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, which lies at the intersection of computer science, biochemistry, and statistics. I am very interested in building computational tools for protein structure simulation that are capable of making experimentally verifiable predictions (and actually testing those predictions). I believe that an integrated approach to bioinformatics that synthesizes proteomic data from multiple tiers of molecular resolution, such as sequence, whole structure, networks, and conserved substructures (ex. catalytic or interaction sites), can lead to a better understanding of molecular mechanisms than any level of resolution independently.

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

  • A Statistical Model to Correct Systematic Bias Introduced by Algorithmic Thresholds in Protein Structural Comparison Algorithms

    
    Fofanov VY, Chen BY, Bryant DH, Moll M, Lichtarge O, Kavraki LE, Kimmel M. IEEE Intl. Conf. on Bioinformatics and Biomedicine (BIBM), Philadelphia, PA, (2008)

  • 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