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Bonnie Kirkpatrick |
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544 Soda Berkeley, CA 94720-1776 bbkirk AT eecs DOT berkeley DOT edu |
| As a Computer Science graduate student at UC Berkely, my interest focuses on computational genetics with an emphasis on pedigrees and phylogenetic analysis. |
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| Information | |||
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CV Photos | |||
| Publications in Refereed Journals and Conferences | |||
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B. Kirkpatrick, J. Rosa, E. Halperin, and R.M. Karp.
Haplotype Inference in Complex Pedigrees. Int. Conf. Comput.
Molecular Biology (RECOMB), 2009.
(pdf, supplement) B. Kirkpatrick, C. Santos-Armendariz, R. M. Karp, and E. Halperin. HaploPool: Improving Haplotype Frequency Estimation through DNA Pools and Phylogenetic Modeling. Bioinformatics. 23: 3048-3055. 2007. (pdf) A. Zemla, B. Geisbrecht, J. Smith, M. Lam, B. Kirkpatrick, M. Wagner, T. Slezak, C. Zhou. STRALCP - Structure Alignment-based Clustering of Proteins. Nucleic Acids Research, 2007. ( advance access) X. Tang, B. Kirkpatrick, S. Thomas, G. Song, and N. Amato. Using motion planning to study RNA folding kinetics. Int. Conf. Comput. Molecular Biology (RECOMB), 2004. (ps, pdf) abstract B. M. Mumey, B. W. Bailey, B. Kirkpatrick, A. J. Jesaitis, T. Angel, and E. A. Dratz. A new method for mapping discontinuous antibody epitopes to reveal structural features of proteins. J. of Computational Biology, 2003. Vol. 10, No. 3-4:555-567. (pdf)
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| Software | |||
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HaploPool -- a
program for estimating haplotype frequencies from genotypes PhyloPed -- a program for phasing individuals in a family
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| Resources and Class Projects | |||
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CIPRES Graduate Student Retreat B. Kirkpatrick, S. Lacoste-Julien, and W. Xu. 2004. Analyzing Root DNS Traffic: A systems perspective. CS 262a final. B. Kirkpatrick, S. Lacoste-Julien, and W. Xu. 2004. Analyzing Root DNS Traffic: A machine learning perspective. CS 281a final. B. Kirkpatrick and B. Klingner. 2004. Turing's Imitation Game: A discussion with the benefit of hind-sight. CS Classics with C.H. Papadimitriou. |
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| Links | |||
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TAMU Web Page | |||