Mapping Discontinuous Antibody Epitopes to Reveal Protein Structure and Changes in Structure Related to Function. - Brendan Mumey; Thomas Angel; Bonnie Kirkpatrick; Brian W. Bailey; P. Hargrave; Algirdas J. Jesaitis; Edward A. Dratz (CSB, 2003)

A New Method for Mapping Discontinuous Antibody Epitopes to Reveal Structural Features of Proteins. - Brendan Mumey; Brian W. Bailey; Bonnie Kirkpatrick; Algirdas J. Jesaitis; Thomas Angel; Edward A. Dratz (J. Comput. Biol., 2003)

Using Motion Planning to Study RNA Folding Kinetics. - Xinyu Tang 002; Bonnie Kirkpatrick; Shawna L. Thomas; Guang Song; Nancy M. Amato (J. Comput. Biol., 2005)

HAPLOPOOL: improving haplotype frequency estimation through DNA pools and phylogenetic modeling. - Bonnie Kirkpatrick; Carlos Santos Armendariz; Richard M. Karp; Eran Halperin (Bioinform., 2007)

Haplotype Inference in Complex Pedigrees. - Bonnie Kirkpatrick; Javier Rosa; Eran Halperin; Richard M. Karp (RECOMB, 2009)

Algorithms for Comparing Pedigree Graphs - Bonnie Kirkpatrick; Yakir Reshef; Hilary K. Finucane; Haitao Jiang; Binhai Zhu; Richard M. Karp (CoRR, 2010)

Haplotype Inference in Complex Pedigrees. - Bonnie Kirkpatrick; Eran Halperin; Richard M. Karp (J. Comput. Biol., 2010)

Efficiently Solvable Perfect Phylogeny Problems on Binary and k-State Data with Missing Values. - Kristian Stevens; Bonnie Kirkpatrick (WABI, 2011)

Haplotypes versus genotypes on pedigrees. - Bonnie Kirkpatrick (Algorithms Mol. Biol., 2011)

Pedigree Reconstruction Using Identity by Descent. - Bonnie Kirkpatrick; Shuai Cheng Li 001; Richard M. Karp; Eran Halperin (J. Comput. Biol., 2011)

Algorithms for Human Genetics. - Bonnie Kirkpatrick (2011)

Non-identifiable Pedigrees and a Bayesian Solution. - Bonnie Kirkpatrick (ISBRA, 2012)

Bayesian Pedigree Analysis using Measure Factorization. - Bonnie Kirkpatrick; Alexandre Bouchard-Côté (NIPS, 2012)

Optimal State-Space Reduction for Pedigree Hidden Markov Models - Bonnie Kirkpatrick; Kay Kirkpatrick (CoRR, 2012)

Comparing Pedigree Graphs. - Bonnie Kirkpatrick; Yakir Reshef; Hilary K. Finucane; Haitao Jiang; Binhai Zhu; Richard M. Karp (J. Comput. Biol., 2012)

Efficient Continuous-Time Markov Chain Estimation. - Monir Hajiaghayi; Bonnie Kirkpatrick; Liangliang Wang; Alexandre Bouchard-Côté (ICML, 2014)

Reachability bounds for chemical reaction networks and strand displacement systems. - Anne Condon; Bonnie Kirkpatrick; Ján Manuch (Nat. Comput., 2014)

Perfect Phylogeny Problems with Missing Values. - Bonnie Kirkpatrick; Kristian Stevens (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Haplotype Inference for Pedigrees with Few Recombinations. - Bonnie Kirkpatrick (ISBRA, 2016)

Fast Computation of the Kinship Coefficients. - Bonnie Kirkpatrick (CoRR, 2016)

Design of nucleic acid strands with long low-barrier folding pathways. - Anne Condon; Bonnie Kirkpatrick; Ján Manuch (Nat. Comput., 2017)