MCB Faculty


Peter Calabrese

Assistant Professor (Research) of Biological Sciences

Contact Information
E-mail: petercal@usc.edu
Phone: (213) 740-2434
Office: RRI 413G

LINKS
Curriculum Vitae
Personal Website
 

Biographical Sketch

Peter Calabrese received his undergraduate degree in mathematics from the University of Maryland, College Park; his Ph.D. in applied mathematics from Cornell University (Rick Durrett thesis advisor); and was a National Science Foundation mathematics post-doctoral fellow at the University of Southern California (Simon Tavaré sponsoring scientist). His research is in the field of computational biology, and he has collaborated with numerous molecular biology laboratories at USC.

Education

  • B.S. Mathematics, University of Maryland, College Park, 1996
  • Ph.D. Applied Mathematics, Cornell University, 2001


  • Postdoctoral Training

    • NSF Math Post-doctoral Fellow, University of Southern California, 2001-2003  

    Description of Research

    Summary Statement of Research Interests
    I am interested in applying probability to problems in biology. I have worked on mathematical modeling both in terms of population genetics and stem cell dynamics. I have developed innovative computational approaches for inference from these complicated models. Perhaps more than most other computational biologists, I like to closely collaborate with biologists in terms of designing and analyzing experiments. I have also been involved with analyzing large genomic datasets. At USC, I have collaborated with the Norman Arnheim, Magnus Nordborg, Myron Goodman, Sergey Nuzhdin, Paul Marjoram, Darryl Shibata, and Simon Tavare.
    Research Keywords
    Computational biology, Population genetics, Mutation mechanisms, Recombination hot spots, Approximate Bayesian Computation

    Publications


    Journal Article
    • Pham, P., Calabrese, P. P., Park, S. J., Goodman, M. F. (2011). Analysis of a single-stranded DNA-scanning process in which activation-induced deoxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity. J Biol Chem. Vol. 286 (28), pp. 24931-42.
    • Choi, S., Yoon, S., Calabrese, P. P., Arnheim, N. (2011). Positive Selection for New Disease Mutations in the Human Germline: Evidence from the Heritable Cancer Syndrome Multiple Endocrine Neoplasia Type 2B. PLoS Genetics. Vol. accepted
    • Yoon, S. R., Qin, J., Glaser, R. L., Wang Jabs, E., Wexler, N. S., Sokol, R., Arnheim, N., Calabrese, P. P. (2009). The ups and downs of mutation frequencies during aging can account for the apert syndrome paternal age effect. PLoS Genet. Vol. 5 (7), pp. e1000558.
    • Arnheim, N., Calabrese, P. P. (2009). Understanding what determines the frequency and pattern of human germline mutations. Nat Rev Genet. Vol. 10 (7), pp. 478-88.
    • Pham, P., Smolka, M. B., Calabrese, P. P., Landolph, A., Zhang, K., Zhou, H., Goodman, M. F. (2008). Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase. J Biol Chem. Vol. 283 (25), pp. 17428-39.
    • Choi, S. K., Yoon, S. R., Calabrese, P. P., Arnheim, N. (2008). A germ-line-selective advantage rather than an increased mutation rate can explain some unexpectedly common human disease mutations. Proc Natl Acad Sci U S A. Vol. 105 (29), pp. 10143-8.
    • Qin, J., Calabrese, P. P., Tiemann-Boege, I., Shinde, D. N., Yoon, S. R., Gelfand, D., Bauer, K., Arnheim, N. (2007). The molecular anatomy of spontaneous germline mutations in human testes. PLoS Biol. Vol. 5 (9), pp. e224.
    • Calabrese, P. P. (2007). A population genetics model with recombination hotspots that are heterogeneous across the population. Proc Natl Acad Sci U S A. Vol. 104 (11), pp. 4748-52.
    • Arnheim, N., Calabrese, P. P., Tiemann-Boege, I. (2007). Mammalian meiotic recombination hot spots. Annu Rev Genet. Vol. 41, pp. 369-99.
    • Tiemann-Boege, I., Calabrese, P. P., Cochran, D. M., Sokol, R., Arnheim, N. (2006). High-resolution recombination patterns in a region of human chromosome 21 measured by sperm typing. PLoS Genet. Vol. 2 (5), pp. e70.
    • Chelico, L., Pham, P., Calabrese, P. P., Goodman, M. F. (2006). APOBEC3G DNA deaminase acts processively 3' --> 5' on single-stranded DNA. Nat Struct Mol Biol. Vol. 13 (5), pp. 392-9.
    • Nordborg, M., Hu, T. T., Ishino, Y., Jhaveri, J., Toomajian, C., Zheng, H., Bakker, E., Calabrese, P. P., Gladstone, J., Goyal, R., Jakobsson, M., Kim, S., Morozov, Y., Padhukasahasram, B., Plagnol, V., Rosenberg, N. A., Shah, C., Wall, J. D., Wang, J., Zhao, K., Kalbfleisch, T., Schulz, V., Kreitman, M., Bergelson, J. (2005). The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. Vol. 3 (7), pp. e196.
    • Calabrese, P. P., Chakravarty, S., Vision, T. J. (2003). Fast identification and statistical evaluation of segmental homologies in comparative maps. Bioinformatics. Vol. 19 Suppl 1, pp. i74-80.
    • Arnheim, N., Calabrese, P. P., Nordborg, M. (2003). Hot and cold spots of recombination in the human genome: the reason we should find them and how this can be achieved. Am J Hum Genet. Vol. 73 (1), pp. 5-16.





  • Department of Biological Sciences
  • University of Southern California
  • Allan Hancock Foundation Building
  • Los Angeles, CA 90089-0371