Mark B. Gerstein

Publication Activity (10 Years)

Years Active: 2007-2023
Publications (10 Years): 9

Top Topics

Protein Protein Interactions

Convolutional Neural Networks

Top Venues

PLoS Comput. Biol.

J. Biomed. Semant.

Publications

Bayo Lau, Prashant S. Emani, Jackson Chapman, Lijing Yao, Tarsus Lam, Paul Merrill, Jonathan Warrell, Mark B. Gerstein, Hugo Y. K. Lam
Insights from incorporating quantum computing into drug design workflows. Bioinform. 39 (1) (2023)
Ho-Joon Lee, Prashant S. Emani, Mark B. Gerstein
Improved prediction of ligand-protein binding affinities by meta-modeling. CoRR (2023)
Bian Li, Yucheng T. Yang, John A. Capra, Mark B. Gerstein
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. PLoS Comput. Biol. 16 (11) (2020)
Fabio C. P. Navarro, Jacob Hoops, Lauren Bellfy, Eliza Cerveira, Qihui Zhu, Chengsheng Zhang, Charles Lee, Mark B. Gerstein
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLoS Comput. Biol. 15 (8) (2019)
Yan Zhang, Shantao Li, Alexej Abyzov, Mark B. Gerstein
Landscape and variation of novel retroduplications in 26 human populations. PLoS Comput. Biol. 13 (6) (2017)
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
Extending gene ontology in the context of extracellular RNA and vesicle communication. J. Biomed. Semant. 7 (2016)
Marghoob Mohiyuddin, John C. Mu, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y. K. Lam
MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinform. 31 (16) (2015)
John C. Mu, Marghoob Mohiyuddin, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y. K. Lam
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinform. 31 (9) (2015)
Daifeng Wang, Koon-Kiu Yan, Cristina Sisu, Chao Cheng, Joel S. Rozowsky, William Meyerson, Mark B. Gerstein
Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors. PLoS Comput. Biol. 11 (4) (2015)
Chong Shou, Nitin Bhardwaj, Hugo Y. K. Lam, Koon-Kiu Yan, Philip M. Kim, Michael Snyder, Mark B. Gerstein
Measuring the Evolutionary Rewiring of Biological Networks. PLoS Comput. Biol. 7 (1) (2011)
Samuel Flores, Mark B. Gerstein
Predicting protein ligand binding motions with the Conformation Explorer. BMC Bioinform. 12 (2011)
Mark B. Gerstein
Human Genome Annotation. ISBRA (2010)
Hugo Y. K. Lam, Philip M. Kim, Janine Mok, Raffi Tonikian, Sachdev S. Sidhu, Benjamin E. Turk, Michael Snyder, Mark B. Gerstein
MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains. BMC Bioinform. 11 (2010)
Gang Fang, Nitin Bhardwaj, Rebecca Robilotto, Mark B. Gerstein
Getting Started in Gene Orthology and Functional Analysis. PLoS Comput. Biol. 6 (3) (2010)
Nitin Bhardwaj, Matthew B. Carson, Alexej Abyzov, Koon-Kiu Yan, Hui Lu, Mark B. Gerstein
Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets. PLoS Comput. Biol. 6 (5) (2010)
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
Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis. PLoS Comput. Biol. 6 (4) (2010)
Zhengdong D. Zhang, Mark B. Gerstein
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model. BMC Bioinform. 11 (2010)
Jiang Du, Robert D. Bjornson, Zhengdong D. Zhang, Yong Kong, Michael Snyder, Mark B. Gerstein
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants. PLoS Comput. Biol. 5 (7) (2009)
Andrey Rzhetsky, Michael R. Seringhaus, Mark B. Gerstein
Getting Started in Text Mining: Part Two. PLoS Comput. Biol. 5 (7) (2009)
Xingyi Guo, Zhaolei Zhang, Mark B. Gerstein, Deyou Zheng
-Acting? PLoS Comput. Biol. 5 (7) (2009)
Hugo Y. K. Lam, Ekta Khurana, Gang Fang, Philip Cayting, Nicholas Carriero, Kei-Hoi Cheung, Mark B. Gerstein
Pseudofam: the pseudogene families database. Nucleic Acids Res. 37 (Database-Issue) (2009)
Yu Xia, Eric A. Franzosa, Mark B. Gerstein
Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate. PLoS Comput. Biol. 5 (6) (2009)
Thomas E. Royce, Nicholas Carriero, Mark B. Gerstein
An efficient pseudomedian filter for tiling microrrays. BMC Bioinform. 8 (2007)
Michael R. Seringhaus, Mark B. Gerstein
Publishing perishing? Towards tomorrow's information architecture. BMC Bioinform. 8 (2007)