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Items: 28

1.

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.

Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC.

Cell. 2018 Feb 22;172(5):1132-1134. doi: 10.1016/j.cell.2018.02.021. No abstract available.

2.

Predicting gene expression in massively parallel reporter assays: A comparative study.

Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N.

Hum Mutat. 2017 Sep;38(9):1240-1250. doi: 10.1002/humu.23197. Epub 2017 Mar 9.

3.

Systematic dissection of genomic features determining transcription factor binding and enhancer function.

Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1291-E1300. doi: 10.1073/pnas.1621150114. Epub 2017 Jan 30.

4.

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.

Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC.

Cell. 2016 Jun 2;165(6):1519-1529. doi: 10.1016/j.cell.2016.04.027. Erratum in: Cell. 2018 Feb 22;172(5):1132-1134.

5.

Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis.

Wagschal A, Najafi-Shoushtari SH, Wang L, Goedeke L, Sinha S, deLemos AS, Black JC, Ramírez CM, Li Y, Tewhey R, Hatoum I, Shah N, Lu Y, Kristo F, Psychogios N, Vrbanac V, Lu YC, Hla T, de Cabo R, Tsang JS, Schadt E, Sabeti PC, Kathiresan S, Cohen DE, Whetstine J, Chung RT, Fernández-Hernando C, Kaplan LM, Bernards A, Gerszten RE, Näär AM.

Nat Med. 2015 Nov;21(11):1290-7. doi: 10.1038/nm.3980. Epub 2015 Oct 26.

6.

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.

Andersen KG, Shapiro BJ, Matranga CB, Sealfon R, Lin AE, Moses LM, Folarin OA, Goba A, Odia I, Ehiane PE, Momoh M, England EM, Winnicki S, Branco LM, Gire SK, Phelan E, Tariyal R, Tewhey R, Omoniwa O, Fullah M, Fonnie R, Fonnie M, Kanneh L, Jalloh S, Gbakie M, Saffa S, Karbo K, Gladden AD, Qu J, Stremlau M, Nekoui M, Finucane HK, Tabrizi S, Vitti JJ, Birren B, Fitzgerald M, McCowan C, Ireland A, Berlin AM, Bochicchio J, Tazon-Vega B, Lennon NJ, Ryan EM, Bjornson Z, Milner DA Jr, Lukens AK, Broodie N, Rowland M, Heinrich M, Akdag M, Schieffelin JS, Levy D, Akpan H, Bausch DG, Rubins K, McCormick JB, Lander ES, Günther S, Hensley L, Okogbenin S; Viral Hemorrhagic Fever Consortium, Schaffner SF, Okokhere PO, Khan SH, Grant DS, Akpede GO, Asogun DA, Gnirke A, Levin JZ, Happi CT, Garry RF, Sabeti PC.

Cell. 2015 Aug 13;162(4):738-50. doi: 10.1016/j.cell.2015.07.020.

7.

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.

Matranga CB, Andersen KG, Winnicki S, Busby M, Gladden AD, Tewhey R, Stremlau M, Berlin A, Gire SK, England E, Moses LM, Mikkelsen TS, Odia I, Ehiane PE, Folarin O, Goba A, Kahn SH, Grant DS, Honko A, Hensley L, Happi C, Garry RF, Malboeuf CM, Birren BW, Gnirke A, Levin JZ, Sabeti PC.

Genome Biol. 2014;15(11):519.

8.

Mechanisms of linezolid resistance among coagulase-negative staphylococci determined by whole-genome sequencing.

Tewhey R, Gu B, Kelesidis T, Charlton C, Bobenchik A, Hindler J, Schork NJ, Humphries RM.

MBio. 2014 May 13;5(3):e00894-14. doi: 10.1128/mBio.00894-14.

9.

A high resolution case study of a patient with recurrent Plasmodium vivax infections shows that relapses were caused by meiotic siblings.

Bright AT, Manary MJ, Tewhey R, Arango EM, Wang T, Schork NJ, Yanow SK, Winzeler EA.

PLoS Negl Trop Dis. 2014 Jun 5;8(6):e2882. doi: 10.1371/journal.pntd.0002882. eCollection 2014 Jun.

10.

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads.

Hernandez D, Tewhey R, Veyrieras JB, Farinelli L, Østerås M, François P, Schrenzel J.

Bioinformatics. 2014 Jan 1;30(1):40-9. doi: 10.1093/bioinformatics/btt590. Epub 2013 Oct 15.

11.

Evidence for the role of EPHX2 gene variants in anorexia nervosa.

Scott-Van Zeeland AA, Bloss CS, Tewhey R, Bansal V, Torkamani A, Libiger O, Duvvuri V, Wineinger N, Galvez L, Darst BF, Smith EN, Carson A, Pham P, Phillips T, Villarasa N, Tisch R, Zhang G, Levy S, Murray S, Chen W, Srinivasan S, Berenson G, Brandt H, Crawford S, Crow S, Fichter MM, Halmi KA, Johnson C, Kaplan AS, La Via M, Mitchell JE, Strober M, Rotondo A, Treasure J, Woodside DB, Bulik CM, Keel P, Klump KL, Lilenfeld L, Plotnicov K, Topol EJ, Shih PB, Magistretti P, Bergen AW, Berrettini W, Kaye W, Schork NJ.

Mol Psychiatry. 2014 Jun;19(6):724-32. doi: 10.1038/mp.2013.91. Epub 2013 Sep 3.

12.

β-Lactam antibiotics targeting PBP1 selectively enhance daptomycin activity against methicillin-resistant Staphylococcus aureus.

Berti AD, Sakoulas G, Nizet V, Tewhey R, Rose WE.

Antimicrob Agents Chemother. 2013 Oct;57(10):5005-12. doi: 10.1128/AAC.00594-13. Epub 2013 Jul 29.

13.

Evolution of high-level daptomycin resistance in Enterococcus faecium during daptomycin therapy is associated with limited mutations in the bacterial genome.

Kelesidis T, Tewhey R, Humphries RM.

J Antimicrob Chemother. 2013 Aug;68(8):1926-8. doi: 10.1093/jac/dkt117. Epub 2013 Apr 11. No abstract available.

14.

Alternative mutational pathways to intermediate resistance to vancomycin in methicillin-resistant Staphylococcus aureus.

Vidaillac C, Gardete S, Tewhey R, Sakoulas G, Kaatz GW, Rose WE, Tomasz A, Rybak MJ.

J Infect Dis. 2013 Jul;208(1):67-74. doi: 10.1093/infdis/jit127. Epub 2013 Mar 28.

15.

Clinical implications of human population differences in genome-wide rates of functional genotypes.

Torkamani A, Pham P, Libiger O, Bansal V, Zhang G, Scott-Van Zeeland AA, Tewhey R, Topol EJ, Schork NJ.

Front Genet. 2012 Nov 1;3:211. doi: 10.3389/fgene.2012.00211. eCollection 2012.

16.

Ceftaroline increases membrane binding and enhances the activity of daptomycin against daptomycin-nonsusceptible vancomycin-intermediate Staphylococcus aureus in a pharmacokinetic/pharmacodynamic model.

Werth BJ, Sakoulas G, Rose WE, Pogliano J, Tewhey R, Rybak MJ.

Antimicrob Agents Chemother. 2013 Jan;57(1):66-73. doi: 10.1128/AAC.01586-12. Epub 2012 Oct 15. Erratum in: Antimicrob Agents Chemother. 2013 Mar;57(3):1565.

17.

Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300.

Tewhey R, Cannavino CR, Leake JA, Bansal V, Topol EJ, Torkamani A, Bradley JS, Schork NJ.

BMC Genomics. 2012 Sep 25;13:508. doi: 10.1186/1471-2164-13-508.

18.

Genotypic and phenotypic evaluation of the evolution of high-level daptomycin nonsusceptibility in vancomycin-resistant Enterococcus faecium.

Humphries RM, Kelesidis T, Tewhey R, Rose WE, Schork N, Nizet V, Sakoulas G.

Antimicrob Agents Chemother. 2012 Nov;56(11):6051-3. doi: 10.1128/AAC.01318-12. Epub 2012 Sep 4.

19.

Whole genome sequencing analysis of Plasmodium vivax using whole genome capture.

Bright AT, Tewhey R, Abeles S, Chuquiyauri R, Llanos-Cuentas A, Ferreira MU, Schork NJ, Vinetz JM, Winzeler EA.

BMC Genomics. 2012 Jun 21;13:262. doi: 10.1186/1471-2164-13-262.

20.

Efficient and cost effective population resequencing by pooling and in-solution hybridization.

Bansal V, Tewhey R, Leproust EM, Schork NJ.

PLoS One. 2011 Mar 30;6(3):e18353. doi: 10.1371/journal.pone.0018353.

21.

The importance of phase information for human genomics.

Tewhey R, Bansal V, Torkamani A, Topol EJ, Schork NJ.

Nat Rev Genet. 2011 Mar;12(3):215-23. doi: 10.1038/nrg2950. Epub 2011 Feb 8. Review.

22.

The next phase in human genetics.

Bansal V, Tewhey R, Topol EJ, Schork NJ.

Nat Biotechnol. 2011 Jan;29(1):38-9. doi: 10.1038/nbt.1757. No abstract available.

PMID:
21221098
23.

Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates.

Sim BM, Chantratita N, Ooi WF, Nandi T, Tewhey R, Wuthiekanun V, Thaipadungpanit J, Tumapa S, Ariyaratne P, Sung WK, Sem XH, Chua HH, Ramnarayanan K, Lin CH, Liu Y, Feil EJ, Glass MB, Tan G, Peacock SJ, Tan P.

Genome Biol. 2010;11(8):R89. doi: 10.1186/gb-2010-11-8-r89. Epub 2010 Aug 27.

24.

Accurate detection and genotyping of SNPs utilizing population sequencing data.

Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA.

Genome Res. 2010 Apr;20(4):537-45. doi: 10.1101/gr.100040.109. Epub 2010 Feb 11.

25.

Microdroplet-based PCR enrichment for large-scale targeted sequencing.

Tewhey R, Warner JB, Nakano M, Libby B, Medkova M, David PH, Kotsopoulos SK, Samuels ML, Hutchison JB, Larson JW, Topol EJ, Weiner MP, Harismendy O, Olson J, Link DR, Frazer KA.

Nat Biotechnol. 2009 Nov;27(11):1025-31. doi: 10.1038/nbt.1583. Epub 2009 Nov 1. Erratum in: Nat Biotechnol. 2010 Feb;28(2):178.

26.

Enrichment of sequencing targets from the human genome by solution hybridization.

Tewhey R, Nakano M, Wang X, Pabón-Peña C, Novak B, Giuffre A, Lin E, Happe S, Roberts DN, LeProust EM, Topol EJ, Harismendy O, Frazer KA.

Genome Biol. 2009;10(10):R116. doi: 10.1186/gb-2009-10-10-r116. Epub 2009 Oct 16.

27.

Common missense variant in the glucokinase regulatory protein gene is associated with increased plasma triglyceride and C-reactive protein but lower fasting glucose concentrations.

Orho-Melander M, Melander O, Guiducci C, Perez-Martinez P, Corella D, Roos C, Tewhey R, Rieder MJ, Hall J, Abecasis G, Tai ES, Welch C, Arnett DK, Lyssenko V, Lindholm E, Saxena R, de Bakker PI, Burtt N, Voight BF, Hirschhorn JN, Tucker KL, Hedner T, Tuomi T, Isomaa B, Eriksson KF, Taskinen MR, Wahlstrand B, Hughes TE, Parnell LD, Lai CQ, Berglund G, Peltonen L, Vartiainen E, Jousilahti P, Havulinna AS, Salomaa V, Nilsson P, Groop L, Altshuler D, Ordovas JM, Kathiresan S.

Diabetes. 2008 Nov;57(11):3112-21. doi: 10.2337/db08-0516. Epub 2008 Aug 4.

28.

Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels.

Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research, Saxena R, Voight BF, Lyssenko V, Burtt NP, de Bakker PI, Chen H, Roix JJ, Kathiresan S, Hirschhorn JN, Daly MJ, Hughes TE, Groop L, Altshuler D, Almgren P, Florez JC, Meyer J, Ardlie K, Bengtsson Boström K, Isomaa B, Lettre G, Lindblad U, Lyon HN, Melander O, Newton-Cheh C, Nilsson P, Orho-Melander M, Råstam L, Speliotes EK, Taskinen MR, Tuomi T, Guiducci C, Berglund A, Carlson J, Gianniny L, Hackett R, Hall L, Holmkvist J, Laurila E, Sjögren M, Sterner M, Surti A, Svensson M, Svensson M, Tewhey R, Blumenstiel B, Parkin M, Defelice M, Barry R, Brodeur W, Camarata J, Chia N, Fava M, Gibbons J, Handsaker B, Healy C, Nguyen K, Gates C, Sougnez C, Gage D, Nizzari M, Gabriel SB, Chirn GW, Ma Q, Parikh H, Richardson D, Ricke D, Purcell S.

Science. 2007 Jun 1;316(5829):1331-6. Epub 2007 Apr 26.

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