Multiple query probabilistic roadmap planning using single query planning primitives. - Kostas E. Bekris; Brian Y. Chen; Andrew M. Ladd; Erion Plaku; Lydia E. Kavraki (IROS, 2003)

Probabilistic Roadmaps of Trees for Parallel Computation of Multiple Query Roadmaps. - Mert Akinc; Kostas E. Bekris; Brian Y. Chen; Andrew M. Ladd; Erion Plaku; Lydia E. Kavraki (ISRR, 2003)

Algorithms for Structural Comparison and Statistical Analysis of 3D Protein Motifs. - Brian Y. Chen; Viacheslav Fofanov; David M. Kristensen; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (Pacific Symposium on Biocomputing, 2005)

Sampling-Based Roadmap of Trees for Parallel Motion Planning. - Erion Plaku; Kostas E. Bekris; Brian Y. Chen; Andrew M. Ladd; Lydia E. Kavraki (IEEE Trans. Robotics, 2005)

Geometric Sieving: Automated Distributed Optimization of 3D Motifs for Protein Function Prediction. - Brian Y. Chen; Viacheslav Fofanov; Drew H. Bryant; Bradley D. Dodson; David M. Kristensen; Andreas Martin Lisewski; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (RECOMB, 2006)

Cavity Scaling: Automated Refinement of Cavity-Aware motifs in protein Function Prediction. - Brian Y. Chen; Drew H. Bryant; Viacheslav Fofanov; David M. Kristensen; Amanda E. Cruess; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (J. Bioinform. Comput. Biol., 2007)

The MASH Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of 3D Motifs. - Brian Y. Chen; Viacheslav Fofanov; Drew H. Bryant; Bradley D. Dodson; David M. Kristensen; Andreas Martin Lisewski; Marek Kimmel; Olivier Lichtarge; Lydia E. Kavraki (J. Comput. Biol., 2007)

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. - David M. Kristensen; R. Matthew Ward; Andreas Martin Lisewski; Serkan Erdin; Brian Y. Chen; Viacheslav Fofanov; Marek Kimmel; Lydia E. Kavraki; Olivier Lichtarge (BMC Bioinform., 2008)

Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction. - Drew H. Bryant; Mark Moll; Brian Y. Chen; Viacheslav Fofanov; Lydia E. Kavraki (BMC Bioinform., 2010)

VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity. - Brian Y. Chen; Barry Honig (PLoS Comput. Biol., 2010)

MarkUs: a server to navigate sequence-structure-function space. - Markus Fischer; Qiangfeng Cliff Zhang; Fabian Dey; Brian Y. Chen; Barry Honig; Donald Petrey (Nucleic Acids Res., 2011)

A volumetric method for representing and comparing regions of electrostatic focusing in molecular structure. - Brian Y. Chen; Debdas Paul (BCB, 2012)

Improving accuracy in binding site comparison with homology modeling. - Brian G. Godshall; Brian Y. Chen (BIBM Workshops, 2012)

VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials. - Brian Y. Chen (PLoS Comput. Biol., 2014)

Investigating Rigidity Properties of Protein Cavities. - Stephanie Mason; Tim Woods; Brian Y. Chen; Filip Jagodzinski (BCB, 2017)

Influential Mutations in the SMAD4 Trimer Complex Can Be Detected from Disruptions of Electrostatic Complementarity. - Bridget E. Nolan; Emily Levenson; Brian Y. Chen (J. Comput. Biol., 2017)

ACM-BCB 2018 Computational Structural Bioinformatics Workshop (CSBW) Chairs' Welcome. - Filip Jagodzinski; Brian Y. Chen; Kevin Molloy (BCB, 2018)

MAPS: Analyzing Peptide Binding Subsites in Major Histocompatibility Complexes. - Jinbu Wang; Brian Y. Chen (BCB, 2018)

A Volumetric Survey of Cavities and Electrostatic Patterns in Protein-RNA Binding Sites. - Devan Bicher; Brian Y. Chen (BCB, 2019)

On Conformations of Peptides Bound to Class I Major Histocompatibility Complexes. - Jinbu Wang; Brian Y. Chen (BCB, 2019)

pClay: A Precise Parallel Algorithm for Comparing Molecular Surfaces. - Georgi D. Georgiev; Kevin F. Dodd; Brian Y. Chen (WABI, 2019)

Precise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials. - Georgi D. Georgiev; Kevin F. Dodd; Brian Y. Chen (Algorithms Mol. Biol., 2020)

A Conical Representation of Hydrogen Bond Geometry for Quantifying Bond Interactions. - Chesphongphach Buranasilp; Brian Y. Chen (BIBM, 2021)

DiffBond: A Method for Predicting Intermolecular Bond Formation. - Justin Z. Tam; Talulla Palumbo; Julie M. Miwa; Brian Y. Chen (BIBM, 2021)

Sparse Interpretation of Graph Convolutional Networks for Multi-modal Diagnosis of Alzheimer's Disease. - Houliang Zhou; Yu Zhang 009; Brian Y. Chen; Li Shen 001; Lifang He 001 (MICCAI (8), 2022)

ColocQuiaL: a QTL-GWAS colocalization pipeline. - Brian Y. Chen; William Bone; Kim Lorenz; Michael Levin 002; Marylyn D. Ritchie; Benjamin F. Voight (Bioinform., 2022)

A Containerization Framework for Bioinformatics Software to Advance Scalability, Portability, and Maintainability. - Justin Z. Tam; Alexandra Chua; Adyn Gallagher; Denice Omene; Danielle Okun; Dominic DiFranzo; Brian Y. Chen (BCB, 2023)

Interpretable Graph Convolutional Network for Alzheimer's Disease Diagnosis using Multi-Modal Imaging Genetics. - Houliang Zhou; Yu Zhang 009; Lifang He 001; Li Shen 001; Brian Y. Chen (BIBM, 2023)

Integrating Multimodal Contrastive Learning and Cross-Modal Attention for Alzheimer's Disease Prediction in Brain Imaging Genetics. - Rong Zhou; Houliang Zhou; Li Shen 001; Brian Y. Chen; Yu Zhang 009; Lifang He 001 (BIBM, 2023)

Attentive Deep Canonical Correlation Analysis for Diagnosing Alzheimer's Disease Using Multimodal Imaging Genetics. - Rong Zhou; Houliang Zhou; Brian Y. Chen; Li Shen 001; Yu Zhang 009; Lifang He 001 (MICCAI (2), 2023)

Personalized Video Summarization by Multimodal Video Understanding. - Brian Y. Chen; Xiangyuan Zhao; Yingnan Zhu (CIKM, 2024)

Multi-Modal Diagnosis of Alzheimer's Disease Using Interpretable Graph Convolutional Networks. - Houliang Zhou; Lifang He 001; Brian Y. Chen; Li Shen 001; Yu Zhang 009 (IEEE Trans. Medical Imaging, 2025)