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Timothy D O'Connor
 

Timothy D O'Connor Ph.D.

Academic Title: Assistant Professor
Primary Appointment: Medicine
timothydoconnor@gmail.com
Location: BIOPARK II, Rm. 653
Phone: 410-706-6784

Personal History:

Timothy O'Connor is a faculty member at the Institute for Genome Sciences (IGS) and an Assistant Professor of Medicine in the Division of Endocrinology, Diabetes and Nutrition at the University of Maryland School of Medicine in Baltimore, Maryland. He is primarily interested in human evolutionary genetics and the evolution of genotype-phenotype architecture for both disease and naturally distributed traits.

  • 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)
  • 2013-present: Assistant Professor, Institute for Genome Sciences at the University of Maryland School of Medicine

Research Interests:

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.


Publications:

O'Connor, T. D., Kiezun, A., Bamshad, M. J., Rich, S. S., Smith, J., Turner, E., NHLBI GO Exome Sequencing Project, ESP Population Genetics and Statistical Analysis Working Group, Leal, S. M., Akey, J. M. (2013) Fine-scale patterns of population stratification confound rare variant association tests. PLoS One 8(7):e65834.

Prado-Martinez, J., Sudmant, P., Kidd, J. M., Li, H., Kelley, J., Lorente-Galdos, B., Veeramah, K., Woerner, A., O'Connor, T. D., Sanpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H., Munch, K., Hobolth, A., Halager, A. E., Malig, M., Gonzalez, J., Hernando, I., Pruefer, K., Pybus, M., Lachmann, M., Alkan, C., Twigg, D., Petit, N., Stevison, L., Baker, C., Hormozdiari, F., Wilson, M. L., Fernandez-Callejo, M., Dabad, M., Camprubi, C., Carvalho, T., Ruiz-Herrera, A., Vives, L., Mele, M., Johnstone, L., Abello, T., Bontrop, R. E., Pusey, A., Lankester, F., Kiyang, J., Lonsdorf, E., Myers, S., Ventura, M., Gagneux, P., Comas, D., Siegismund, H., Gut, M., Fulton, L., Kondova, I., Tishkoff, S., Mullikin, J. C., Bergl, R., Wilson, R. K., Gut, I. G., Hahn, B. H., Gonder, K. M., Ryder, O., Navarro, A., Akey, J. M., Bertranpetit, J., Reich, D., Mailund, T., Schrierup, M., Hvilsom, C., Andres, A., Wall, J., Bustamante, C. D., Hammer, M., Eichler, E. E., Marques-Bonet, T. (2013) Great ape genome diversity and population history. Nature Adv. Acc.

Fu, W., O'Connor, T. D., Jun, G., Kang, H. M., Abecasis, G., Leal, S. M., Gabriel, S., Rieder, M. J., Altshuler, D., Shendure, J, Nickerson, D. A., Bamshad, M. J., Population Genetics Working Group, Broad GO, Seattle GO, NHLBI Exome Sequencing Project, Akey, J. M. (2012) Analysis of 6,515 exomes reveals a very recent origin of most human protein-coding variants. Nature 493:216-220.

Tennessen, J. A.*, Bigham, A.*, O'Connor, T. D.* Fu, W., Kenny, E. E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G., Kang, H. M., Jordan, D., Leal, S. M., Gabriel, S., Rieder, M. J., Abecasis, G., Altshuler, D., Nickerson, D. A., Boerwinkle, E, Sunyaev, S., Bustamante, C. D., Bamshad, M. J., Akey, J. M., Broad GO, Seattle GO, on behalf of the NHLBI Exome Sequencing Project (2012) Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337:64-69.

Scally, A., Dutheil, J. Y., Hillier, L. W., Jordan, G. E., Goodhead, I., Herrero, J., Hobolth, A., Lappalainen, T., Mailund, T., Marques-Bonet, T., McCarthy, S., Montgomery, S. H., Schwalie, P. C., Y. Amy Tang, Ward, M. C., Xue, Y., Yngvadottir, B., Alkan, C., Andersen, L. N., Ayub, Q., Ball, E. V., Beal, K., Bradley, B. J., Chen, Y., Clee, C. M., Fitzgerald, S., Graves, T. A., Gu, Y., Heath, P., Heger, A., Karakoc, E., Kolb-Kokocinski, A., Laird, G. K., Lunter, G., Meader, S., Mort, M., Mullikin, J. C., Munch, K., O'Connor, T. D., Phillips, A. D., Prado-Martinez, J., Rogers, A. S., Sajjadian, S., Schmidt, D., Shaw, K., Simpson, J. T., Stenson, P. D., Turner, D. J., Vigilant, L., Vilella, A. J., Whitener, W., Zhu, B., Cooper, D. N., de Jong, P., Dermitzakis, E. T., Eichler, E. E., Flicek, P., Goldman, N., Mundy, N. I., Ning, Z., Odom, D. T., Ponting, C. P., Quail, M. A., Ryder, O. A., Searle, S. M., Warren, W. C., Wilson, R. K., Schierup, M. H., Rogers, J., Tyler-Smith, C. Durbin, R.. (2012) Insights into the evolution of the great apes provided by the gorilla genome sequence. Nature 483:169-175.

Tennessen, J. A.*, O'Connor, T. D.*, Bamshad M. J., Akey, J.M. (2011) The promise and limitations of population exomics for human evolution studies. Genome Biology 12:127.

O'Connor, T. D., Sundberg, K., Carroll, H. D., Clement, M. J., Snell, Q. O. (2010) Analysis of long branch extraction and long branch shortening. BMC Genomics 11(suppl2):S14.

O'Connor, T. D., Mundy, N. I. (2009) Genotypeâ?"phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate. Bioinformatics 25(12): i94-i100.

Sundberg, K., O'Connor, T. D., Carroll H. D., Clement, M. J., Snell, Q. O. (2008) Using parsimony to guide maximum likelihood searches. International Journal of Computational Biology and Drug Design 1(1):74-87.

Carroll, H. D., Beckstead, W. A., O'Connor, T. D., Ebbert, M. T. W., Clement, M. J., Snell, Q. O., McClellan, D. A. (2007) DNA reference alignment benchmarks based on tertiary structure of encoded proteins. Bioinformatics 23(19):2648-2649.