Mark Gerstein

Lukas Habegger, Suganthi Balasubramanian, David Z. Chen, Ekta Khurana, Andrea Sboner, Arif Harmanci, Joel S. Rozowsky, Declan Clarke, Michael Snyder, Mark Gerstein: VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics 28(17): 2267-2269 (2012)

Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel S. Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein: RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics 27(2): 281-283 (2011)

Alexej Abyzov, Mark Gerstein: AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinformatics 27(5): 595-603 (2011)

Justin Jee, Joel S. Rozowsky, Kevin Y. Yip, Lucas Lochovsky, Robert D. Bjornson, Guoneng Zhong, Zhengdong D. Zhang, Yutao Fu, Jie Wang, Zhiping Weng, Mark Gerstein: ACT: aggregation and correlation toolbox for analyses of genome tracks. Bioinformatics 27(8): 1152-1154 (2011)

Chao Cheng, Renqiang Min, Mark Gerstein: TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. Bioinformatics 27(23): 3221-3227 (2011)

Alexander Karpikov, Joel S. Rozowsky, Mark Gerstein: Tiling array data analysis: a multiscale approach using wavelets. BMC Bioinformatics 12: 57 (2011)

Samuel Flores, Mark B. Gerstein: Predicting protein ligand binding motions with the Conformation Explorer. BMC Bioinformatics 12: 417 (2011)

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 Computational Biology 7(1) (2011)

Chao Cheng, Koon-Kiu Yan, Woochang Hwang, Jiang Qian, Nitin Bhardwaj, Joel S. Rozowsky, Zhi John Lu, Wei Niu, Pedro Alves, Masaomi Kato, Michael Snyder, Mark Gerstein: Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data. PLoS Computational Biology 7(11) (2011)

Dov Greenbaum, Andrea Sboner, Xinmeng Jasmine Mu, Mark Gerstein: Genomics and Privacy: Implications of the New Reality of Closed Data for the Field. PLoS Computational Biology 7(12) (2011)

Matthew Holford, Ekta Khurana, Kei-Hoi Cheung, Mark Gerstein: Using semantic web rules to reason on an ontology of pseudogenes. Bioinformatics [ISMB] 26(12): 71-78 (2010)

Nitin Bhardwaj, Mark Gerstein, Hui Lu: Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique. BMC Bioinformatics 11(S-1): 6 (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 Bioinformatics 11: 243 (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 Bioinformatics 11: 539 (2010)

Neil Voss, Mark Gerstein: 3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Research 38(Web-Server-Issue): 555-562 (2010)

Gang Fang, Nitin Bhardwaj, Rebecca Robilotto, Mark B. Gerstein: Getting Started in Gene Orthology and Functional Analysis. PLoS Computational Biology 6(3) (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 Computational Biology 6(4) (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 Computational Biology 6(5) (2010)

Mark Gerstein: Analysis of molecular networks. BCB 2010: 1

Nitin Bhardwaj, Mark Gerstein: Dynamic and static analysis of transcriptional regulatory networks in a hierarchical context. GENSiPS 2010: 1

Koon-Kiu Yan, Mark Gerstein: Hierarchical analysis of regulatory networks and cross-disciplinary comparison with the Linux call graph. GENSiPS 2010: 1

Mark B. Gerstein: Human Genome Annotation. ISBRA 2010: 50-51

Kevin Y. Yip, Mark Gerstein: Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. Bioinformatics 25(2): 243-250 (2009)

Kevin Y. Yip, Philip M. Kim, Drew McDermott, Mark Gerstein: Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. BMC Bioinformatics 10 (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 Research 37(Database-Issue): 738-743 (2009)

Yu Xia, Eric A. Franzosa, Mark B. Gerstein: Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate. PLoS Computational Biology 5(6) (2009)

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 Computational Biology 5(7) (2009)

Xingyi Guo, Zhaolei Zhang, Mark B. Gerstein, Deyou Zheng: Small RNAs Originated from Pseudogenes: cis- or trans-Acting? PLoS Computational Biology 5(7) (2009)

Andrey Rzhetsky, Michael R. Seringhaus, Mark B. Gerstein: Getting Started in Text Mining: Part Two. PLoS Computational Biology 5(7) (2009)

Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew McDermott, Mark Gerstein: An integrated system for studying residue coevolution in proteins. Bioinformatics 24(2): 290-292 (2008)

Philip E. Bourne, J. Lynn Fink, Mark Gerstein: Open Access: Taking Full Advantage of the Content. PLoS Computational Biology 4(3) (2008)

Zhengdong D. Zhang, Joel S. Rozowsky, Michael Snyder, Joseph T. Chang, Mark Gerstein: Modeling ChIP Sequencing In Silico with Applications. PLoS Computational Biology 4(8) (2008)

Thomas E. Royce, Joel S. Rozowsky, Mark Gerstein: Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics 23(8): 988-997 (2007)

Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein: The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics 23(8): 1048 (2007)

Haiyuan Yu, Ronald Jansen, Gustavo Stolovitzky, Mark Gerstein: Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. Bioinformatics 23(16): 2163-2173 (2007)

Andrew K. Smith, Kei-Hoi Cheung, Michael Krauthammer, Martin H. Schultz, Mark Gerstein: Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. Bioinformatics 23(22): 3073-3079 (2007)

Samuel Flores, Mark Gerstein: FlexOracle: predicting flexible hinges by identification of stable domains. BMC Bioinformatics 8 (2007)

Samuel Flores, Long J. Lu, Julie Yang, Nicholas Carriero, Mark Gerstein: Hinge Atlas: relating protein sequence to sites of structural flexibility. BMC Bioinformatics 8 (2007)

Thomas E. Royce, Nicholas Carriero, Mark B. Gerstein: An efficient pseudomedian filter for tiling microrrays. BMC Bioinformatics 8 (2007)

Michael R. Seringhaus, Mark B. Gerstein: Publishing perishing? Towards tomorrow's information architecture. BMC Bioinformatics 8 (2007)

Andrew K. Smith, Kei-Hoi Cheung, Kevin Y. Yip, Martin H. Schultz, Mark Gerstein: LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. BMC Bioinformatics 8(S-3) (2007)

Eric Z. Yu, Anne E. Counterman Burba, Mark Gerstein: PARE: A tool for comparing protein abundance and mRNA expression data. BMC Bioinformatics 8 (2007)

Mark Gerstein, Dov Greenbaum, Kei-Hoi Cheung, Perry L. Miller: An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective. Journal of Biomedical Informatics 40(1): 73-79 (2007)

John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul M. Harrison, Mark Gerstein: Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Research 35(Database-Issue): 55-60 (2007)

Mark Gerstein, Shawn M. Douglas: RNAi Development. PLoS Computational Biology 3(4) (2007)

Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein: The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics. PLoS Computational Biology 3(4) (2007)

Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, Mark Gerstein: Predicting interactions in protein networks by completing defective cliques. Bioinformatics 22(7): 823-829 (2006)

Zhaolei Zhang, Nicholas Carriero, Deyou Zheng, John E. Karro, Paul M. Harrison, Mark Gerstein: PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics 22(12): 1437-1439 (2006)

Anne E. Counterman Burba, Ursula Lehnert, Eric Z. Yu, Mark Gerstein: Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins. Bioinformatics 22(22): 2735-2738 (2006)

Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein: The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics 22(23): 2968-2970 (2006)

Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, Martin H. Schultz, Michael Snyder, Mark Gerstein: A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinformatics 22(24): 3016-3024 (2006)

Samuel Flores, Nathaniel Echols, Duncan Milburn, Brandon Hespenheide, Kevin Keating, Jason Lu, Stephen Wells, Eric Z. Yu, Michael Thorpe, Mark Gerstein: The Database of Macromolecular Motions: new features added at the decade mark. Nucleic Acids Research 34(Database-Issue): 296-301 (2006)

Yang Liu, Jianrong Li, Lee T. Sam, Chern-Sing Goh, Mark Gerstein, Yves A. Lussier: An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits. PLoS Computational Biology 2(11) (2006)

Nicholas Carriero, Michael V. Osier, Kei-Hoi Cheung, Perry L. Miller, Mark Gerstein, Hongyu Zhao, Baolin Wu, Scott Rifkin, Joseph T. Chang, Heping Zhang, Kevin White, Kenneth Williams, Martin H. Schultz: Case Report: A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies. JAMIA 12(1): 90-98 (2005)

Dov Greenbaum, Andrew K. Smith, Mark Gerstein: Editorial. Nucleic Acids Research 33(Database-Issue): 3-4 (2005)

Kei-Hoi Cheung, Kevin Y. Yip, Andrew K. Smith, Remko de Knikker, Andy Masiar, Mark Gerstein: YeastHub: a semantic web use case for integrating data in the life sciences domain. ISMB (Supplement of Bioinformatics) 2005: 85-96

Joel S. Rozowsky, Paul Bertone, Thomas E. Royce, Sherman Weissman, Michael Snyder, Mark Gerstein: Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites. BSB 2005: 28-29

Vadim Alexandrov, Mark Gerstein: Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. BMC Bioinformatics 5: 2 (2004)

Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao: Information assessment on predicting protein-protein interactions. BMC Bioinformatics 5: 154 (2004)

Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder: Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. Journal of Computational Biology 11(4): 766-785 (2004)

Kei-Hoi Cheung, Deyun Pan, Andrew K. Smith, Michael R. Seringhaus, Shawn M. Douglas, Mark Gerstein: A XML-Based Approach to Integrating Heterogeneous Yeast Genome Data. METMBS 2004: 236-242

Jiang Qian, Jimmy J. Lin, Nicholas M. Luscombe, Haiyuan Yu, Mark Gerstein: Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics 19(15): 1917-1926 (2003)

Nathaniel Echols, Duncan Milburn, Mark Gerstein: MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Research 31(1): 478-482 (2003)

Nicholas M. Luscombe, Thomas E. Royce, Paul Bertone, Nathaniel Echols, Christine E. Horak, Joseph T. Chang, Michael Snyder, Mark Gerstein: ExpressYourself: a modular platform for processing and visualizing microarray data. Nucleic Acids Research 31(13): 3477-3482 (2003)

Mark Gerstein: Computational Proteomics: Genome-scale Analysis of Protein Structure, Function, & Evolution(Invited Talk). German Conference on Bioinformatics 2003: 53

Dov Greenbaum, Ronald Jansen, Mark Gerstein: Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 18(4): 585-596 (2002)

Jerry Tsai, Mark Gerstein: Calculations of protein volumes: sensitivity analysis and parameter database. Bioinformatics 18(7): 985-995 (2002)

Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder: Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. WABI 2002: 419-433

Jerry Tsai, Neil Voss, Mark Gerstein: Determining the minimum number of types necessary to represent the sizes of protein atoms. Bioinformatics 17(10): 949-956 (2001)

Paul Bertone, Yuval Kluger, Ning Lan, Deyou Zheng, Dinesh Christendat, Adelinda Yee, Aled M. Edwards, Cheryl H. Arrowsmith, Gaetano T. Montelione, Mark Gerstein: SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Research 29(13): 2884-2898 (2001)

Kei-Hoi Cheung, Yang Liu, Anuj Kumar, Michael Snyder, Mark Gerstein, Perry L. Miller: An XML Application For Genomic Data Interoperation. BIBE 2001: 97-103

Mark Gerstein: Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinformatics 14(8): 707-714 (1998)

Mark Gerstein: [Invited Lecture] A Structural Census of Genomes: Comparing Bacterial, Eukaryotic, and Archaea Genomes in Terms of Protein Structure. German Conference on Bioinformatics 1998

Mark Gerstein, Michael Levitt: Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures. ISMB 1996: 59-67

Mark Gerstein, Russ B. Altman: Using a measure of structural variation to define a core for the globins. Computer Applications in the Biosciences 11(6): 633-644 (1995)

Russ B. Altman, Mark Gerstein: Finding an Average Core Structure: Application to the Globins. ISMB 1994: 19-27