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B. Kirkpatrick and M. Mnich. Efficient haplotype inference for
pedigrees with few recombinations. unpublished manuscript, 2011.
B. Kirkpatrick and K. Kirkpatrick. Optimal state-space
reduction for pedigree Hidden Markov Models. unpublished
manuscript, 2011. (preprint)
B. Kirkpatrick, Y. Reshef, H. Finucane, H. Jiang, B. Zhu, R. M.
Karp. Comparing pedigree graphs. J. Comput. Biol. 2012.
(preprint)
B. Kirkpatrick. Non-Identifiable Pedigrees and a Bayesian
Solution. Int. Symp. on Bioinformatics
Res. and Appl. (ISBRA), 2012.
(abstract,
paper)
B. Kirkpatrick, S.C. Li, R. M. Karp, and E. Halperin. Pedigree
reconstruction using identity by descent. J. Comput. Biol.,
18(11):1481-93, 2011. (abstract)
K. Stephens and B. Kirkpatrick. Efficiently solvable perfect
phylogeny problems on binary and k-state data with missing values.
11th Workshop on Algorithms in Bioinformatics (WABI), 2011. (pdf)
B. Kirkpatrick. Algorithms for human genetics. UC Berkeley, EECS,
Ph.D. Thesis. 2011.
(pdf)
B. Kirkpatrick, S.C. Li, R. M. Karp, and E. Halperin. Pedigree
reconstruction using identity by descent. Int. Conf.
on Research in Comput. Molecular Biology (RECOMB), 2011. (pdf)
B. Kirkpatrick. Haplotypes versus genotypes on pedigrees.
Algorithms Mol. Biol., 2011. (pdf)
B. Kirkpatrick. Haplotypes versus genotypes on pedigrees.
10th Workshop on Algorithms in Bioinformatics (WABI), 2010.
(pdf, appendix)
B. Kirkpatrick, E. Halperin, and R.M. Karp.
Haplotype inference in complex pedigrees. J. Comput. Biol. 17(3):
269-280,
2010.
(pdf,supplement)
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.
Comput. Biol., 2003. Vol. 10, No. 3-4:555-567. (pdf)
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