• TEES Assistant Research Scientist
Shawna Thomas

Educational Background

  • Ph.D. in Computer Science, Texas A&M University, College Station, TX 1/02 – 5/10
  • B.S. in Computer Engineering, Texas A&M University, College Station, TX 8/98 – 12/01

Research Interests

  • Studying the folding and motion of molecules using motion planning techniques from robotics. In particular, developing new techniques for modeling protein transitions between two or more known target states. Supervising changes to the research group’s common C++ code base.

Awards & Honors

  • IBM Ph.D. Fellowship, 2008–2009
  • IBM Fran Allen Ph.D. Fellowship, 2007–2008
  • Graduate Assistance in Areas of National Need Fellowship, 2006–2007
  • Philanthropic Educational Organization Scholar Award, 2005–2006
  • NSF Graduate Research Fellowship, 2002–2005
  • Astronaut Scholarship, 2000–2001
  • Lechner Scholarship, Fall 1998–Fall 2001
  • Graduate Research Excellence Award, Department of Computer Science, 2007–2008
  • Mentoring Award, Department of Computer Science, 2007–2008 Undergraduate Research Excellence Award, Department of Computer Science, 2001–2002
  • CRA Distributed Mentor Program Award, Summer 2001
  • University Undergraduate Research Fellow, 2000–2001
  • Best Senior Thesis, Computer Science Group, Spring 2001
  • Best Senior Thesis Presentation, Computer Science Group, Spring 2001
  • Undergraduate Summer Research Grant, Summer 2000
  • Best Presentation, Computer Science Group, Summer 2000

Selected Publications

  • “A Motion Planning Approach to Studying Molecular Motions.” Lydia Tapia, Shawna Thomas, Nancy M. Amato, in Communications in Information and Systems (CIS), 10(1): 53–68, 2010.
  • “Reachable Distance Space: Efficient Sampling-Based Planning for Spatially Constrained Systems.” Xinyu Tang, Shawna THomas, Philip Coleman, Nancy M. Amato, in the International Journal of Robotics Research (IJRR), 29(7): 916–934, 2010.
  • “An Unsupervised Adaptive Strategy for Constructing Probabilistic Roadmaps.” Lydia Tapia, Shawna Thomas, Bryan Boyd, NancyM. Amato, in Proc. of the IEEE International Conference on Robotics and Automation (ICRA), Kobe, Japan, May 2009, pp. 4037–4044. (acceptance rate: 43%)
  • “Planning with Reachable Distances.” Xinyu Tang, Shawna Thomas, NancyM. Amato, in Proc. of the International Workshop on the Algorithmic Foundations of Robotics (WAFR), Guanajuato,M´exico, December 2008.
  • “Simulating RNA Folding Kinetics on Approximated Energy Landscapes.” Xinyu Tang, Shawna Thomas, Lydia Tapia, David Giedroc, Nancy M. Amato, in the Journal of Molecular Biology (JMB), 3811(4): 1055-1067, 2008.
  • “Kinetics Analysis Methods for Approximate Folding Landscapes.” Lydia Tapia, Xinyu Tang, Shawna Thomas, and Nancy M. Amato, in Proc. of the International Conference on Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational Biology (ECCB) Vienna, Austria, published in Bioinformatics, 23(13): i539–i548, July 2007. (acceptance rate: 15%)
  • “Simulating Protein Motions with Rigidity Analysis.” Shawna Thomas, Xinyu Tang, Lydia Tapia, and Nancy M. Amato, in Journal of Computational Biology (JCB), 14(6): 839–855, July 2007. A preliminary version appeared in [13].
  • “Planning with Reachable Distances: Fast Enforcement of Closure Constraints.” Xinyu Tang, Shawna Thomas, and Nancy M. Amato, in Proc. of the IEEE International Conference on Robotics and Automation (ICRA), Roma, Italy, April 2007, pp. 2694–2699. (acceptance rate: 44%)
  • “Biasing Samplers to ImproveMotion Planning Performance.” Shawna Thomas, Marco Morales, Xinyu Tang, and Nancy M. Amato, in Proc. of the IEEE International Conference on Robotics and Automation (ICRA), Roma, Italy, April 2007, pp. 1625–1630. (acceptance rate: 44%)
  • “Tools for Simulating and Analyzing RNA Folding Kinetics.” Xinyu Tang, Shawna Thomas, Lydia Tapia, and Nancy M. Amato, in Proc. of the International Conference on Research in Computational Molecular Biology (RECOMB), Oakland, CA, April 2007, pp. 268–282. (acceptance rate: 21%)