Brian Chen

  • Ph.D.
  • Assistant Professor
  • Department of Computer Science and Engineering, Lehigh University

Research Interests

Structural Bioinformatics Computational and Structural Biology

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About

I am an assistant professor in the Department of Computer Science and Engineering within the P. C. Rossin College of Engineering and Applied Sciences at Lehigh University. My research focuses primarily on structural bioinformatics.

I was a postdoctoral research scientist at Barry Honig's Lab at the Howard Hughes Medical Institute, the Department of Biochemistry and Molecular Biophysics, and the Center for Computational Biology and Bioinformatics at Columbia University. At Columbia, I gained considerable exposure to research in structural biology, biophysics, and protein crystallography.

I earned a Ph.D. from Rice University's Department of Computer Science for my work on protein function annotation. My advisor was Dr. Lydia Kavraki. While at Rice, I had the pleasure to learn quite a bit about structural bioinformatics, robotics, graphics, and distributed systems.

I received a B.A. in Mathematics and a B.A. in Computer Science from Rutgers College at Rutgers University, the State University of New Jersey, in 2000. While at Rutgers, I had the opportunity to do a summer project with János Komlós, and some signal processing with William Craelius.

Publications

MarkUs: a server to navigate sequence-structure-function space.

Fischer M, Zhang Q, Dey F, Chen B, Honig B, Petrey D

Nucleic acids research (2011)

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Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction

Bryant D, Moll M, Chen B, Fofanov V, Kavraki L

BMC bioinformatics (2010)

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Mapping of ligand-binding cavities in proteins.

Andersson C, Chen B, Linusson A

Proteins: Structure, Function, and Bioinformatics (2010)

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Multivariate assessment of virtual screening experiments

Andersson C, Chen B, Linusson A

Journal of Chemometrics (2010)

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VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity

Chen B, Honig B

PLoS Computational Biology (2010)

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A statistical model to correct systematic bias introduced by algorithmic thresholds in protein structural comparison algorithms

Fofanov V, Chen B, Bryant D, Moll M, Lichtarge O, Kavraki L, Kimmel M

Computational Structural Bioinformatics Workshop, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008). (2008)

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Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

Kristensen D, Ward R, Lisewski A, Erdin S, Chen B, Fofanov V, Kimmel M, Kavraki L, Lichtarge O

BMC Bioinformatics (2008)

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Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction.

Chen B, Bryant D, Fofanov V, Kristensen D, Cruess A, Kimmel M, Lichtarge O, Kavraki L

Journal of bioinformatics and computational biology (2007)

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Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

Chen B, Bryant D, Cruess A, Bylund J, Fofanov V, Kristensen D, Kimmel M, Lichtarge O, Kavraki L

Computational Systems Bioinformatics Conference (CSB2007) (2007)

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The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.

Chen B, Fofanov V, Bryant D, Dodson B, Kristensen D, Lisewski A, Kimmel M, Lichtarge O, Kavraki L

Journal of Computational Biology (2007)

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Cavity-aware motifs reduce false positives in protein function prediction.

Chen B, Bryant D, Fofanov V, Kristensen D, Cruess A, Kimmel M, Lichtarge O, Kavraki L

Proceedings of the 2006 IEEE Computational Systems Bioinformatics Conference (CSB 2006) (2006)

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Geometric Sieving : Automated Distributed Optimization of 3D Motifs for Protein Function Prediction

Chen B, Fofanov V, Bryant D, Dodson B, Kristensen D, Lisewski A, Kimmel M, Lichtarge O, Kavraki L

Proceedings of The Tenth Annual International Conference on Computational Molecular Biology (RECOMB 2006) (2006)

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Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

Kristensen D, Chen B, Fofanov V, Ward R, Lisewski A, Kimmel M, Kavraki L, Lichtarge O

Protein Science (2006)

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Algorithms for structural comparison and statistical analysis of 3D protein motifs.

Chen B, Fofanov V, Kristensen D, Kimmel M, Lichtarge O, Kavraki L

Pacific Symposium on Biocomputing. (2005)

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Sampling-based roadmap of trees for parallel motion planning

Plaku E, Bekris K, Chen B, Ladd a, Kavraki L

IEEE Transactions on Robotics (2005)

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Multiple query probabilistic roadmap planning using single query planning primitives

Bekris K, Chen B, Ladd A, Plaku E, Kavraki L

Proceedings 2003 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2003) (2003)

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Professional experience

Assistant Professor

Department of Computer Science and Engineering, Lehigh University

August 2010 - Present

Postdoctoral Research Scientist

Howard Hughes Medical Institute, Dept. of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University

December 2006 - July 2010 (3 years 7 months)

Research Assistant

Rice University Department of Computer Science

August 2000 - November 2006 (6 years 3 months)

Education history

Rice University

Ph.D.

August 2000 - November 2006 (6 years 3 months)

Rutgers University Rutgers Business School

Computer Science and Mathematics

August 1996 - May 2000 (3 years 9 months)