CASTp: Computed Atlas of Surface Topography of proteins. - T. Andrew Binkowski; Shapor Naghibzadeh; Jie Liang 002 (Nucleic Acids Res., 2003)

Developing optimal non-linear scoring function for protein design. - Changyu Hu II; Xiang Li; Jie Liang 002 (Bioinform., 2004)

pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins. - T. Andrew Binkowski; Patrick Freeman; Jie Liang 002 (Nucleic Acids Res., 2004)

topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. - Nathan O. Stitziel; T. Andrew Binkowski; Yan Yuan Tseng; Simon Kasif; Jie Liang 002 (Nucleic Acids Res., 2004)

Automated method for predicting enzyme functional surfaces and locating key residues with accuracy and specificity. - Yan Yuan Tseng; Jie Liang 002 (EMBC, 2006)

CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. - Joe Dundas; Zheng Ouyang; Jeffery Tseng; T. Andrew Binkowski; Yaron Turpaz; Jie Liang 002 (Nucleic Acids Res., 2006)

Foreword. - Piotr Berman; Bhaskar DasGupta; Jie Liang 002 (Algorithmica, 2007)

Topology independent protein structural alignment. - Joe Dundas; T. Andrew Binkowski; Bhaskar DasGupta; Jie Liang 002 (BMC Bioinform., 2007)

Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability. - Youfang Cao; Jie Liang 002 (BMC Syst. Biol., 2008)

Novel Approach to Structure-Based Pharmacophore Search Using Computational Geometry and Shape Matching Techniques. - Jerry Osagie Ebalunode; Zheng Ouyang; Jie Liang 002; Weifan Zheng (J. Chem. Inf. Model., 2008)

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity. - Jie Liang 002; Hong Qian (J. Comput. Sci. Technol., 2009)

Mechanical forces mediate localized topological change in epithelia. - Yingzi Li; Hammad Naveed; Sema Kachalo; Lisa X. Xu; Jie Liang 002 (EMBC, 2011)

GPU-accelerated Chemical Similarity Assessment for Large Scale Databases. - Marco Maggioni; Marco D. Santambrogio; Jie Liang 002 (ICCS, 2011)

Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesis. - Youfang Cao; Hammad Naveed; Claire Liang; Jie Liang 002 (EMBC, 2013)

Dynamic mechanical finite element model of biological cells for studying cellular pattern formation. - Jieling Zhao; Hammad Naveed; Sema Kachalo; Youfang Cao; Wei Tian 003; Jie Liang 002 (EMBC, 2013)

GPU-Based Steady-State Solution of the Chemical Master Equation. - Marco Maggioni; Tanya Y. Berger-Wolf; Jie Liang 002 (IPDPS Workshops, 2013)

Grand Challenges in Interfacing Engineering With Life Sciences and Medicine. - Bin He 002; Richard Baird; Robert J. Butera; Aniruddha Datta; Steven George; Bruce Hecht; Alfred O. Hero III; Gianluca Lazzi; Raphael C. Lee; Jie Liang 002; Michael R. Neuman; Grace C. Y. Peng; et al. (IEEE Trans. Biomed. Eng., 2013)

Computational predictions of structures of multichromosomes of budding yeast. - Gamze Gürsoy; Yun Xu; Jie Liang 002 (EMBC, 2014)

Effects of mechanical properties on tumor invasion: Insights from a cellular model. - Yingzi Li; Hammad Naveed; Jie Liang 002; Lisa X. Xu (EMBC, 2014)

Exact computation of probability landscape of stochastic networks of Single Input and Coupled Toggle Switch Modules. - Anna Terebus; Youfang Cao; Jie Liang 002 (EMBC, 2014)

Roles of regulated internalization in the polarization of cell surface receptors. - Wei Tian 003; Youfang Cao; Amber Ismael; David Stone; Jie Liang 002 (EMBC, 2014)

Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method. - Ke Tang; Jinfeng Zhang; Jie Liang 002 (PLoS Comput. Biol., 2014)

Guest Editorial EMBC 2014. - Walter G. Besio; Leslie Ying; Jie Liang 002; Nigel H. Lovell; Carmen C. Y. Poon; May D. Wang (IEEE J. Biomed. Health Informatics, 2015)

Mechanisms of stochastic focusing and defocusing in biological reaction networks: Insight from accurate Chemical Master Equation (ACME) solutions. - Gamze Giirsoy; Anna Terebus; Youfang Cao; Jie Liang 002 (EMBC, 2016)

Accurate Chemical Master Equation Solution Using Multi-Finite Buffers. - Youfang Cao; Anna Terebus; Jie Liang 002 (Multiscale Model. Simul., 2016)

Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins. - Wei Tian 003; Meishan Lin; Hammad Naveed; Jie Liang 002 (Bioinform., 2017)

PRODIGEN: visualizing the probability landscape of stochastic gene regulatory networks in state and time space. - Chihua Ma; Timothy Luciani; Anna Terebus; Jie Liang 002; G. Elisabeta Marai (BMC Bioinform., 2017)

Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model. - Gamze Gürsoy; Yun Xu; Jie Liang 002 (PLoS Comput. Biol., 2017)

Guest Editorial IEEE BHI 2016. - Stephen Redmond; Jie Liang 002; Constantinos S. Pattichis (IEEE J. Biomed. Health Informatics, 2017)

On quantification of geometry and topology of protein pockets and channels for assessing mutation effects. - Wei Tian 003; Jie Liang 002 (BHI, 2018)

A general method for predicting amino acid residues experiencing hydrogen exchange. - Boshen Wang; Alan Perez-Rathke; Renhao Li; Jie Liang 002 (BHI, 2018)

CASTp 3.0: computed atlas of surface topography of proteins. - Wei Tian 003; Chang Chen; Xue Lei; Jieling Zhao; Jie Liang 002 (Nucleic Acids Res., 2018)

Guest Editorial IEEE BHI 2017. - Jie Liang 002; Michalis E. Zervakis; Julien Penders (IEEE J. Biomed. Health Informatics, 2018)

Predicting Oncogenic Missense Mutations. - Xue Lei; Boshen Wang; Alan Perez-Rathke; Wei Tian 003; Chia-Yi Chou; Yan-Yuan Tseng; Jie Liang 002 (BHI, 2019)

Alterations in Chromatin Folding Patterns in Cancer Variant-Enriched Loci. - Alan Perez-Rathke; Samira Mali; Lin Du; Jie Liang 002 (BHI, 2019)

Structure-based Method for Predicting Deleterious Missense SNPs. - Boshen Wang; Wei Tian 003; Xue Lei; Alan Perez-Rathke; Yan Yuan Tseng; Jie Liang 002 (BHI, 2019)

Sensitivities of Regulation Intensities in Feed-Forward Loops with Multistability. - Anna Terebus; Youfang Cao; Jie Liang 002 (EMBC, 2019)

Evolution of coagulation-fragmentation stochastic processes using accurate chemical master equation approach. - Farid Manuchehrfar; Wei Tian 003; Tom Chou; Jie Liang 002 (Commun. Inf. Syst., 2019)

Guest Editorial on the Special Issue on Integrating Informatics and Technology for Precision Medicine. - Constantinos S. Pattichis; Constantinos Pitris; Jie Liang 002; Yuan-Ting Zhang (IEEE J. Biomed. Health Informatics, 2019)

Inferring initial state of the ancestral network of cellular fate decision: a case study of phage lambda. - Yiyu Pang; Jie Liang 002 (EMBC, 2021)

Modeling and simulation of nuclear architecture reorganization process using a phase field approach. - Qing Cheng 003; Pourya Delafrouz; Jie Liang 002; Chun Liu 009; Jie Shen 001 (CoRR, 2021)

Modeling and simulation of cell nuclear architecture reorganization process. - Qing Cheng 003; Pourya Delafrouz; Jie Liang 002; Chun Liu 009; Jie Shen 001 (J. Comput. Phys., 2022)

Predicting Pathology of Missense Mutations through Protein-Specific Evolutionary Pattern. - Bowei Ye; Boshen Wang; Jie Liang 002 (EMBC, 2023)

Structure-based pathogenicity relationship identifier for predicting effects of single missense variants and discovery of higher-order cancer susceptibility clusters of mutations. - Boshen Wang; Xue Lei; Wei Tian 003; Alan Perez-Rathke; Yan-Yuan Tseng; Jie Liang 002 (Briefings Bioinform., 2023)

Predicting Functional Surface Topographies Combining Topological Data Analysis and Deep Learning Across the Human Protein Universe. - Bowei Ye; Jie Liang 002 (EMBC, 2024)

ALPHAGMUT: A Rationale-Guided Alpha Shape Graph Neural Network to Evaluate Mutation Effects. - Boshen Wang; Bowei Ye; Lin Xu; Jie Liang 002 (CoRR, 2024)