Book Chapters


Explaining Small Molecule Binding Specificity with Volumetric Representations of Protein Binding Sites
Ziyi Guo and Brian Y. Chen. In Algorithms and Methods in Structural Bioinformatics, Nurit Haspel, Filip Jagodzinski and Kevin Malloy, Editors. Springer Nature 2022. ISBN: 978-3-031-05913-1. https://doi.org/10.1007/978-3-031-05914-8
Chapter 39: Volumetric Alignment of Protein-Binding Cavities
Ruobing Chen, Brian Y. Chen and Katya Scheinberg. In Advances and Trends in Optimization with Engineering Applications , Society for Industrial and Applied Mathematics (SIAM), 2017. ISBN: 978-1-61197-467-6.


Refereed Journal Publications


Evolving information complexity of coarsening materials microstructures
Jeffrey M. Rickman, Katayun Barmak, Brian Y. Chen and Matthew Patrick Scientific Reports 13, num 22390 (2023). doi.org/10.1038/s41598-023-49759-x
HBcompare: Classifying Ligand Binding Preferences with Hydrogen Bond Topology
Justin Z Tam, Zhaoming Kong, Omar Ahmed, Lifang He, and Brian Y. Chen MDPI Biomolecules 12(11), 1589 (2022). doi.org/10.3390/biom12111589
Analysis of Protein-Protein Interactions for Intermolecular Bond Prediction
Justin Z Tam, Talulla Palumbo, Julie M Miwa, and Brian Y. Chen MDPI Molecules 27, 6178 (2022). doi.org/10.3390/molecules27196178
Sex and Location Differences in Verification Status of Physician-Held Social Media Platform Accounts
Deborah Rupert, Kanan Shah, Brian Y. Chen, Avital Y. O'Glasser, Michael Schiml, Shikha Jain and Fumiko Chino JAMA Network Open 5(8):e2225671. (2022)
doi:10.1001/jamanetworkopen.2022.25671
Precise Parallel Volumetric Comparison of Molecular Surfaces and Electrostatic Isopotentials
Georgi D. Georgiev, Kevin F. Dodd and Brian Y. Chen, Algorithms for Molecular Biology 15, 11 (2020). https://doi.org/10.1186/s13015-020-00168-z
Exploring Protein Cavities through Rigidity Analysis
Stephanie Mason, Brian Y. Chen and Filip Jagodzinski, Molecules, 23(2), 351, 2018. doi:10.3390/molecules23020351
Ricin uses arginine 235 as an anchor residue to bind to P-proteins of the ribosomal stalk
Yijun Zhou, Xiao-Ping Li, Brian Y. Chen and Nilgun E. Tumer, Nature Scientific Reports 7:42912, 2017. doi:10.1038/srep42912
Influential Mutations in the SMAD4 Trimer Complex Can Be Detected from Disruptions of Electrostatic Complementarity
Bridget E. Nolan, Emily Levenson and Brian Y. Chen, Journal of Computational Biology, January 2017, 24(1): 68-78. doi:10.1089/cmb.2016.0162.
Conformational Sampling Reveals Amino Acids with a Steric Influence on Specificity
Ziyi Guo and Brian Y. Chen, Journal of Computational Biology 22(9), pp 861-875, 2015.
VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials
Brian Y. Chen, PLoS Computational Biology, 10(8): e1003792. doi:10.1371/ journal. pcbi. 1003792, 2014.
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.
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


Attentive Deep Canonical Correlation Analysis for Diagnosing Alzheimer's Disease Using Multimodal Imaging Genetics
Rong Zhou, Houliang Zhou, Brian Y. Chen, Li Shen, Yu Zhang and Lifang He In the 26th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI 2023). Vancouver, Canada, October 2023.
Integrating Multimodal Contrastive Learning and Cross-Modal Attention for Alzheimer's Disease Prediction in Brain Imaging Genetics
Rong Zhou, Houliang Zhou, Li Shen, Brian Y. Chen, Yu Zhang, and Lifang He In the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2023). Instanbul, Turkey, Dec 2023.
Interpretable Graph Convolutional Network for Alzheimer's Disease Diagnosis using Multi-Modal Imaging Genetics
Houliang Zhou, Yu Zhang, Lifang He, Li Shen, Brian Y. Chen In the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2023). Instanbul, Turkey, Dec 2023.
A Containerization Framework for Bioinformatics Software to Advance Scalability, Portability, and Maintainability
Justin Tam, Alexandra Chua, Adyn Gallagher, Denice Omene, Danielle Okun, Dominic DiFranzo and Brian Y. Chen In Computational Structural Bioinformatics Workshop 2023 (CSBW 2023). Houston, TX, Sept 2023. Best paper Finalist.
Immediate effects of posture correction girdle on adolescents with early scoliosis
Pak Yiu Liu, Joanne Yip, Brian Y. Chen, Lifang He, Jason Cheung, Kit Lun Yick, Sun Pui Ng, Hong Kong In 13th International Conference on Applied Human Factors and Ergonomics (AHFE 2022). New York City, NY, July 2022. AHFE 2022 Best paper award.
Sparse interpretation of graph convolutional networks for multi-modal diagnosis of Alzheimer's disease
Houliang Zhou, Yu Zhang, Brian Y. Chen, Shen Li, Lifang He In the 25th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2022). Singapore, Sept 2022.

Interpretable Graph Convolutional Network of Multi-Modality Brain Imaging for Alzheimer's Disease Diagnosis
Houliang Zhou, Lifang He, Yu Zhang, Li Shen, and Brian Y. Chen Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI 2022). Kolkata, India, March 2022.

DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity
Felix M. Quintana, Zhaoming Kong, Lifang He, and Brian Y. Chen Proceedings of The Pacific Symposium on Biocomputing (PSB 2022), World Scientific. Big Island, HI, January 2022.

DiffBond: A Method for Predicting Intermolecular Bond Formation
Justin Tam, Talulla Palumbo, Julie M. Miwa, and Brian Y. Chen Proceedings of the CSBW (Computational Structural Biology Workshop) at BIBM 2021: IEEE International Conference on Bioinformatics and Biomedicine . Dec. 2021.
A Conical Representation of Hydrogen Bond Geometry for Quantifying Bond Interactions
Chesphongphach Buranasilp and Brian Y. Chen Proceedings of the CSBW (Computational Structural Biology Workshop) at BIBM 2021: IEEE International Conference on Bioinformatics and Biomedicine. Dec. 2021. Best paper award, CSBW 2021.
pClay: A Precise Parallel Algorithm for Comparing Molecular Surfaces.
Georgi D. Georgiev, Kevin F. Dodd, and Brian Y. Chen 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) 2019. Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik.. Sept. 2019.
On Conformations of peptides bound to class I Major Histocompatibility Complexes.
Jinbu Wang and Brian Y. Chen Proceedings of the CSBW (Computational Structural Biology Workshop) at ACM-BCB'19: ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Sept. 2019.
A Volumetric Survey of Cavities and Electrostatic Patterns in Protein-RNA Binding Sites.
Devan Bicher and Brian Y. Chen Proceedings of the CSBW (Computational Structural Biology Workshop) at ACM-BCB'19: ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Sept. 2019.
MAPS: Analyzing Peptide Binding Subsites in Major Histocompatibility Complexes
Jinbu Wang and Brian Y. Chen Proceedings of the CSBW (Computational Structural Biology Workshop) at ACM-BCB'18: ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics.
Investigating Rigidity Properties of Protein Cavities
Stephanie Mason, Tim Woods, Brian Y. Chen, and Filip Jagodzinski Proceedings of the CSBW (Computational Structural Biology Workshop) at ACM-BCB'17: ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics.
A Map of Binding Cavity Conformations Reveals Differences in Binding Specificity
Ziyi Guo and Brian Y. Chen Proceedings of the IEEE 2016 International Conference on Bioinformatics and Biomedicine (BIBM), pp 1246-52. Shenzhen, December 2016.
A Statistical Model of Electrostatic Isopotential Variation in Serine Protease Binding Cavities
Rachel Y. Okun and Brian Y. Chen Proceedings of the Computational Structural Bioinformatics Workshop (CSBW), pp 1246-52. Washington, DC, November 2015.
Predicting Protein-Ligand Binding Specificity Based on Ensemble Clustering
Ziyi Guo and Brian Y. Chen Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp 1239-44. Washington, DC, November 2015.
Superposition of Protein Structures Using Electrostatic Isopotentials
Ziyi Guo, Juliana Hong, Katya Scheinberg and Brian Y. Chen Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015), pp 75-82. Washington, DC, November 2015..
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). 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.
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 5th ACM Conference on Bioinformatics, Computational Biology and Biomedicine (BCB 2014), pp 445-454. Newport Beach, CA, September, 2014.
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), pp 662-669. Philadelphia, PA, Oct 2012.
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.
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.


Non-refereed Conference Abstracts

(Computational Materials Science)


Development of an Automated Reciprocal-Space Navigator in a JEOL FEMTUS Platform
Surui Huang, Brian Y. Chen, Aparna Bharati, Martin P. Harmer, M Watanabe Microscopy and Microanalysis 29 (Supplement 1), 728-729, 2023. doi.org/10.1093/micmic/ozad067.359
Examination of Discontinuous Changes in Grain Boundary Velocity Induced by Grain Boundary Transformations
Christopher J. Marvel, Caroline Riedel, Houliang Zhou, Benjamin Zalatan, Brian Y. Chen, and Martin P. Harmer, Proceedings of the 47th International Conference and Expo on Advanced Ceramics and Composites (ICACC2023)
Push-Button Microscopy: Automated Instrument Alignment and Reciprocal-space Navigation using Pygem
Surui Huang, Jack Kellerk, Brian Y. Chen, Aparna Bharati, Masashi Watanabe, Patrick Cantwell, Chris Marvel and Martin Harmer, Microscopy and Microanalysis 28, S1 (2022). doi:10.1017/S1431927622011771


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

Algorithms for discovering mutations that alter binding specificity
Invited to: American Chemical Society, National Meeting, August 20-24 2017, Washington, DC.
Computational detection of steric and electrostatic influences on protein binding specificity
Invited to: American Chemical Society, Northeast Regional Meeting, October 5-8, 2016, Binghamton, NY.
A System for the Volumetric Analysis of Protein Structure
Invited to: Department of Computer Science, Rutgers University, Piscataway, NJ, Spring 2014.
Volumetric and Electrostatic Dissection of Protein-Ligand and Protein-Protein Interactions
Invited to: Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, Spring 2014.
Automatically Detecting Influences on Protein Binding Specificity
Invited to: Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, November 26, 2012.
Deconstructing the Molecular World
Invited to: Genomic Informatics Center, Hankyong National University, Korea, May 15, 2012.
Geometric and Statistical Techniques for Predicting Structural Influences on Protein-Ligand Binding Specificity
Invited to: Departmental Colloquium, Dept. of Computer Science, Texas A&M, College Station, TX, March 5, 2012.
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.