Timothy D. O'Connor, PhD

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.

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

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. 

Kessler, M. D., Bateman, N. W., Conrads, T. P., Maxwell, G. L., Dunning Hotopp, J. C., O’Connor, T. D. (2019) Ancestral characterization of 1018 cancer cell lines highlights disparities, and reveals gene expression and mutational differences. Cancer. 125(12):2076-2088.                                 https://www.ncbi.nlm.nih.gov/pubmed/30865299 

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

Harris, D. N., Song, W., Shetty, A. C., Levano, K. S., Cáceres, O., Padilla, C., Borda, V., Tarazona, D., Trujillo, O., Sanchez, C., Kessler, M. D., Galarza, M., Capristano, S., Montejo, H., Flores-Villanueva, P. O., Tarazona-Santos, E., O'Connor, T. D.*, Guio, H.* (2018) Evolutionary genomic dynamics of Peruvians before, during, and after the Inca Empire. Proceedings of the National Academy of Science USA. 115(28):E6526-E6535. 29946025 

Taliun, D.*, Harris, D. N.*, Kessler, M. D.*, Carlson, J.*, Szpiech, Z. A.*, Torres, R.*, Gagliano Taliun, S. A.*, Corvelo, A.*, Gogarten, S. M., Kang, H. Min, Pitsillides, A. N., LeFaive, J., Lee, S.-B., Tian, X., Browning, B. L., Das, S., Clarke, W. E., Emde, A.-Katrin, Loesch, D. P., Shetty, A. C., Blackwell, T. W., Wong, Q., Aguet, F.çois, Albert, C., Alonso, A., Ardlie, K. G., Aslibekyan, S., Auer, P. L., Barnard, J., Barr, R. Graham, Becker, L. C., Beer, R. L., Benjamin, E. J., Bielak, L. F., Blangero, J., Boehnke, M., Bowden, D. W., Brody, J. A., Burchard, E. G., Cade, B. E., Casella, J. F., Chalazan, B., Chen, Y.-D. I., Cho, M., Choi, S. Hoan, Chung, M. K., Clish, C. B., Correa, A., Curran, J.  E., Darbar, D., Daya, M., Andrade, M. de, DeMeo, D. L., Dutcher, S., Ellinor, P. T., Emery, L. S., Forer, L., Fornage, M., Franceschini, N., Fuchsberger, C., Fullerton, S. M., Germer, S., Gottlieb, D. J., Guo, X., Hall, M. E., He, J., Heard-Costa, N. L., Heckbert, S. R., Irvin, M. R., Johnson, A. D., Kardia, S. L.R., Kelly, T., Kelly, S., Kiel, D. P., Klemmer, R., Kooperberg, C., Köttgen, A., Lange, L. A., Lasky-Su, J., Levy, D., Lin, X., Lin, K.-Han, Liu, C., Lori, G., Lubitz, S. A., Lunetta, K. L., Mak, A. C.Y., Manichaikul, A., Manning, A. K., Mathias, R. A., McGarvey, S. T., Meigs, J. B., Mikulla, J. L., Minear, M. A., Mitchell, B., Montasser, M. E., Montgomery, C., Morrison, A. C., Murabito, J. M., Natarajan, P., Nelson, S. C., North, K. E., O'Connell, J.  R., Palmer, N. D., Pankratz, N., Peloso, G. M., Peyser, P. A., Psaty, B. M., Rao, D.C., Redline, S., Reiner, A. P., Roden, D., Rotter, J. I., Ruczinski, I., Sarnowski, C.é, Schoenherr, S., Seo, J.-Sun, Seshadri, S., Shoemaker, M. Benjamin, Smith, A. V., Smith, N. L., Smith, J. A., Sotoodehnia, N., Stilp, A. M., Tang, W., Taylor, K. D., Thornton, T. A., Tracy, R. P., Vasan, R. S., Viaud-Martinez, K., Vrieze, S., Weeks, D. E, Weir, B. S., Weiss, S. T., Weng, L. Chen, Willer, C. J., Zhao, X., Arnett, D. K., Ashley-Koch, A. E., Barnes, K. C., Boerwinkle, E., Gabriel, S., Gibbs, R., Rice, K. M., Rich, S. S., Silverman, E., Qasba, P., Gan, W., Trans-Omics for Precision Medicine (TOPMed) Program, TOPMed Population Genetics Working Group, Papanicolaou, G. J., Nickerson, D. A., Browning, S. R., Zody, M. C., Zöllner, S., Wilson, J. G., Cupples, L. A., Laurie, C. C.*, Jaquish, C. E.*, Hernandez, R. D.*, O'Connor, T. D.*, Abecasis, G. R.* Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. (under review). https://www.biorxiv.org/content/10.1101/563866v1 

Shetty, A. C., Jacob, C. G., Huang, F., Li, Y., Agrawal, S., Saunders, D. L., Lon, C., Fukuda, M. M., Ringwald, P., Ashley, E. A., Han, K. T., Hlaing, T. M., Nyunt, M. M., Silva, J. C., Stewart, K. E., Plowe, C. V., O'Connor, T. D.*, Takala-Harrison, S.*, and Artemisinin Resistance Confirmation, Characterization, and Containment (ARC3), Artemisinin Resistance Containment and Elimination (ARCE), Tracking Resistance to Artemisinin Collaboration (TRAC), and MalariaGEN Plasmodium falciparum Community Project. Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns. Nature Communications. 10:2665. https://www.nature.com/articles/s41467-019-10121-3