Profiles Research Networking Software The University of Chicago
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BARBARA STRANGER

TitleASSISTANT PROFESSOR     
InstitutionUniversity of Chicago
DepartmentMEDICINE
AddressChicago IL 60637

 Overview 
 overview
The overriding research interest of the lab is trying to disentangle the relationship between genotype and phenotype, and to understand the forces shaping functional genetic variation in humans. We use a combination of experimental and computational approaches: We employ high-throughput functional genomics and genome-wide association analysis (GWAS) to identify variable regions of the genome with functional effects on the transcriptome and proteome, and to investigate the context-specificity of these patterns. At the same time, we examine the levels and patterns of genetic variation within and between human populations, and between human and other species to identify regions of the genome with patterns of variation suggestive of natural selection.


 Bibliographic 
 selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. 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. Bedside Back to Bench: Building Bridges between Basic and Clinical Genomic Research. Cell. 2017 Mar 23; 169(1):6-12.
    View in: PubMed
  2. Brynedal B, Choi J, Raj T, Bjornson R, Stranger BE, Neale BM, Voight BF, Cotsapas C. Large-Scale trans-eQTLs Affect Hundreds of Transcripts and Mediate Patterns of Transcriptional Co-regulation. Am J Hum Genet. 2017 Apr 06; 100(4):581-591.
    View in: PubMed
  3. Khramtsova EA, Stranger BE. Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results. Bioinformatics. 2017 Feb 01; 33(3):432-434.
    View in: PubMed
  4. 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. Neuroblastoma survivors are at increased risk for second malignancies: A report from the International Neuroblastoma Risk Group Project. Eur J Cancer. 2017 Feb; 72:177-185.
    View in: PubMed
  5. Raj T, Chibnik LB, McCabe C, Wong A, Replogle JM, Yu L, Gao S, Unverzagt FW, Stranger B, Murrell J, Barnes L, Hendrie HC, Foroud T, Krichevsky A, Bennett DA, Hall KS, Evans DA, De Jager PL. Genetic architecture of age-related cognitive decline in African Americans. Neurol Genet. 2017 Feb; 3(1):e125.
    View in: PubMed
  6. 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. Integrative genomics reveals hypoxia inducible genes that are associated with a poor prognosis in neuroblastoma patients. Oncotarget. 2016 Nov 22; 7(47):76816-76826.
    View in: PubMed
  7. Khramtsova EA, Stranger BE. Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results. Bioinformatics. 2016 Oct 14.
    View in: PubMed
  8. Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LS. Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx. Am J Hum Genet. 2016 Apr 07; 98(4):697-708.
    View in: PubMed
  9. 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. The transcriptional landscape of age in human peripheral blood. Nat Commun. 2015 Oct 22; 6:8570.
    View in: PubMed
  10. Croteau-Chonka DC, Rogers AJ, Raj T, McGeachie MJ, Qiu W, Ziniti JP, Stubbs BJ, Liang L, Martinez FD, Strunk RC, Lemanske RF, Liu AH, Stranger BE, Carey VJ, Raby BA. Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation. PLoS One. 2015; 10(10):e0140758.
    View in: PubMed
  11. Trynka G, Westra HJ, Slowikowski K, Hu X, Xu H, Stranger BE, Klein RJ, Han B, Raychaudhuri S. Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci. Am J Hum Genet. 2015 Jul 02; 97(1):139-52.
    View in: PubMed
  12. Sul JH, Raj T, de Jong S, de Bakker PI, Raychaudhuri S, Ophoff RA, Stranger BE, Eskin E, Han B. Accurate and fast multiple-testing correction in eQTL studies. Am J Hum Genet. 2015 Jun 04; 96(6):857-68.
    View in: PubMed
  13. Tilburgs T, Crespo ÂC, van der Zwan A, Rybalov B, Raj T, Stranger B, Gardner L, Moffett A, Strominger JL. Human HLA-G+ extravillous trophoblasts: Immune-activating cells that interact with decidual leukocytes. Proc Natl Acad Sci U S A. 2015 Jun 09; 112(23):7219-24.
    View in: PubMed
  14. Gamazon ER, Stranger BE. The impact of human copy number variation on gene expression. Brief Funct Genomics. 2015 Sep; 14(5):352-7.
    View in: PubMed
  15. De Jager PL, Hacohen N, Mathis D, Regev A, Stranger BE, Benoist C. ImmVar project: Insights and design considerations for future studies of "healthy" immune variation. Semin Immunol. 2015 Feb; 27(1):51-7.
    View in: PubMed
  16. Ye CJ, Feng T, Kwon HK, Raj T, Wilson MT, Asinovski N, McCabe C, Lee MH, Frohlich I, Paik HI, Zaitlen N, Hacohen N, Stranger B, De Jager P, Mathis D, Regev A, Benoist C. Intersection of population variation and autoimmunity genetics in human T cell activation. Science. 2014 Sep 12; 345(6202):1254665.
    View in: PubMed
  17. 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. Regulation of gene expression in autoimmune disease loci and the genetic basis of proliferation in CD4+ effector memory T cells. PLoS Genet. 2014 Jun; 10(6):e1004404.
    View in: PubMed
  18. Li Q, Stram A, Chen C, Kar S, Gayther S, Pharoah P, Haiman C, Stranger B, Kraft P, Freedman ML. Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types. Hum Mol Genet. 2014 Oct 01; 23(19):5294-302.
    View in: PubMed
  19. 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. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science. 2014 May 02; 344(6183):519-23.
    View in: PubMed
  20. 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. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science. 2014 Mar 07; 343(6175):1246980.
    View in: PubMed
  21. 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. Interindividual variation in human T regulatory cells. Proc Natl Acad Sci U S A. 2014 Mar 25; 111(12):E1111-20.
    View in: PubMed
  22. Gamazon ER, Stranger BE. Genomics of alternative splicing: evolution, development and pathophysiology. Hum Genet. 2014 Jun; 133(6):679-87.
    View in: PubMed
  23. 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. CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility. Hum Mol Genet. 2014 May 15; 23(10):2729-36.
    View in: PubMed
  24. 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, 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. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature. 2014 Feb 20; 506(7488):376-81.
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  25. Patsopoulos NA, Barcellos LF, Hintzen RQ, Schaefer C, van Duijn CM, Noble JA, Raj T. Fine-mapping the genetic association of the major histocompatibility complex in multiple sclerosis: HLA and non-HLA effects. PLoS Genet. 2013 Nov; 9(11):e1003926.
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  26. Stranger BE, Raj T. Genetics of human gene expression. Curr Opin Genet Dev. 2013 Dec; 23(6):627-34.
    View in: PubMed
  27. Gokcumen O, Zhu Q, Mulder LC, Iskow RC, Austermann C, Scharer CD, Raj T, Boss JM, Sunyaev S, Price A, Stranger B, Simon V, Lee C. Balancing selection on a regulatory region exhibiting ancient variation that predates human-neandertal divergence. PLoS Genet. 2013 Apr; 9(4):e1003404.
    View in: PubMed
  28. 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, 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. Genome-wide association study and gene expression analysis identifies CD84 as a predictor of response to etanercept therapy in rheumatoid arthritis. PLoS Genet. 2013 Mar; 9(3):e1003394.
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  29. Raj T, Kuchroo M, Replogle JM, Raychaudhuri S, Stranger BE, De Jager PL. Common risk alleles for inflammatory diseases are targets of recent positive selection. Am J Hum Genet. 2013 Apr 04; 92(4):517-29.
    View in: PubMed
  30. Li Q, Seo JH, Stranger B, McKenna A, Pe'er I, Laframboise T, Brown M, Tyekucheva S, Freedman ML. Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell. 2013 Jan 31; 152(3):633-41.
    View in: PubMed
  31. Trynka G, Sandor C, Han B, Xu H, Stranger BE, Liu XS, Raychaudhuri S. Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet. 2013 Feb; 45(2):124-30.
    View in: PubMed
  32. Stranger BE, De Jager PL. Coordinating GWAS results with gene expression in a systems immunologic paradigm in autoimmunity. Curr Opin Immunol. 2012 Oct; 24(5):544-51.
    View in: PubMed
  33. Dimas AS, Nica AC, Montgomery SB, Stranger BE, Raj T, Buil A, Giger T, Lappalainen T, Gutierrez-Arcelus M. Sex-biased genetic effects on gene regulation in humans. Genome Res. 2012 Dec; 22(12):2368-75.
    View in: PubMed
  34. 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. Analysis of case-control association studies with known risk variants. Bioinformatics. 2012 Jul 01; 28(13):1729-37.
    View in: PubMed
  35. 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. Patterns of cis regulatory variation in diverse human populations. PLoS Genet. 2012; 8(4):e1002639.
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  36. Raj T, Shulman JM, Keenan BT, Chibnik LB, Evans DA, Bennett DA, Stranger BE, De Jager PL. Alzheimer disease susceptibility loci: evidence for a protein network under natural selection. Am J Hum Genet. 2012 Apr 06; 90(4):720-6.
    View in: PubMed
  37. Stranger BE, Björkegren J, Dolan ME, Ritchie MD. Systems and genome-wide approaches unite to provide a route to personalized medicine. Genome Med. 2012; 4(3):29.
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  38. 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. Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis. Proc Natl Acad Sci U S A. 2012 Jan 10; 109(2):529-34.
    View in: PubMed
  39. Stranger BE, Stahl EA, Raj T. Progress and promise of genome-wide association studies for human complex trait genetics. Genetics. 2011 Feb; 187(2):367-83.
    View in: PubMed
  40. Yang TP, Beazley C, Montgomery SB, Dimas AS, Gutierrez-Arcelus M, Stranger BE, Deloukas P, Dermitzakis ET. Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics. 2010 Oct 01; 26(19):2474-6.
    View in: PubMed
  41. Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, Barroso I, Dermitzakis ET. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet. 2010 Apr 01; 6(4):e1000895.
    View in: PubMed
  42. 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. Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease. Hum Mol Genet. 2010 May 01; 19(9):1828-39.
    View in: PubMed
  43. 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. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science. 2009 Sep 04; 325(5945):1246-50.
    View in: PubMed
  44. Kudaravalli S, Veyrieras JB, Stranger BE, Dermitzakis ET, Pritchard JK. Gene expression levels are a target of recent natural selection in the human genome. Mol Biol Evol. 2009 Mar; 26(3):649-58.
    View in: PubMed
  45. Dimas AS, Stranger BE, Beazley C, Finn RD, Ingle CE, Forrest MS, Ritchie ME, Deloukas P, Tavaré S, Dermitzakis ET. Modifier effects between regulatory and protein-coding variation. PLoS Genet. 2008 Oct; 4(10):e1000244.
    View in: PubMed
  46. Johnston CM, Lovell FL, Leongamornlert DA, Stranger BE, Dermitzakis ET, Ross MT. Large-scale population study of human cell lines indicates that dosage compensation is virtually complete. PLoS Genet. 2008 Jan; 4(1):e9.
    View in: PubMed
  47. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES. Genome-wide detection and characterization of positive selection in human populations. Nature. 2007 Oct 18; 449(7164):913-8.
    View in: PubMed
  48. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18; 449(7164):851-61.
    View in: PubMed
  49. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, Montgomery S, Tavaré S, Deloukas P, Dermitzakis ET. Population genomics of human gene expression. Nat Genet. 2007 Oct; 39(10):1217-24.
    View in: PubMed
  50. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14; 447(7146):799-816.
    View in: PubMed
  51. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, Tavaré S, Deloukas P, Hurles ME, Dermitzakis ET. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007 Feb 09; 315(5813):848-53.
    View in: PubMed
  52. Bird CP, Stranger BE, Liu M, Thomas DJ, Ingle CE, Beazley C, Miller W, Hurles ME, Dermitzakis ET. Fast-evolving noncoding sequences in the human genome. Genome Biol. 2007; 8(6):R118.
    View in: PubMed
  53. 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. Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol. 2007; 8(10):R228.
    View in: PubMed
  54. Bird CP, Stranger BE, Dermitzakis ET. Functional variation and evolution of non-coding DNA. Curr Opin Genet Dev. 2006 Dec; 16(6):559-64.
    View in: PubMed
  55. Dermitzakis ET, Stranger BE. Genetic variation in human gene expression. Mamm Genome. 2006 Jun; 17(6):503-8.
    View in: PubMed
  56. Stranger BE, Dermitzakis ET. From DNA to RNA to disease and back: the 'central dogma' of regulatory disease variation. Hum Genomics. 2006 Jun; 2(6):383-90.
    View in: PubMed
  57. Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, Lyle R, Hunt S, Kahl B, Antonarakis SE, Tavaré S, Deloukas P, Dermitzakis ET. Genome-wide associations of gene expression variation in humans. PLoS Genet. 2005 Dec; 1(6):e78.
    View in: PubMed
  58. Stranger BE, Dermitzakis ET. The genetics of regulatory variation in the human genome. Hum Genomics. 2005 Jun; 2(2):126-31.
    View in: PubMed
  59. Stranger BE, Mitchell-Olds T. Nucleotide variation at the myrosinase-encoding locus, TGG1, and quantitative myrosinase enzyme activity variation in Arabidopsis thaliana. Mol Ecol. 2005 Jan; 14(1):295-309.
    View in: PubMed
  60. Ramos-Onsins SE, Stranger BE, Mitchell-Olds T, Aguadé M. Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata. Genetics. 2004 Jan; 166(1):373-88.
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