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Timothy D. O'Connor, PhD

Academic Title:

Assistant Professor

Primary Appointment:



Health Sciences Facility III, 670 West Baltimore St, Baltimore 21201

Phone (Primary):


Education and Training

2001-2007: B.S. Bioinformatics, Brigham Young University
2007-2011: Ph.D. Evolutionary Genetics, University of Cambridge (Dr. Nicholas I. Mundy)
2007-2011: Gates Cambridge Scholar
2010-2013: Senior Research Fellow, Dept. of Genome Science, University of Washington (Dr. Joshua Akey)


My laboratory explores the effects of evolution and population structure on the genomic architecture of disease and other phenotypes. One of the biggest questions of modern genetics and evolution is to understand the complex connection between genes, environment, and phenotype. We want to understand the origin of phenotypic diversity. We believe this will require the integration of many data types, scientific disciplines, and a heavy reliance on evolutionary theory. As we move forward in developing theories and addressing this important problem it will be important to combine evolutionary genetics and systems biology. My lab has a track record of developing new algorithms and statistics to interdisciplinary biological problems as well as the use of large multifaceted data sets, particularly the output of next-generation sequencing. We are especially interested in the recent evolution of New World populations such as Hispanic Americans, African Americans, and the Old Order Amish.

Research/Clinical Keywords

Human Evolutionary Genetics, Computational Biology, Next-Generation Sequence Analysis,Genotype/Phenotype Architecture

Highlighted Publications

Tennessen JA*, Bigham AW*, O'Connor TD*, Fu W, Kenny EE, Gravel S, McGee S, Do R, Liu X, Jun G, Kang HM, Jordan D, Leal SM, Gabriel S, Rieder MJ, Abecasis G, Altshuler D, Nickerson DA, Boerwinkle E, Sunyaev S, Bustamante CD, Bamshad MJ, Akey JM. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science. 2012 Jul 6;337(6090):64-9. PubMed PMID: 22604720

O'Connor TD, Fu W, Mychaleckyj JC, Logsdon B, Auer P, Carlson CS, Leal SM, Smith JD, Rieder MJ, Bamshad MJ, Nickerson DA, Akey JM. Rare variation facilitates inferences of fine-scale population structure in humans. Mol Biol Evol. 2015 Mar;32(3):653-60. PubMed PMID: 25415970

Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, Akey JM. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature. 2013 Jan 10;493(7431):216-20. PubMed PMID: 23201682

Kessler MD, Yerges-Armstrong L, Taub MA, Shetty AC, Maloney K, Jeng LJB, Ruczinski I, Levin AM, Williams LK, Beaty TH, Mathias RA, Barnes KC, CAAPA Consortium, O’Connor, TD. Challenges and disparities in the application of personalized genomic medicine to populations with African Ancestry. Nature Communications. 2016

Mathias RA, Taub TA, Gignoux CR, Fu W, Musharoff S, O'Connor TD, Vergara C, Torgerson DG, Pino-Yanes M, Shringarpure SS, Huang L, Rafaels N, Boorgula MP, Johnston HR, Ortega VE, Levin AM, Song W, Torres R, Padhukasahasram B, Eng C, Mejia-Mejia D-A, Ferguson T, Qin ZS, Scott AF, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Kumar R, Avila PC, Williams LK, Watson H, Ware LB, Olopade C, Olopade O, Oliveira R, Ober C, Nicolae DL, Meyers D, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker E, Araujo MI, Herrera-Paz EF, Gietzen K, Grus WE, Bamshad M, Bustamante CD, Kenny EE, Hernandez RD, Beaty TH, Ruczinski I, Akey J, CAAPA, Barnes KC. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome. Nature Communications. 2016  

Additional Publication Citations

Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. Insights into hominid evolution from the gorilla genome sequence. Nature. 2012 Mar 7;483(7388):169-75. PubMed PMID: 22398555.

Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T. Great ape genetic diversity and population history. Nature. 2013 Jul 25;499(7459):471-5. PubMed PMID: 23823723.

Bradley BJ, Snowdon CT, McGrew WC, Lawler RR, Guevara EE, McIntosh A, O’Connor T. Non-human primates avoid the detrimental effects of prenatal androgen exposure in mixed-sex litters: combined demographic, behavioral, and genetic analyses. American Journal of Primatology. 2016 July 29. PubMed PMID: 27434275.

Fu W, O'Connor TD, Akey JM. Genetic architecture of quantitative traits and complex diseases. Curr Opin Genet Dev. 2013 Dec;23(6):678-83. PubMed PMID: 24287334.

O'Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E, Leal SM, Akey JM. Fine-scale patterns of population stratification confound rare variant association tests. PLoS One. 2013;8(7):e65834. PubMed PMID: 23861739.

O'Connor TD. AdmixKJump: identifying population structure in recently diverged groups. Source Code Biol Med. 2015;10(1):2. PubMed PMID: 25678934.