B Kirkpatrick

Bonnie Kirkpatrick

587 Soda
Berkeley, CA 94720-1776
(510) 642-3560
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.

Information

CV
Schedule
Photos

Publications in Refereed Journals and Conferences

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. pp. 252-261. (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)

Software
HaploPool -- a program for estimating haplotype frequencies from genotypes

Resources and Class Projects
Career Opportunities for EECS PhDs
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.

Links
MSU Web Page
TAMU Web Page

Resources and Class Projects
Career Opportunities for EECS PhDs 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.