Mark B. Gerstein

27 papers Journal 26Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems.
CoRR
Yunyang Li, Zaishuo Xia, Lin Huang, Xinran Wei, Han Yang, Sam Harshe, Zun Wang, Chang Liu, Jia Zhang, Bin Shao, Mark B. Gerstein
2024 J jnl
BioCoder: a benchmark for bioinformatics code generation with large language models.
Bioinform.
Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark B. Gerstein
2024 J jnl
Improved Prediction of Ligand-Protein Binding Affinities by Meta-modeling.
J. Chem. Inf. Model.
Ho-Joon Lee, Prashant S. Emani, Mark B. Gerstein
2023 J jnl
Improved prediction of ligand-protein binding affinities by meta-modeling.
CoRR
Ho-Joon Lee, Prashant S. Emani, Mark B. Gerstein
2023 J jnl
Insights from incorporating quantum computing into drug design workflows.
Bioinform.
Bayo Lau, Prashant S. Emani, Jackson Chapman, Lijing Yao, Tarsus Lam, Paul Merrill, Jonathan Warrell, Mark B. Gerstein, Hugo Y. K. Lam
2020 J jnl
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks.
PLoS Comput. Biol.
Bian Li, Yucheng T. Yang, John A. Capra, Mark B. Gerstein
2019 J jnl
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.
PLoS Comput. Biol.
Fabio C. P. Navarro, Jacob Hoops, Lauren Bellfy, Eliza Cerveira, Qihui Zhu, Chengsheng Zhang, Charles Lee, Mark B. Gerstein
2017 J jnl
Landscape and variation of novel retroduplications in 26 human populations.
PLoS Comput. Biol.
Yan Zhang, Shantao Li, Alexej Abyzov, Mark B. Gerstein
2016 J jnl
Extending gene ontology in the context of extracellular RNA and vesicle communication.
J. Biomed. Semant.
Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E. Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B. Gerstein, Andrew F. Hill, Robert R. Kitchen, Jan Lötvall, Tushar Patel
2015 J jnl
Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors.
PLoS Comput. Biol.
Daifeng Wang, Koon-Kiu Yan, Cristina Sisu, Chao Cheng, Joel S. Rozowsky, William Meyerson, Mark B. Gerstein
2015 J jnl
MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.
Bioinform.
Marghoob Mohiyuddin, John C. Mu, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y. K. Lam
2015 J jnl
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.
Bioinform.
John C. Mu, Marghoob Mohiyuddin, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y. K. Lam
2011 J jnl
Measuring the Evolutionary Rewiring of Biological Networks.
PLoS Comput. Biol.
Chong Shou, Nitin Bhardwaj, Hugo Y. K. Lam, Koon-Kiu Yan, Philip M. Kim, Michael Snyder, Mark B. Gerstein
2011 J jnl
Predicting protein ligand binding motions with the Conformation Explorer.
BMC Bioinform.
Samuel Flores, Mark B. Gerstein
2010 J jnl
Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets.
PLoS Comput. Biol.
Nitin Bhardwaj, Matthew B. Carson, Alexej Abyzov, Koon-Kiu Yan, Hui Lu, Mark B. Gerstein
2010 J jnl
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model.
BMC Bioinform.
Zhengdong D. Zhang, Mark B. Gerstein
2010 J jnl
Getting Started in Gene Orthology and Functional Analysis.
PLoS Comput. Biol.
Gang Fang, Nitin Bhardwaj, Rebecca Robilotto, Mark B. Gerstein
2010 — conf
Human Genome Annotation.
ISBRA
Mark B. Gerstein
2010 J jnl
MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains.
BMC Bioinform.
Hugo Y. K. Lam, Philip M. Kim, Janine Mok, Raffi Tonikian, Sachdev S. Sidhu, Benjamin E. Turk, Michael Snyder, Mark B. Gerstein
2010 J jnl
Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis.
PLoS Comput. Biol.
Younghee Lee, Xinan Yang, Yong Huang, Hanli Fan, Qingbei Zhang, Youngfei Wu, Jianrong Li, Rifat Hasina, Chao Cheng, Mark W. Lingen, Mark B. Gerstein, Ralph R. Weichselbaum, H. Rosie Xing, Yves A. Lussier
2009 J jnl
Getting Started in Text Mining: Part Two.
PLoS Comput. Biol.
Andrey Rzhetsky, Michael R. Seringhaus, Mark B. Gerstein
2009 J jnl
Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate.
PLoS Comput. Biol.
Yu Xia, Eric A. Franzosa, Mark B. Gerstein
2009 J jnl
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants.
PLoS Comput. Biol.
Jiang Du, Robert D. Bjornson, Zhengdong D. Zhang, Yong Kong, Michael Snyder, Mark B. Gerstein
2009 J jnl
Pseudofam: the pseudogene families database.
Nucleic Acids Res.
Hugo Y. K. Lam, Ekta Khurana, Gang Fang, Philip Cayting, Nicholas Carriero, Kei-Hoi Cheung, Mark B. Gerstein
2009 J jnl
Small RNAs Originated from Pseudogenes:
PLoS Comput. Biol.
Xingyi Guo, Zhaolei Zhang, Mark B. Gerstein, Deyou Zheng
2007 J jnl
An efficient pseudomedian filter for tiling microrrays.
BMC Bioinform.
Thomas E. Royce, Nicholas Carriero, Mark B. Gerstein
2007 J jnl
Publishing perishing? Towards tomorrow's information architecture.
BMC Bioinform.
Michael R. Seringhaus, Mark B. Gerstein