Bonnie Kirkpatrick
 544 Soda
University of California Berkeley
Berkeley, CA 94720-1776
bbkirk AT eecs DOT berkeley DOT edu


Education
Ph.D., Computer Science University of California Berkeley, expected 2009
M.S., Computer Science University of California Berkeley, 2007
B.S., Computer Science
      Minors: Mathematics and French,
Montana State University, Bozeman, MT, 2004
Diploma Beaverhead County High School, Dillon, MT, 2000


Merit Awards
NSF Graduate Research Fellowship, 2005-present
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,
      One of thirty recipients nationwide.
 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 for Undergraduates,
      One of thirty-three recipients nationwide.
 2001


Professional Experience
Researcher,   Bioinformatics Group, International Computer Science Institute, Aug 2005 - present
Developing SNP analysis techniques to detect genetic variation in populations

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.

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

Tutor,   Montana State University-Bozeman, Jan - May 2002
Tutored for an upper-level computer theory class.

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


Teaching Experience
Software Engineering, Upper division undergraduate, UC Berkeley, Fall 2006
Mentored and managed two software development teams of six and seven students with Prof. George Necula.


Publications in Refereed Journals and Conferences
  1. 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)

  2. 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).

  3. 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. (ps, pdf) abstract

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


Unrefereed Publications, Technical Reports, and Posters
  1. Kirkpatrick, B. UC Berkeley, EECS, Masters Report. 2007. (pdf) abstract

  2. B. Kirkpatrick. Constructing Phylogenies from Partial Characters. DOE CSGF Conference. Jun 2005.

  3. B. Kirkpatrick and B. Klingner. Turing's Imitation Game: a discussion with the benefit of hindsight. UC Berkeley. Nov 2004.

  4. 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. (ps, pdf)

  5. B. Mumey, T. Angel, B. Kirkpatrick, B. Bailey, P. Hargrave, A. Jesaitis, and E. Dratz. Mapping Discontinuous Antibody Epitopes to Reveal Protein Structure and Changes in Structure Related to Function. Poster at Computational Systems Bioinformatics (CSB), 2003, Stanford University.

  6. 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 Member, Computer Science Dept, Montana State University, 2002-2003
Mentor, PEAKS (gifted and talented 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
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.