Refereed Journal Publications



PDF coming soon!
VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials
Brian Y. Chen, PLoS Computational Biology, in press.
PDF coming soon!
Isolating Influential Regions of Electrostatic Focusing in Protein and DNA Structure
Seth Blumenthal, Yisheng Tang, Wenjie Yang, and Brian Y. Chen, IEEE Transactions in Computational Biology and Bioinformatics, 10(5), pp 1188-1198, 2013.
PDF coming soon!
An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility
Brian G. Godshall, Yisheng Tang, Wenjie Yang, and Brian Y. Chen BMC Structural Biology, BMC Structural Biology 13.Suppl 1 (2013): S10.
Modeling Regionalized Volumetric Differences in Protein-Ligand Binding Cavities
Brian Y. Chen and Soutir Bandyopadhyay. Invited to: Proteome Science, doi:10.1186/1477-5956-10-S1-S6, 10(Suppl 1):S6, 2012.
A Regionalizable Statistical Model of Intersecting Regions in Protein-Ligand Binding Cavities
Brian Y. Chen and Soutir Bandyopadhyay. Invited to: Journal of Bioinformatics and Computational Biology, doi: 10.1142/S0219720012420048, 2012.
MarkUs: a Server to Navigate Sequence–Structure–Function Space
Markus Fischer, Qiangfeng Cliff Zhang, Fabian Dey, Brian Y. Chen, Barry Honig, and Donald Petrey. Nucleic Acids Research, doi:10.1093/nar/gkr468, pp. 1-5, 2011.
Multivariate Assessment of Virtual Screening Experiments
C. David Andersson, Brian Y. Chen, Anna Linusson Journal of Chemometrics, vol. 24(11-12), pp. 757-67, 2010.
VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity
Brian Y. Chen and Barry Honig. PLOS Computational Biology. 6(8): e1000881. doi:10.1371/journal.pcbi.1000881, 2010.
Analysis of Substructural Variation in Families of Enzymatic Proteins with Applications to Protein Function Prediction
Drew H. Bryant, Mark Moll, Brian Y. Chen, Viacheslav Y. Fofanov, and Lydia E. Kavraki. BMC Bioinformatics, vol. 11:242, 2010.
Mapping of Ligand-Binding Cavities in Proteins
C. David Andersson, Brian Y. Chen, Anna Linusson. PROTEINS: Structure, Function, and Bioinformatics, vol. 78(6), pp. 1408-22, 2010.
Prediction of Enzyme Function Based on 3D Templates of Evolutionarily Important Amino Acids
David M. Kristensen, Robert M. Ward, Andreas M. Lisewski, Serkan Erdin, Brian Y. Chen, Viacheslav Y. Fofanov, Marek Kimmel, Lydia E. Kavraki, Olivier Lichtarge. BMC Bioinformatics, vol. 9:17, 2008.
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. Invited to: Journal of Bioinformatics and Computational Biology, vol. 5(2a), pp. 353-382, 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. Invited to: Journal of Computational Biology, vol. 14(6), pp. 791-816, 2007.
Recurrent Use of Evolutionary Importance for Functional Annotation of Proteins Based on Local Structural Similarity
David M. Kristensen, Brian Y. Chen, Viacheslav Y. Fofanov, R. Matthew Ward, A. Martin Lisewski, Marek Kimmel, Lydia E. Kavraki, and Olivier Lichtarge. Protein Science, vol. 15(6), pp. 1530-6, 2006.
Sampling-Based Roadmap of Trees for Parallel Motion Planning
Erion Plaku, Konstantinos E. Bekris, Brian Y. Chen, Andrew M. Ladd, Lydia E. Kavraki. IEEE Transactions on Robotics, vol. 21(4), pp. 587-608, 2005.



Refereed Conference Publications

PDF coming soon!
Variational Bayesian Clustering on Protein Cavity Conformations for Detecting Influential Amino Acids
Ziyi Guo and Brian Y. Chen Proceedings of the Computational Structural Bioinformatics Workshop (CSBW 2014), (accepted). Newport Beach, CA, September, 2014.
A gesture-based interface for the exploration and classification of protein binding cavities
Zachary A. Daniels, Steven R. Stinson, Shenchi Tian, Evan Mulbry, and Brian Y. Chen Proceedings of the 2014 workshop on Mobile augmented reality and robotic technology-based systems (MARS 2014), pp 47-50. Bretton Woods, NH, June 2014.
PDF coming soon!
A Flexible Volumetric Comparison of Protein Cavities can Reveal Patterns in Ligand Binding Specificity
Ziyi Guo, Trevor Kuhlengel, Steven Stinson, Seth Blumenthal, Soutir Bandyopadhyay and Brian Y. Chen Proceedings of the 5rd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (BCB 2014), pp 445-454. Newport Beach, CA, September, 2014.
PDF coming soon!
Improving Accuracy in Binding Site Comparison with Homology Modeling
Brian G. Godshall and Brian Y. Chen Proceedings of the Computational Structural Bioinformatics Workshop (CSBW 2012), (accepted). Philadelphia, PA, Oct 2012.
PDF coming soon!
A Volumetric Method for Representing and Comparing Regions of Electrostatic Focusing in Molecular Structure
Brian Y. Chen and Debdas Paul. Proceedings of the 3rd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (BCB 2012), pp 242-249. Orlando, FL, October 2012.
PDF coming soon!
Aligning Ligand Binding Cavities by Optimizing Superposed Volume
Ruobing Chen, Katya Scheinberg, and Brian Y. Chen. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), pp 1-5. Philadelphia, PA, October 2012.
A Statistical Model of Overlapping Volume in Ligand Binding Cavities
Brian Y. Chen and Soutir Bandyopadhyay. Proceedings of the Computational Structural Bioinformatics Workshop (CSBW 2011), pp. 424-31. Atlanta, GA, November 2011.
VASP-S: A Volumetric Analysis and Statistical Model for Predicting Steric Influences on Protein-Ligand Binding Specificity
Brian Y. Chen and Soutir Bandyopadhyay. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), pp. 22-9. Atlanta, GA, November 2011.
A Statistical Model to Correct Systematic Bias Introduced by Algorithmic Thresholds in Protein Structural Comparison Algorithms
Viacheslav Y. Fofanov*, Brian Y. Chen*, Drew H. Bryant, Mark Moll, Olivier Lichtarge, Lydia Kavraki, and Marek Kimmel. Computational Structural Bioinformatics Workshop, IEEE International Conference on Bioinformatics and Biomedicine (BIBM 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.
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. Also appeared in: Research in Computational Molecular Biology, Lecture Notes in Computer Science, Volume 3909/2006, Springer Berlin / Heidelberg. S. Istrail, P. Pevzner, and M.Waterman, ed. pp. 500-15.
Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs
Brian Y. Chen*, Viacheslav Y. Fofanov*, David M. Kristensen, Marek Kimmel, Olivier Lichtarge, Lydia E. Kavraki. Proceedings of The Pacific Symposium on Biocomputing (PSB 2005), pp. 334-345, World Scientific. Big Island, HI, January 2005.

Multiple Query Probabilistic Roadmap Planning Using Single Query Planning Primitives
Konstantinos E. Bekris, Brian Y. Chen, Andrew M. Ladd, Erion Plaku, and Lydia E. Kavraki. IEEE/RJS International Conference on Intelligent Robots and Systems (IROS), pp. 656-661. Las Vegas, NV, October 2003.
Probabilistic Roadmaps of Trees for Parallel Computation of Multiple Query Roadmaps
Mert Akinc, Konstantinos E. Bekris, Brian Y. Chen, Andrew M. Ladd, Erion Plaku, and Lydia E. Kavraki. Invited to: Eleventh International Symposium of Robotics Research (ISRR), Siena, Italy, 2003. Also appeared in: Springer-Verlag, Springer Tracts in Advanced Robotics (STAR), editors D. Paolo and R. Chatila, vol. 15, pp. 80-89.



Theses

Geometry-based Methods for Protein Function Prediction
Brian Y. Chen, Thesis, Doctor of Philosophy. Rice University Department of Computer Science, Houston, Texas. Fall, 2006.
Structural Pattern Matching for Functional Annotation of Proteins
Brian Y. Chen, Thesis, Masters of Science. Rice University Department of Computer Science, Houston, Texas. Spring, 2003.



Selected Talks

Comparing Solid Representations of Protein Cavities to Reveal Influences on Protein-Ligand Binding Specificity
Invited to: 2011 SIAM Conference on Geometric and Physical Modeling, Minisymposium on Geometry in Macromolecular Modeling, Orlando, FL, Oct 25, 2011.
An Algorithm for Discovering Steric Influences on Protein-Ligand Binding Specificity
Invited to: Departmental Colloquia, Dept. of Computer Science, George Mason University. Fairfax, VA, Oct 11, 2011.
Cavity-Aware Motifs Reduce False Positives in Protein Function Prediction
2006 IEEE Computational Systems Bioinformatics Conference (CSB 2006), Stanford University, Palo Alto, CA. August 14-18, 2006.
Geometric Refinement of Active Site Motifs for Improved Annotation of Protein Function
Invited to: 2006 NLM Informatics Training Conference, Vanderbilt University, Nashville, TN. June 27-28, 2006.
Geometric Sieving: Automated Distributed Optimization of 3D-Motifs for Protein Function Prediction
Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2006), Venice, Italy. April 2-5, 2006.
Optimizing 3D-Motifs for Protein Function Prediction
Houston Society for Engineering in Medicine and Biology (HSEMB2006), University of Houston, Houston, Texas. February 9, 2006.
Geometric and Statistical Analysis of 3D Protein Substructures using Match Augmentation
DIMACS Workshop on Information Processing by Protein Structures, Rutgers University, Piscataway, New Jersey. June 23, 2005.
Geometric Pattern Matching for Biological Problems
Invited to: John P. McGovern Town Meeting on Biocomputing and Imaging, Texas Medical Center, Houston, TX. March 2, 2005.
Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs
Pacific Symposium on Biocomputing (PSB 2005), Big Island, Hawaii. January 5, 2005.
Structural Pattern Matching for Functional Annotation of Proteins
Houston Society for Engineering in Medicine and Biology (HSEMB2003), University of Houston, Houston, Texas. April 3, 2003.