Publications

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2015

B. Y. Chen, “Conformational Sampling Reveals Amino Acids with a Steric Influence on Specificity”, Journal of Computational Biology, p. accepted, 2015.
Z. Guo, Hong, J., Scheinberg, K., and Chen, B. Y., “Superposition of Protein Structures using Electrostatic Isopotentials”, Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015), p. in review, 2015.

2014

Z. Guo, Kuhlengel, T. K., Stinson, S. R., Blumenthal, S., Bandyopadhyay, S., and Chen, B. Y., “A Flexible Volumetric Comparison of Protein Cavities can Reveal Patterns in Ligand Binding Specificity”, in Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2014, pp. 445-454.
Z. A. Daniels, Stinson, S. R., Tian, S., Mulbry, E., and Chen, B. Y., “A gesture-based interface for the exploration and classification of protein binding cavities”, in Proceedings of the 2014 workshop on Mobile augmented reality and robotic technology-based systems, 2014, pp. 47–50.
B. Y. Chen, “VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials”, PLoS Comp Biol, p. e1003792, 2014.
Z. Guo and Chen, B. Y., “Predicting Small Molecule Substrate Specificity for Protein Function Annotation”, in Handbook of Computational Molecular Biology, M. Singh and Aluru, S. in review: CRC Press, 2014.
R. Chen, Guo, Z., Chen, B. Y., and Scheinberg, K., “Methodologies and Software for Derivative-free Optimization”, in Optimization Methods in Engineering, in review: Society for Industrial and Applied Mathematics, 2014.

2013

B. G. Godshall, Tang, Y., Yang, W., and Chen, B. Y., “An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility”, BMC struct biol, vol. 13, p. S10, 2013.
S. Blumenthal, Tang, Y., Yang, W., and Chen, B. Y., “Isolating Influential Regions of Electrostatic Focusing in Protein and DNA Structure”, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 10, pp. 1188–1198, 2013.

2012

R. Chen, Scheinberg, K., and Chen, B. Y., “Aligning ligand binding cavities by optimizing superposed volume”, Proceedings (IEEE Int Conf Bioinformatics Biomed), pp. 1–5, 2012.
B. Y. Chen and Paul, D., “A volumetric method for representing and comparing regions of electrostatic focusing in molecular structure”, in Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2012, pp. 242–249.
B. G. Godshall and Chen, B. Y., “Improving accuracy in binding site comparison with homology modeling”, Proceedings (IEEE Int Conf Bioinformatics Biomed), pp. 662–669, 2012.
B. Y. Chen and Bandyopadhyay, S., “Modeling regionalized volumetric differences in protein-ligand binding cavities”, Proteome Sci, vol. 10, p. S6, 2012.
B. Y. Chen and Bandyopadhyay, S., “A Regionalizable Statistical Model Of Intersecting Regions In Protein-Ligand Binding Cavities”, J Bioinform Comput Biol, vol. 10, 2012.

2011

M. Fischer, Zhang, Q., Dey, F., Chen, B. Y., Honig, B., and Petrey, D., “MarkUs: a server to navigate sequence-structure-function space.”, Nucleic Acids Res, pp. 1–5, 2011.
B. Y. Chen and Bandyopadhyay, S., “VASP-S: A Volumetric Analysis and Statistical Model for Predicting Steric Influences on Protein-Ligand Binding Specificity”, Proceedings (IEEE Int Conf Bioinformatics Biomed), pp. 22-9, 2011.
B. Y. Chen and Bandyopadhyay, S., “A Statistical Model of Overlapping Volume in Ligand Binding Cavities”, in Proceedings of the Computational Structural Bioinformatics Workshop (CSBW 2011), 2011, pp. 424-31.

2010

D. C. Andersson, Chen, B. Y., and Linusson, A., “Mapping of ligand-binding cavities in proteins.”, Proteins: Structure, Function and Bioinformatics, vol. 78, pp. 1408–22, 2010.
D. C. Andersson, Chen, B. Y., and Linusson, A., “Multivariate assessment of virtual screening experiments”, Journal of Chemometrics, vol. 24, pp. 757–767, 2010.
D. H. Bryant, Moll, M., Chen, B. Y., Fofanov, V. Y., and Kavraki, L. E., “Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction”, BMC Bioinformatics, vol. 11, 2010.
B. Y. Chen and Honig, B., “VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity”, PLoS Comput Biol, vol. 6, p. 11, 2010.

2008

D. M. Kristensen, Ward, R. M., Lisewski, A. M., Erdin, S., Chen, B. Y., Fofanov, V. Y., Kimmel, M., Kavraki, L. E., and Lichtarge, O., “Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.”, BMC Bioinformatics, vol. 9, p. 17, 2008.
V. Y. Fofanov, Chen, B. Y., Bryant, D. H., Moll, M., Lichtarge, O., Kavraki, L. E., and Kimmel, M., “A statistical model to correct systematic bias introduced by algorithmic thresholds in protein structural comparison algorithms”, 2008 IEEE International Conference on Bioinformatics and Biomeidcine Workshops, pp. 1–8, 2008.

2007

B. Y. Chen, Fofanov, V. Y., Bryant, D. H., Dodson, B. D., Kristensen, D. M., Lisewski, A. M., Kimmel, M., Lichtarge, O., and Kavraki, L. E., “The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs.”, J Comp Biol, vol. 14, pp. 791–816, 2007.
B. Y. Chen, Bryant, D. H., Fofanov, V. Y., Kristensen, D. M., Cruess, A. E., Kimmel, M., Lichtarge, O., and Kavraki, L. E., “Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction.”, J Bioinform Comput Biol, vol. 5, pp. 353–82, 2007.
B. Y. Chen, Bryant, D. H., Cruess, A. E., Bylund, J. H., Fofanov, V. Y., Kristensen, D. M., Kimmel, M., Lichtarge, O., and Kavraki, L. E., “Composite motifs integrating multiple protein structures increase sensitivity for function prediction.”, in Computational Systems Bioinformatics Conference (CSB2007), 2007, vol. 6, pp. 343–55.

2006

B. Y. Chen, Bryant, D. H., Fofanov, V. Y., Kristensen, D. M., Cruess, A. E., Kimmel, M., Lichtarge, O., and Kavraki, L. E., “Cavity-aware motifs reduce false positives in protein function prediction.”, in Proceedings of the 2006 IEEE Computational Systems Bioinformatics Conference (CSB 2006), 2006, pp. 311–23.
B. Y. Chen, Fofanov, V. Y., Bryant, D. H., Dodson, B. D., Kristensen, D. M., Lisewski, A. M., Kimmel, M., Lichtarge, O., and Kavraki, L. E., “Geometric Sieving : Automated Distributed Optimization of 3D Motifs for Protein Function Prediction”, in Proceedings of The Tenth Annual International Conference on Computational Molecular Biology (RECOMB 2006), 2006, pp. 500–515.
D. M. Kristensen, Chen, B. Y., Fofanov, V., Ward, R. M., Lisewski, A. M., Kimmel, M., Kavraki, L. E., and Lichtarge, O., “Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity”, Protein Sci, vol. 15, pp. 1530–1536, 2006.

2005

E. Plaku, Bekris, K. E., Chen, B. Y., Ladd, A. M., and Kavraki, L. E., “Sampling-based roadmap of trees for parallel motion planning”, IEEE Transactions on Robotics, vol. 21, pp. 597–608, 2005.
B. Y. Chen, Fofanov, V. Y., Kristensen, D. M., Kimmel, M., Lichtarge, O., and Kavraki, L. E., “Algorithms for structural comparison and statistical analysis of 3D protein motifs.”, in Pacific Symposium on Biocomputing., 2005, vol. 345, pp. 334–45.

2003

M. Akinc, Bekris, K. E., Chen, B. Y., Ladd, A. M., Plaku, E., and Kavraki, L. E., “Probabilistic Roadmap of Trees for Parallel Computation of Multiple Query Roadmaps”, in Eleventh International Symposium of Robotics Research (ISRR), 2003, pp. 80–89.
K. E. Bekris, Chen, B. Y., Ladd, A. M., Plaku, E., and Kavraki, L. E., “Multiple query probabilistic roadmap planning using single query planning primitives”, in Proceedings 2003 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2003), 2003, vol. 01, pp. 656–661.