Brian Chen, Ph.D.
Bethlehem, Pennsylvania, United States
Research field: Computer and Information Science
Structural Bioinformatics, Computational and Structural Biology
Publications
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Journal Article (11)
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Markus Fischer, Qiangfeng Cliff Zhang, Fabian Dey et al. (2011) MarkUs: a server to navigate sequence-structure-function space., 1-5. In Nucleic acids research.Download PDF (2.53 MB)
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Drew H Bryant, Mark Moll, Brian Y Chen et al. (2010) Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. In BMC bioinformatics 11 (242).Download PDF (3.81 MB)
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C. David Andersson, Brian Y Chen, Anna Linusson (2010) Mapping of ligand-binding cavities in proteins., 1408-22. In Proteins: Structure, Function, and Bioinformatics 78 (6).Download PDF (1.22 MB)
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C. David Andersson, Brian Y Chen, Anna Linusson (2010) Multivariate assessment of virtual screening experiments, 757-767. In Journal of Chemometrics 24 (11-12).Download PDF (432.72 KB)
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Brian Y Chen, Barry Honig (2010) VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity, 11. In PLoS Computational Biology 6 (8).Download PDF (925.94 KB)
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David M Kristensen, R Matthew Ward, Andreas Martin Lisewski et al. (2008) Prediction of enzyme function based on 3D templates of evolutionarily important amino acids., 17. In BMC Bioinformatics.Download PDF (2.11 MB)
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Brian Y Chen, Drew H Bryant, Viacheslav Y Fofanov et al. (2007) Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction., 353-82. In Journal of bioinformatics and computational biology 5 (2a).Download PDF (2.19 MB)
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Brian Y Chen, Drew H Bryant, Amanda E Cruess et al. (2007) Composite motifs integrating multiple protein structures increase sensitivity for function prediction., 343-55. In Computational Systems Bioinformatics Conference (CSB2007).Download PDF (419.71 KB)
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Brian Y Chen, Viacheslav Y Fofanov, Drew H Bryant et al. (2007) The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs., 791-816. In Journal of Computational Biology 14 (6).Download PDF (4 MB)
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David M Kristensen, Brian Y Chen, Viacheslav Y Fofanov et al. (2006) Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity, 1530-1536. In Protein Science 15 (6).Download PDF (402.35 KB)
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Conference Proceedings (5)
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V.Y. Fofanov, Brian Y Chen, Drew H Bryant et al. (2008) A statistical model to correct systematic bias introduced by algorithmic thresholds in protein structural comparison algorithms, 1-8. In Computational Structural Bioinformatics Workshop, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008)..Download PDF (678.93 KB)
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Brian Y Chen, Drew H Bryant, Viacheslav Y Fofanov et al. (2006) Cavity-aware motifs reduce false positives in protein function prediction., 311-23. In Proceedings of the 2006 IEEE Computational Systems Bioinformatics Conference (CSB 2006).Download PDF (1.65 MB)
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Brian Y Chen, Viacheslav Y Fofanov, Drew H Bryant et al. (2006) Geometric Sieving : Automated Distributed Optimization of 3D Motifs for Protein Function Prediction, 500-515. In Proceedings of The Tenth Annual International Conference on Computational Molecular Biology (RECOMB 2006).Download PDF (617.03 KB)
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Brian Y Chen, Viacheslav Y Fofanov, David M Kristensen et al. (2005) Algorithms for structural comparison and statistical analysis of 3D protein motifs., 334-45. In Pacific Symposium on Biocomputing..Download PDF (327.45 KB)
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K.E. Bekris, Brian Y Chen, A.M. Ladd et al. (2003) Multiple query probabilistic roadmap planning using single query planning primitives, 656-661. In Proceedings 2003 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2003) 01 (October).Download PDF (419.55 KB)
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Awards and Grants
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May 2011Sigma Xi Honorific Society, full member, 2011. View website
Biographical Information
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.
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.
CV
Professional Experience
2010 - Present
Assistant Professor at Department of Computer Science and Engineering, Lehigh University
Bethlehem, Pennsylvania, United States
Bethlehem, Pennsylvania, United States
Dec 2006 - Jul 2010
Postdoctoral Research Scientist at Howard Hughes Medical Institute, Dept. of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University
New York, New York, United States
New York, New York, United States
Aug 2000 - Nov 2006
Research Assistant at Computer Science, Rice University
Houston, Texas, United States
Houston, Texas, United States
Education
Aug 2000 - Nov 2006
Rice University
in Houston, Texas, United States
Ph.D.
Ph.D.
Aug 1996 - May 2000
Rutgers University
in Piscataway, New Jersey, United States
Computer Science and Mathematics
Computer Science and Mathematics
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