About Me

I am a Computer Science graduate student in Dr. Lydia Kavraki's Physical and Biological Computing Group.

Currently, most of my work is related to the analysis of 3-dimensional protein structures. I am very interested in building computational tools for protein structure simulation that are capable making experimentally verifiable predictions (and actually testing those predictions).

 

Awards

  • National Science Foundation Graduate Research Fellowship, 2008
  • John and Ellen Tietze Fellowship, 2008
  • Janessa Shapiro Award, 2007
  • James S. Waters Creativity Award, 2007
  • First Place, Engineering Division, Rice Undergraduate Research Symposium Poster Contest, 2007
  • Outstanding Senior Design Project Award for ”Nanosorter: A High-Throughput Nanoshell Sorting Device”, 2007
  • Outstanding Contributions to Research Award, 2007
  • Texas Space Grant Consortium Scholarship Award, 2006
  • W.M. Keck Center Undergraduate Research Training Program Fellowship, 2005
  • Brown Undergraduate Research Internship Award, 2004

Curriculum Vitae

  • Education

    • Rice University
      , 2003-2007:
      B.S. in Bioengineering (BSBE) Awarded May, 2007
      Specialization: Cellular and Molecular Engineering
    • Rice University
      , 2008-present:
      PhD Student in Computer Science

  • Work Experience

    • Genentech, Inc.
      , South San Francisco, CA, June-December, 2007
      Internship with the Department of Early-Stage Purification
      • Implemented a lab- and pilot-scale, non-chromatography process for monoclonal antibody (mAb) purification
      • Optimized purification process parameters for improved mAb yield and time-efficiency
      • Utilized a robotic wet lab station for automated, high-throughput parameter sweeping

  • Publications

    • Composite Motifs Integrating Multiple Protein Structures Increase Sensitivity For Function Prediction

      Brian Y. Chen, Drew H. Bryant, Amanda E. Cruess, Joseph H. Bylund, Viacheslav Y. Fofanov, David M. Kristensen, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki. Proceedings of the 2007 IEEE Computational Systems Bioinformatics Conference (CSB 2007), pp. 343-55. San Diego, CA, August 2007.
    • The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs

      Brian Y. Chen, Viacheslav Y. Fofanov, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, Andreas M. Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki. Journal of Computational Biology, vol. 14(6), pp. 791-816, 2007.
    • Cavity Scaling: Automated Refinement of cavity aware motifs in protein function prediction

      Brian Y. Chen, Drew H. Bryant, Viacheslav Y. Fofanov, David M. Kristensen, Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge and Lydia E. Kavraki. Journal of Bioinformatics and Computational Biology, vol. 5(2a), pp. 353-382, 2007.
    • Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction

      Brian Y. Chen*, Drew H. Bryant*, Viacheslav Y. Fofanov, David M. Kristensen, Amanda E. Cruess, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki. Proceedings of the 2006 IEEE Computational Systems Bioinformatics Conference (CSB 2006), pp. 311-23. Palo Alto, CA, August 2006.
    • Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction

      Brian Y. Chen*, Viacheslav Y. Fofanov*, Drew H. Bryant, Bradley D. Dodson, David M. Kristensen, A. Martin Lisewski, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki. Proceedings of The Tenth Annual International Conference on Computational Molecular Biology (RECOMB 2006), pp. 500-15. Venice, Italy, April 2006.

My Two Dogs

I have two lovable dachshund/chihuahua mixes (aka Chiweenies).

Above is Tobias, ~3 years old

Above is Jonas, ~1 year old

Tobias on a roadtrip