Publications

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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. 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.
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.
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.

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.

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.

2008

2007

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.

2005

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.
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