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Items: 1 to 50 of 63

1.

ImmGen report: sexual dimorphism in the immune system transcriptome.

Gal-Oz ST, Maier B, Yoshida H, Seddu K, Elbaz N, Czysz C, Zuk O, Stranger BE, Ner-Gaon H, Shay T.

Nat Commun. 2019 Sep 20;10(1):4295. doi: 10.1038/s41467-019-12348-6.

2.

Pharmacogenomic genotypes define genetic ancestry in patients and enable population-specific genomic implementation.

Hernandez W, Danahey K, Pei X, Yeo KJ, Leung E, Volchenboum SL, Ratain MJ, Meltzer DO, Stranger BE, Perera MA, O'Donnell PH.

Pharmacogenomics J. 2019 Sep 11. doi: 10.1038/s41397-019-0095-z. [Epub ahead of print]

PMID:
31506565
3.

Author Correction: The role of sex in the genomics of human complex traits.

Khramtsova EA, Davis LK, Stranger BE.

Nat Rev Genet. 2019 Aug;20(8):494. doi: 10.1038/s41576-019-0148-9.

PMID:
31253947
4.

The new science of sex differences in neuropsychiatric traits.

Davis LK, Stranger BE.

Am J Med Genet B Neuropsychiatr Genet. 2019 Sep;180(6):333-334. doi: 10.1002/ajmg.b.32747. Epub 2019 Jun 24. No abstract available.

PMID:
31237066
5.

5-Hydroxymethylcytosine Profiles Are Prognostic of Outcome in Neuroblastoma and Reveal Transcriptional Networks That Correlate With Tumor Phenotype.

Applebaum MA, Barr EK, Karpus J, Nie J, Zhang Z, Armstrong AE, Uppal S, Sukhanova M, Zhang W, Chlenski A, Salwen HR, Wilkinson E, Dobratic M, Grossman R, Godley LA, Stranger BE, He C, Cohn SL.

JCO Precis Oncol. 2019;3. doi: 10.1200/PO.18.00402. Epub 2019 May 16.

6.

Sex differences in gene expression in response to ischemia in the human left ventricular myocardium.

Stone G, Choi A, Meritxell O, Gorham J, Heydarpour M, Seidman CE, Seidman JG, Aranki SF, Body SC, Carey VJ, Raby BA, Stranger BE, Muehlschlegel JD.

Hum Mol Genet. 2019 May 15;28(10):1682-1693. doi: 10.1093/hmg/ddz014.

PMID:
30649309
7.

The role of sex in the genomics of human complex traits.

Khramtsova EA, Davis LK, Stranger BE.

Nat Rev Genet. 2019 Mar;20(3):173-190. doi: 10.1038/s41576-018-0083-1. Review. Erratum in: Nat Rev Genet. 2019 Jun 28;:.

PMID:
30581192
8.

Sex differences in the genetic architecture of obsessive-compulsive disorder.

Khramtsova EA, Heldman R, Derks EM, Yu D; Tourette Syndrome/Obsessive-Compulsive Disorder Working Group of the Psychiatric Genomics Consortium, Davis LK, Stranger BE.

Am J Med Genet B Neuropsychiatr Genet. 2019 Sep;180(6):351-364. doi: 10.1002/ajmg.b.32687. Epub 2018 Nov 20.

PMID:
30456828
9.

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection.

Ye CJ, Chen J, Villani AC, Gate RE, Subramaniam M, Bhangale T, Lee MN, Raj T, Raychowdhury R, Li W, Rogel N, Simmons S, Imboywa SH, Chipendo PI, McCabe C, Lee MH, Frohlich IY, Stranger BE, De Jager PL, Regev A, Behrens T, Hacohen N.

Genome Res. 2018 Dec;28(12):1812-1825. doi: 10.1101/gr.240390.118. Epub 2018 Nov 16.

10.

Evaluation of Genetic Predisposition for MYCN-Amplified Neuroblastoma.

Hungate EA, Applebaum MA, Skol AD, Vaksman Z, Diamond M, McDaniel L, Volchenboum SL, Stranger BE, Maris JM, Diskin SJ, Onel K, Cohn SL.

J Natl Cancer Inst. 2017 Oct 1;109(10). doi: 10.1093/jnci/djx093.

11.

Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research.

Manolio TA, Fowler DM, Starita LM, Haendel MA, MacArthur DG, Biesecker LG, Worthey E, Chisholm RL, Green ED, Jacob HJ, McLeod HL, Roden D, Rodriguez LL, Williams MS, Cooper GM, Cox NJ, Herman GE, Kingsmore S, Lo C, Lutz C, MacRae CA, Nussbaum RL, Ordovas JM, Ramos EM, Robinson PN, Rubinstein WS, Seidman C, Stranger BE, Wang H, Westerfield M, Bult C.

Cell. 2017 Mar 23;169(1):6-12. doi: 10.1016/j.cell.2017.03.005.

12.

Large-Scale trans-eQTLs Affect Hundreds of Transcripts and Mediate Patterns of Transcriptional Co-regulation.

Brynedal B, Choi J, Raj T, Bjornson R, Stranger BE, Neale BM, Voight BF, Cotsapas C.

Am J Hum Genet. 2017 Apr 6;100(4):581-591. doi: 10.1016/j.ajhg.2017.02.004. Epub 2017 Mar 9.

13.

Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results.

Khramtsova EA, Stranger BE.

Bioinformatics. 2017 Feb 1;33(3):432-434. doi: 10.1093/bioinformatics/btw641.

14.

Neuroblastoma survivors are at increased risk for second malignancies: A report from the International Neuroblastoma Risk Group Project.

Applebaum MA, Vaksman Z, Lee SM, Hungate EA, Henderson TO, London WB, Pinto N, Volchenboum SL, Park JR, Naranjo A, Hero B, Pearson AD, Stranger BE, Cohn SL, Diskin SJ.

Eur J Cancer. 2017 Feb;72:177-185. doi: 10.1016/j.ejca.2016.11.022. Epub 2016 Dec 26.

15.

Integrative genomics reveals hypoxia inducible genes that are associated with a poor prognosis in neuroblastoma patients.

Applebaum MA, Jha AR, Kao C, Hernandez KM, DeWane G, Salwen HR, Chlenski A, Dobratic M, Mariani CJ, Godley LA, Prabhakar N, White K, Stranger BE, Cohn SL.

Oncotarget. 2016 Nov 22;7(47):76816-76826. doi: 10.18632/oncotarget.12713.

16.

Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx.

Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LS.

Am J Hum Genet. 2016 Apr 7;98(4):697-708. doi: 10.1016/j.ajhg.2016.02.020. Epub 2016 Mar 31.

17.

The transcriptional landscape of age in human peripheral blood.

Peters MJ, Joehanes R, Pilling LC, Schurmann C, Conneely KN, Powell J, Reinmaa E, Sutphin GL, Zhernakova A, Schramm K, Wilson YA, Kobes S, Tukiainen T; NABEC/UKBEC Consortium, Ramos YF, Göring HH, Fornage M, Liu Y, Gharib SA, Stranger BE, De Jager PL, Aviv A, Levy D, Murabito JM, Munson PJ, Huan T, Hofman A, Uitterlinden AG, Rivadeneira F, van Rooij J, Stolk L, Broer L, Verbiest MM, Jhamai M, Arp P, Metspalu A, Tserel L, Milani L, Samani NJ, Peterson P, Kasela S, Codd V, Peters A, Ward-Caviness CK, Herder C, Waldenberger M, Roden M, Singmann P, Zeilinger S, Illig T, Homuth G, Grabe HJ, Völzke H, Steil L, Kocher T, Murray A, Melzer D, Yaghootkar H, Bandinelli S, Moses EK, Kent JW, Curran JE, Johnson MP, Williams-Blangero S, Westra HJ, McRae AF, Smith JA, Kardia SL, Hovatta I, Perola M, Ripatti S, Salomaa V, Henders AK, Martin NG, Smith AK, Mehta D, Binder EB, Nylocks KM, Kennedy EM, Klengel T, Ding J, Suchy-Dicey AM, Enquobahrie DA, Brody J, Rotter JI, Chen YD, Houwing-Duistermaat J, Kloppenburg M, Slagboom PE, Helmer Q, den Hollander W, Bean S, Raj T, Bakhshi N, Wang QP, Oyston LJ, Psaty BM, Tracy RP, Montgomery GW, Turner ST, Blangero J, Meulenbelt I, Ressler KJ, Yang J, Franke L, Kettunen J, Visscher PM, Neely GG, Korstanje R, Hanson RL, Prokisch H, Ferrucci L, Esko T, Teumer A, van Meurs JB, Johnson AD.

Nat Commun. 2015 Oct 22;6:8570. doi: 10.1038/ncomms9570.

18.

Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation.

Croteau-Chonka DC, Rogers AJ, Raj T, McGeachie MJ, Qiu W, Ziniti JP, Stubbs BJ, Liang L, Martinez FD, Strunk RC, Lemanske RF Jr, Liu AH, Stranger BE, Carey VJ, Raby BA.

PLoS One. 2015 Oct 16;10(10):e0140758. doi: 10.1371/journal.pone.0140758. eCollection 2015. Review.

19.

Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci.

Trynka G, Westra HJ, Slowikowski K, Hu X, Xu H, Stranger BE, Klein RJ, Han B, Raychaudhuri S.

Am J Hum Genet. 2015 Jul 2;97(1):139-52. doi: 10.1016/j.ajhg.2015.05.016.

20.

Accurate and fast multiple-testing correction in eQTL studies.

Sul JH, Raj T, de Jong S, de Bakker PI, Raychaudhuri S, Ophoff RA, Stranger BE, Eskin E, Han B.

Am J Hum Genet. 2015 Jun 4;96(6):857-68. doi: 10.1016/j.ajhg.2015.04.012. Epub 2015 May 28.

21.

The impact of human copy number variation on gene expression.

Gamazon ER, Stranger BE.

Brief Funct Genomics. 2015 Sep;14(5):352-7. doi: 10.1093/bfgp/elv017. Epub 2015 Apr 27. Review.

22.

ImmVar project: Insights and design considerations for future studies of "healthy" immune variation.

De Jager PL, Hacohen N, Mathis D, Regev A, Stranger BE, Benoist C.

Semin Immunol. 2015 Feb;27(1):51-7. doi: 10.1016/j.smim.2015.03.003. Epub 2015 Mar 25. Review.

PMID:
25819567
23.

Regulation of gene expression in autoimmune disease loci and the genetic basis of proliferation in CD4+ effector memory T cells.

Hu X, Kim H, Raj T, Brennan PJ, Trynka G, Teslovich N, Slowikowski K, Chen WM, Onengut S, Baecher-Allan C, De Jager PL, Rich SS, Stranger BE, Brenner MB, Raychaudhuri S.

PLoS Genet. 2014 Jun 26;10(6):e1004404. doi: 10.1371/journal.pgen.1004404. eCollection 2014 Jun.

24.

Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes.

Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL.

Science. 2014 May 2;344(6183):519-23. doi: 10.1126/science.1249547.

25.

Interindividual variation in human T regulatory cells.

Ferraro A, D'Alise AM, Raj T, Asinovski N, Phillips R, Ergun A, Replogle JM, Bernier A, Laffel L, Stranger BE, De Jager PL, Mathis D, Benoist C.

Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):E1111-20. doi: 10.1073/pnas.1401343111. Epub 2014 Mar 7.

26.

Common genetic variants modulate pathogen-sensing responses in human dendritic cells.

Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N.

Science. 2014 Mar 7;343(6175):1246980. doi: 10.1126/science.1246980.

27.

Genetics of rheumatoid arthritis contributes to biology and drug discovery.

Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Yoshida S, Graham RR, Manoharan A, Ortmann W, Bhangale T, Denny JC, Carroll RJ, Eyler AE, Greenberg JD, Kremer JM, Pappas DA, Jiang L, Yin J, Ye L, Su DF, Yang J, Xie G, Keystone E, Westra HJ, Esko T, Metspalu A, Zhou X, Gupta N, Mirel D, Stahl EA, Diogo D, Cui J, Liao K, Guo MH, Myouzen K, Kawaguchi T, Coenen MJ, van Riel PL, van de Laar MA, Guchelaar HJ, Huizinga TW, Dieudé P, Mariette X, Bridges SL Jr, Zhernakova A, Toes RE, Tak PP, Miceli-Richard C, Bang SY, Lee HS, Martin J, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Rantapää-Dahlqvist S, Arlestig L, Choi HK, Kamatani Y, Galan P, Lathrop M; RACI consortium; GARNET consortium, Eyre S, Bowes J, Barton A, de Vries N, Moreland LW, Criswell LA, Karlson EW, Taniguchi A, Yamada R, Kubo M, Liu JS, Bae SC, Worthington J, Padyukov L, Klareskog L, Gregersen PK, Raychaudhuri S, Stranger BE, De Jager PL, Franke L, Visscher PM, Brown MA, Yamanaka H, Mimori T, Takahashi A, Xu H, Behrens TW, Siminovitch KA, Momohara S, Matsuda F, Yamamoto K, Plenge RM.

Nature. 2014 Feb 20;506(7488):376-81. doi: 10.1038/nature12873. Epub 2013 Dec 25.

28.

CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility.

Raj T, Ryan KJ, Replogle JM, Chibnik LB, Rosenkrantz L, Tang A, Rothamel K, Stranger BE, Bennett DA, Evans DA, De Jager PL, Bradshaw EM.

Hum Mol Genet. 2014 May 15;23(10):2729-36. doi: 10.1093/hmg/ddt666. Epub 2013 Dec 30.

29.

Genomics of alternative splicing: evolution, development and pathophysiology.

Gamazon ER, Stranger BE.

Hum Genet. 2014 Jun;133(6):679-87. doi: 10.1007/s00439-013-1411-3. Epub 2014 Jan 1. Review.

PMID:
24378600
30.

Fine-mapping the genetic association of the major histocompatibility complex in multiple sclerosis: HLA and non-HLA effects.

Patsopoulos NA, Barcellos LF, Hintzen RQ, Schaefer C, van Duijn CM, Noble JA, Raj T; IMSGC; ANZgene, Gourraud PA, Stranger BE, Oksenberg J, Olsson T, Taylor BV, Sawcer S, Hafler DA, Carrington M, De Jager PL, de Bakker PI.

PLoS Genet. 2013 Nov;9(11):e1003926. doi: 10.1371/journal.pgen.1003926. Epub 2013 Nov 21.

31.

Genetics of human gene expression.

Stranger BE, Raj T.

Curr Opin Genet Dev. 2013 Dec;23(6):627-34. doi: 10.1016/j.gde.2013.10.004. Epub 2013 Nov 14. Review.

PMID:
24238872
32.

Genome-wide association study and gene expression analysis identifies CD84 as a predictor of response to etanercept therapy in rheumatoid arthritis.

Cui J, Stahl EA, Saevarsdottir S, Miceli C, Diogo D, Trynka G, Raj T, Mirkov MU, Canhao H, Ikari K, Terao C, Okada Y, Wedrén S, Askling J, Yamanaka H, Momohara S, Taniguchi A, Ohmura K, Matsuda F, Mimori T, Gupta N, Kuchroo M, Morgan AW, Isaacs JD, Wilson AG, Hyrich KL, Herenius M, Doorenspleet ME, Tak PP, Crusius JB, van der Horst-Bruinsma IE, Wolbink GJ, van Riel PL, van de Laar M, Guchelaar HJ, Shadick NA, Allaart CF, Huizinga TW, Toes RE, Kimberly RP, Bridges SL Jr, Criswell LA, Moreland LW, Fonseca JE, de Vries N, Stranger BE, De Jager PL, Raychaudhuri S, Weinblatt ME, Gregersen PK, Mariette X, Barton A, Padyukov L, Coenen MJ, Karlson EW, Plenge RM.

PLoS Genet. 2013 Mar;9(3):e1003394. doi: 10.1371/journal.pgen.1003394. Epub 2013 Mar 28.

33.

Common risk alleles for inflammatory diseases are targets of recent positive selection.

Raj T, Kuchroo M, Replogle JM, Raychaudhuri S, Stranger BE, De Jager PL.

Am J Hum Genet. 2013 Apr 4;92(4):517-29. doi: 10.1016/j.ajhg.2013.03.001. Epub 2013 Mar 21.

34.

Chromatin marks identify critical cell types for fine mapping complex trait variants.

Trynka G, Sandor C, Han B, Xu H, Stranger BE, Liu XS, Raychaudhuri S.

Nat Genet. 2013 Feb;45(2):124-30. doi: 10.1038/ng.2504. Epub 2012 Dec 23.

35.

Coordinating GWAS results with gene expression in a systems immunologic paradigm in autoimmunity.

Stranger BE, De Jager PL.

Curr Opin Immunol. 2012 Oct;24(5):544-51. doi: 10.1016/j.coi.2012.09.002. Epub 2012 Oct 3. Review.

36.

Sex-biased genetic effects on gene regulation in humans.

Dimas AS, Nica AC, Montgomery SB, Stranger BE, Raj T, Buil A, Giger T, Lappalainen T, Gutierrez-Arcelus M; MuTHER Consortium, McCarthy MI, Dermitzakis ET.

Genome Res. 2012 Dec;22(12):2368-75. doi: 10.1101/gr.134981.111. Epub 2012 Sep 7.

37.

Analysis of case-control association studies with known risk variants.

Zaitlen N, Pasaniuc B, Patterson N, Pollack S, Voight B, Groop L, Altshuler D, Henderson BE, Kolonel LN, Le Marchand L, Waters K, Haiman CA, Stranger BE, Dermitzakis ET, Kraft P, Price AL.

Bioinformatics. 2012 Jul 1;28(13):1729-37. doi: 10.1093/bioinformatics/bts259. Epub 2012 May 3.

38.

Patterns of cis regulatory variation in diverse human populations.

Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET.

PLoS Genet. 2012;8(4):e1002639. doi: 10.1371/journal.pgen.1002639. Epub 2012 Apr 19.

39.

Systems and genome-wide approaches unite to provide a route to personalized medicine.

Stranger BE, Björkegren J, Dolan ME, Ritchie MD.

Genome Med. 2012 Mar 30;4(3):29. doi: 10.1186/gm328. eCollection 2012.

40.

Alzheimer disease susceptibility loci: evidence for a protein network under natural selection.

Raj T, Shulman JM, Keenan BT, Chibnik LB, Evans DA, Bennett DA, Stranger BE, De Jager PL.

Am J Hum Genet. 2012 Apr 6;90(4):720-6. doi: 10.1016/j.ajhg.2012.02.022.

41.

Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis.

Brown KH, Dobrinski KP, Lee AS, Gokcumen O, Mills RE, Shi X, Chong WW, Chen JY, Yoo P, David S, Peterson SM, Raj T, Choy KW, Stranger BE, Williamson RE, Zon LI, Freeman JL, Lee C.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):529-34. doi: 10.1073/pnas.1112163109. Epub 2011 Dec 27.

42.

Progress and promise of genome-wide association studies for human complex trait genetics.

Stranger BE, Stahl EA, Raj T.

Genetics. 2011 Feb;187(2):367-83. doi: 10.1534/genetics.110.120907. Epub 2010 Nov 29. Review.

43.

Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies.

Yang TP, Beazley C, Montgomery SB, Dimas AS, Gutierrez-Arcelus M, Stranger BE, Deloukas P, Dermitzakis ET.

Bioinformatics. 2010 Oct 1;26(19):2474-6. doi: 10.1093/bioinformatics/btq452. Epub 2010 Aug 10.

44.

Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.

Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, Barroso I, Dermitzakis ET.

PLoS Genet. 2010 Apr 1;6(4):e1000895. doi: 10.1371/journal.pgen.1000895.

45.

Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease.

Prescott NJ, Dominy KM, Kubo M, Lewis CM, Fisher SA, Redon R, Huang N, Stranger BE, Blaszczyk K, Hudspith B, Parkes G, Hosono N, Yamazaki K, Onnie CM, Forbes A, Dermitzakis ET, Nakamura Y, Mansfield JC, Sanderson J, Hurles ME, Roberts RG, Mathew CG.

Hum Mol Genet. 2010 May 1;19(9):1828-39. doi: 10.1093/hmg/ddq041. Epub 2010 Jan 27.

46.

Common regulatory variation impacts gene expression in a cell type-dependent manner.

Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Gutierrez Arcelus M, Sekowska M, Gagnebin M, Nisbett J, Deloukas P, Dermitzakis ET, Antonarakis SE.

Science. 2009 Sep 4;325(5945):1246-50. doi: 10.1126/science.1174148. Epub 2009 Jul 30.

47.

Gene expression levels are a target of recent natural selection in the human genome.

Kudaravalli S, Veyrieras JB, Stranger BE, Dermitzakis ET, Pritchard JK.

Mol Biol Evol. 2009 Mar;26(3):649-58. doi: 10.1093/molbev/msn289. Epub 2008 Dec 17.

48.

Modifier effects between regulatory and protein-coding variation.

Dimas AS, Stranger BE, Beazley C, Finn RD, Ingle CE, Forrest MS, Ritchie ME, Deloukas P, Tavaré S, Dermitzakis ET.

PLoS Genet. 2008 Oct;4(10):e1000244. doi: 10.1371/journal.pgen.1000244. Epub 2008 Oct 31.

49.

Large-scale population study of human cell lines indicates that dosage compensation is virtually complete.

Johnston CM, Lovell FL, Leongamornlert DA, Stranger BE, Dermitzakis ET, Ross MT.

PLoS Genet. 2008 Jan;4(1):e9. doi: 10.1371/journal.pgen.0040009. Epub 2007 Dec 13.

50.

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

Marioni JC, Thorne NP, Valsesia A, Fitzgerald T, Redon R, Fiegler H, Andrews TD, Stranger BE, Lynch AG, Dermitzakis ET, Carter NP, Tavaré S, Hurles ME.

Genome Biol. 2007;8(10):R228.

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