B Kirkpatrick
 www.bowtiecomputing.com
bbkirk@bowtiecomputing.com


Education
Ph.D. in Computer Science University of California Berkeley, 2011
M.S. in Computer Science University of California Berkeley, 2007
B.S. in Computer Science
 Montana State University, Bozeman, MT, 2004


Merit Awards
Fernbach Fewlloship at LLNL (declined), 2012
Google Anita Borg Memorial Scholarship, 2010
NSF Graduate Research Fellowship, 2005-2010
DOE Computational Science Graduate Fellowship, 2004-2008
Siebel Award for Leadership and Academic Excellence, 2005-2006
Barry M. Goldwater Scholarship, 2003-2004
Micron Scholarship, 2002-2004
Computing Research Association Distributed Mentor Project, 2002, 2003
Phi Kappa Phi Outstanding Junior Award Honorable Mention, 2003
Montana Space Grant Consortium Scholarship, 2001-2003
Undergraduate Scholars Program Research Scholarship, 2001-2003
Award for Excellence, 2004
National Partnership for Advanced Computing Infrastructure-Research Experience, 2001


Professional Experience
Founder & Researcher,   Computer Science Bowtie Computing Nov 2023 - present
 
Founder & Researcher,   Computer Science Intrepid Net Computing Aug 2015 - Nov 2023
 
Assistant Professor,   Computer Science University of Miami Jan 2014 - Aug 2015
 
Visiting Professor,   Computer Science University of Maine Jul 2013 - Jan 2014
 
Post-doc,   Bioinformatics, and Empirical & Theoretical Algorithmics (Beta) Lab, University of British Columbia, Jul 2011 - Jul 2013
Investigating probabilistic models with combinatorial state-spaces.
Working on applications to RNA folding, pedigree analysis, and cancer genetics.
Researcher,   Bioinformatics Group, International Computer Science Institute, Aug 2005 - Jun 2011
Developing SNP analysis techniques to analyze genetic variation in populations.
Studying both family relationships and population-genetic relationships.
Researcher,   Bioinformatics Group, Lawrence Livermore National Laboratory, Jun 2005 - Aug 2005
Discovering structurally conserved regions of related proteins.
Researcher,   Mumey Laboratory, Montana State University-Bozeman, Jul 2001-2004
Mapped discontinuous antibody epitopes to reveal structural features of proteins.
Researcher,   PARASOL Lab, Texas A&M University, Jun 2002 - Sept 2003
Explored protein and RNA folding landscapes using robotic motion-planning techniques.

Consulting,   A New Arrival, Inc., Silver Star, MT, Jan 2002 - May 2003
Advised an adoption agency on electronic security for confidential documents.

Researcher,   Center for Computational Biology, Montana State University-Bozeman, Jun - Dec 2001
Achieved end-user configurability of scientific data in semistructured databases.


Teaching Experience
CSC 210: Computing for Scientists University of Miami, Spring 2015
CSC 210: Computing for Scientists University of Miami, Fall 2014
CSC 527: Theory of Computing University of Miami, Spring 2014
CPSC 445: Algorithms in Bioinformatics University of British Columbia Spring 2013
Combinatorics and Discrete Probability, UC Berkeley, Fall 2010
Software Engineering, UC Berkeley, Spring 2009
Combinatorics and Discrete Probability, UC Berkeley, Fall 2008
Software Engineering, UC Berkeley, Fall 2006
Tutor for CS Theory, Montana State University-Bozeman, Spring 2002


Publications in Refereed Journals and Conferences

  1. B. Kirkpatrick. Cliques in graphs. TIPS. 2022. (paper)

  2. B. Kirkpatrick. Cycles in graphs. TIPS. 2022. (paper)

  3. B. Kirkpatrick. A polynomial-time algorithm for graph isomorphism. TIPS. 2016. (paper)

  4. B. Kirkpatrick. Computer security is algorithmically intractable. 2018. TIPS, SIAM CSE 2019. (paper)

  5. B. Kirkpatrick, S. Ge, and L. Wang. Efficient computation of the kinship coefficients. Bioinformatics. bty725. 2018. (paper, software)

  6. S. Ge, L. Wang, and B. Kirkpatrick. Efficient computation of the kinship coefficients. RECOMB Satellite Meeting on Genetics. 2017.

  7. A. Condon, B. Kirkpatrick, and J. Manuch. Design of nucleic acid strands with long low-barrier folding pathways. Natural Computing, 2017.

  8. B. Kirkpatrick. Haplotype inference for pedigrees with few recombinations. arXiv:1602.04270. Int. Symp. on Bioinformatics Res. and Appl. (ISBRA). 2016.

  9. F. Lindsten, A. M. Johansen, C. A. Naesseth, B. Kirkpatrick, T. B. Schön, J. Aston, A. Bouchard-Côté. Divide-and-conquer with sequential Monte carlo. arXiv:1406.4993. Journal of Computational and Graphical Statistics. 2016.

  10. A. Condon, B. Kirkpatrick, and J. Manuch. Reachability bounds for chemical reaction networks and strand displacement systems. Natural Computing, 13(4):499-516, 2014.

  11. M. Hajiaghayi, B. Kirkpatrick, L. Wang and A. Bouchard-Côté. Efficient Continuous-Time Markov Chain Estimation. International Conference on Machine Learning (ICML). 2014.

  12. B. Kirkpatrick and K. Stevens. Perfect phylogeny problems with missing values. IEEE Transactions on Computational Biology and Bioinformatics, 11(5):928-941, 2014.

  13. B. Kirkpatrick, M. Hajiaghayi, and A. Condon. A new model for approximating RNA folding trajectories and population kinetics. Computational Science & Discovery, 6(1), 2013.

  14. A. Bouchard-Côté and B. Kirkpatrick. Bayesian pedigree analysis using measure factorization. NIPS: Neural Information Processing Systems 25, 2012.

  15. A. Condon, B. Kirkpatrick and J. Manuch. Reachability bounds for chemical reaction networks and strand displacement systems, 18th International Conference on DNA Computing and Molecular Programming, Springer-Verlag Lecture Notes in Computer Science 7433:43-57, 2012.

  16. B. Kirkpatrick, Y. Reshef, H. Finucane, H. Jiang, B. Zhu, R. M. Karp. Comparing pedigree graphs. J. Comput. Biol., 19(9):998-1014, 2012.

  17. B. Kirkpatrick. Non-identifiable pedigrees and a Bayesian solution. Int. Symp. on Bioinformatics Res. and Appl. (ISBRA), 2012. arXiv:1602.08183, 2016.

  18. K. Stevens 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.

  19. 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.

  20. 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.

  21. B. Kirkpatrick. Haplotypes versus genotypes on pedigrees. Algorithms Mol. Biol., 6(10), 2011.

  22. B. Kirkpatrick. Haplotypes versus genotypes on pedigrees. 10th Workshop on Algorithms in Bioinformatics (WABI), 2010.

  23. B. Kirkpatrick, E. Halperin, and R.M. Karp. Haplotype inference in complex pedigrees. J. Comput. Biol., 17(3): 269-280, 2010.

  24. B. Kirkpatrick, J. Rosa, E. Halperin, and R.M. Karp. Haplotype inference in complex pedigrees. Int. Conf. Comput. Molecular Biology (RECOMB), 2009.

  25. 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.

  26. 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.

  27. X. Tang, B. Kirkpatrick, S. Thomas, G. Song, and N. M. Amato. Using motion planning to study RNA folding kinetics. J. Comput. Biol., 12(6):862-881, 2005.

  28. 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), pp. 252-261, 2004.

  29. 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., 10(3-4):555-567, 2003.


Manuscripts

  1. B. Kirkpatrick and K. Kirkpatrick. Optimal space reduction for pedigree hidden Markov models. arXiv:1202.2468. submitted, 2011.

  2. B. Kirkpatrick and A. Bouchard-Côté. Correcting for cryptic relatedness in genome-wide association studies. arXiv:1602.07956. submitted, 2016.

  3. B. Kirkpatrick. Efficient Computation with Large Pedigrees. 2015.


Unrefereed Publications, White-Papers, Technical Reports, and Posters

  1. B. Kirkpatrick. Expenditure accounting algorithm. TIPS. 2023. (paper)

  2. B. Kirkpatrick. Symmetric graph algorithms. TIPS. 2021. (paper)

  3. B. Kirkpatrick. Properties of hacks. TIPS. 2020. (paper)

  4. B. Kirkpatrick. Precision in network time. TIPS. 2020. (paper)

  5. B. Kirkpatrick. Properties of network time. TIPS. 2020. (paper)

  6. B. Kirkpatrick. Quantum communication. TIPS. 2018. (paper)

  7. B. Kirkpatrick. Panther shadow: a Linux worm analysis. www.intrepidnetcomputing.com. 2018. (defendIT(TM))

  8. B. Kirkpatrick. Panther shadow: a Linux worm. www.intrepidnetcomputing.com. 2018. (pdf)

  9. B. Kirkpatrick. DHCP Worm. 2017. (dfendIT(TM))

  10. B. Kirkpatrick. Cybersecurity in Bosie. www.intrepidnetcomputing.com. 2016. (pdf)

  11. B. Kirkpatrick. Cybersecurity in Salt Lake. www.intrepidnetcomputing.com. 2016. (pdf)

  12. B. Kirkpatrick. Cybersecurity in Miami. www.intrepidnetcomputing.com. 2016. (pdf)

  13. B. Kirkpatrick. Cybersecurity in Montana. www.intrepidnetcomputing.com. 2016. (pdf)

  14. B. Kirkpatrick. Open letter to genetics researchers. TIPS. 2016. (letter)

  15. B. Kirkpatrick. Recovery with 2-Step Verification. 2016. (defendIT(TM))

  16. B. Kirkpatrick. Statistical Forensics. 2016. (defendIT(TM))

  17. B. Kirkpatrick. Hacking as an anathema to computer science. TIPS. 2015. (paper)

  18. B. Kirkpatrick. Patching buffer over-runs using compilers. www.intrepidnetcomputing.com. 2015. (defendIT(TM))

  19. B. Kirkpatrick. USB Trojan detection using a USB drive. www.intrepidnetcomputing.com. 2015. (defendIT(TM))

  20. B. Kirkpatrick. Encouraging vulnerability bounties. TIPS. 2015. (paper)

  21. B. Kirkpatrick. Algorithms for human genetics. UC Berkeley, EECS, Ph.D. Thesis. 2011.

  22. B. Kirkpatrick. Pedigree reconstruction using identity by descent. CS 294-26 final, 2008. Technical Report No. UCB/EECS-2010-43. 2010.

  23. B. Kirkpatrick, X. Tang, S. Thomas, and N. Amato. Modeling RNA folding landscapes with probabilistic roadmap methods. Technical Report, TR03-004, Parasol Lab, Department of Computer Science, Texas A&M University, Aug 2003. Technical Report.

  24. B. Kirkpatrick, G. Song, X. Tang, and N. Amato. Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures. CRA-DMP/USRG, Texas A&M University, Aug 2002.


Extracurricular Activities
Co-President, Women in CS and EE, UC Berkeley, 2006-2008
Organizing Committee Chair, CIPRES Graduate Student Meeting, 2005
Ambassador, College of Engineering, Montana State University, 2002-2004
Faculty Search Committee, Computer Science Dept, Montana State University, 2002-2003
Mentor, PEAKS (gifted program), Bozeman Public Schools, 2003
Webmaster, Women in CS and EE, UC Berkeley, 2005-2006
Vice President and Treasurer, Association of Computing Machinery, 2003-2004
Secretary and Treasurer, Association of Computing Machinery, 2001-2002
President, Campus T'ai Chi / Kung Fu Club, 2001-2004
Web and Public Relations Coordinator, Recycling Club, Montana State University, 2003-2004
Active Member, Association of Women in Computing, 2000-2004
Volunteer Group Leader, Expanding Your Horizons, 2001-2003
Student Volunteer, Computational Systems Bioinformatics Conference, 2004
Student Volunteer, Supercomputing Conference, 2001
Participant, CRA Graduate Cohort, 2005
Attendee, Grace Hopper Celebration of Women in Computing Conference, 2002-2006


Skills
Natural Languages: French (moderate fluency), English (native fluency)
Programming Languages: C++, Perl, Java, R, Matlab, Lisp, PHP, Assembly, and Pascal
Internet Skills: Web site development, CGI, HTML, JavaScript, and XML
Databases: Oracle and MySQL


References
Available on request.