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, Davies C, Williams A, Turpaz Y.

BMC Genomics. 2006 Dec 27;7:325.

22.

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

MAQC Consortium, Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W Jr.

Nat Biotechnol. 2006 Sep;24(9):1151-61.

23.

Using RNA sample titrations to assess microarray platform performance and normalization techniques.

Shippy R, Fulmer-Smentek S, Jensen RV, Jones WD, Wolber PK, Johnson CD, Pine PS, Boysen C, Guo X, Chudin E, Sun YA, Willey JC, Thierry-Mieg J, Thierry-Mieg D, Setterquist RA, Wilson M, Lucas AB, Novoradovskaya N, Papallo A, Turpaz Y, Baker SC, Warrington JA, Shi L, Herman D.

Nat Biotechnol. 2006 Sep;24(9):1123-31.

24.

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues.

Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W116-8.

25.

Use of a mixed tissue RNA design for performance assessments on multiple microarray formats.

Thompson KL, Rosenzweig BA, Pine PS, Retief J, Turpaz Y, Afshari CA, Hamadeh HK, Damore MA, Boedigheimer M, Blomme E, Ciurlionis R, Waring JF, Fuscoe JC, Paules R, Tucker CJ, Fare T, Coffey EM, He Y, Collins PJ, Jarnagin K, Fujimoto S, Ganter B, Kiser G, Kaysser-Kranich T, Sina J, Sistare FD.

Nucleic Acids Res. 2005 Dec 23;33(22):e187.

26.

The DNA architectural protein HMGB1 facilitates RTA-mediated viral gene expression in gamma-2 herpesviruses.

Song MJ, Hwang S, Wong W, Round J, Martinez-Guzman D, Turpaz Y, Liang J, Wong B, Johnson RC, Carey M, Sun R.

J Virol. 2004 Dec;78(23):12940-50.

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