Mark Gerstein

According to our database1, Mark Gerstein authored at least 94 papers between 1994 and 2019.

Collaborative distances:



In proceedings 
PhD thesis 





GENCODE reference annotation for the human and mouse genomes.
Nucleic Acids Research, 2019

Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology.
IEEE/ACM Trans. Comput. Biology Bioinform., 2018

Rank Projection Trees for Multilevel Neural Network Interpretation.
CoRR, 2018

MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool.
Bioinformatics, 2018

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.
Bioinformatics, 2018

Landscape and variation of novel retroduplications in 26 human populations.
PLoS Computational Biology, 2017

MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.
PLoS Computational Biology, 2017

HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.
Bioinformatics, 2017

DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks.
PLoS Computational Biology, 2016

Extending gene ontology in the context of extracellular RNA and vesicle communication.
J. Biomedical Semantics, 2016

Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors.
PLoS Computational Biology, 2015

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.
Bioinformatics, 2015

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.
Bioinformatics, 2015

High-order neural networks and kernel methods for peptide-MHC binding prediction.
Bioinformatics, 2015

Comparative analysis of regulatory information and circuits across distant species Open.
Nature, 2014

Interpretable Sparse High-Order Boltzmann Machines.
Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, 2014

Interpretation of Genomic Variants Using a Unified Biological Network Approach.
PLoS Computational Biology, 2013

Identification of yeast cell cycle regulated genes based on genomic features.
BMC Systems Biology, 2013

Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar.
Proceedings of the ACM Conference on Bioinformatics, 2013

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.
Bioinformatics, 2012

Measuring the Evolutionary Rewiring of Biological Networks.
PLoS Computational Biology, 2011

Genomics and Privacy: Implications of the New Reality of Closed Data for the Field.
PLoS Computational Biology, 2011

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data.
PLoS Computational Biology, 2011

Tiling array data analysis: a multiscale approach using wavelets.
BMC Bioinformatics, 2011

Predicting protein ligand binding motions with the Conformation Explorer.
BMC Bioinformatics, 2011

ACT: aggregation and correlation toolbox for analyses of genome tracks.
Bioinformatics, 2011

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
Bioinformatics, 2011

TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles.
Bioinformatics, 2011

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
Bioinformatics, 2011

Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis.
PLoS Computational Biology, 2010

Getting Started in Gene Orthology and Functional Analysis.
PLoS Computational Biology, 2010

Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets.
PLoS Computational Biology, 2010

3V: cavity, channel and cleft volume calculator and extractor.
Nucleic Acids Research, 2010

Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model.
BMC Bioinformatics, 2010

MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains.
BMC Bioinformatics, 2010

Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique.
BMC Bioinformatics, 2010

Using semantic web rules to reason on an ontology of pseudogenes.
Bioinformatics [ISMB], 2010

Human Genome Annotation.
Proceedings of the Bioinformatics Research and Applications, 6th International Symposium, 2010

Hierarchical analysis of regulatory networks and cross-disciplinary comparison with the Linux call graph.
Proceedings of the 2010 IEEE International Workshop on Genomic Signal Processing and Statistics, 2010

Dynamic and static analysis of transcriptional regulatory networks in a hierarchical context.
Proceedings of the 2010 IEEE International Workshop on Genomic Signal Processing and Statistics, 2010

Analysis of molecular networks.
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate.
PLoS Computational Biology, 2009

Getting Started in Text Mining: Part Two.
PLoS Computational Biology, 2009

Small RNAs Originated from Pseudogenes: cis- or trans-Acting?
PLoS Computational Biology, 2009

Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants.
PLoS Computational Biology, 2009

Pseudofam: the pseudogene families database.
Nucleic Acids Research, 2009

Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.
BMC Bioinformatics, 2009

Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions.
Bioinformatics, 2009

Modeling ChIP Sequencing In Silico with Applications.
PLoS Computational Biology, 2008

Open Access: Taking Full Advantage of the Content.
PLoS Computational Biology, 2008

An integrated system for studying residue coevolution in proteins.
Bioinformatics, 2008

The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics.
PLoS Computational Biology, 2007

RNAi Development.
PLoS Computational Biology, 2007 a comprehensive database and comparison platform for pseudogene annotation.
Nucleic Acids Research, 2007

An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective.
Journal of Biomedical Informatics, 2007

PARE: A tool for comparing protein abundance and mRNA expression data.
BMC Bioinformatics, 2007

LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.
BMC Bioinformatics, 2007

Publishing perishing? Towards tomorrow's information architecture.
BMC Bioinformatics, 2007

An efficient pseudomedian filter for tiling microrrays.
BMC Bioinformatics, 2007

Hinge Atlas: relating protein sequence to sites of structural flexibility.
BMC Bioinformatics, 2007

FlexOracle: predicting flexible hinges by identification of stable domains.
BMC Bioinformatics, 2007

Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.
Bioinformatics, 2007

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
Bioinformatics, 2007

Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.
Bioinformatics, 2007

Assessing the need for sequence-based normalization in tiling microarray experiments.
Bioinformatics, 2007

An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits.
PLoS Computational Biology, 2006

The Database of Macromolecular Motions: new features added at the decade mark.
Nucleic Acids Research, 2006

PseudoPipe: an automated pseudogene identification pipeline.
Bioinformatics, 2006

Predicting interactions in protein networks by completing defective cliques.
Bioinformatics, 2006

A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.
Bioinformatics, 2006

Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.
Bioinformatics, 2006

Nucleic Acids Research, 2005

Case Report: A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies.
JAMIA, 2005

Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2005

YeastHub: a semantic web use case for integrating data in the life sciences domain.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search.
Journal of Computational Biology, 2004

Information assessment on predicting protein-protein interactions.
BMC Bioinformatics, 2004

Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.
BMC Bioinformatics, 2004

A XML-Based Approach to Integrating Heterogeneous Yeast Genome Data.
Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Scienes, 2004

ExpressYourself: a modular platform for processing and visualizing microarray data
Nucleic Acids Research, 2003

MolMovDB: analysis and visualization of conformational change and structural flexibility.
Nucleic Acids Research, 2003

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
Bioinformatics, 2003

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

Calculations of protein volumes: sensitivity analysis and parameter database.
Bioinformatics, 2002

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, 2002

SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.
Nucleic Acids Research, 2001

Determining the minimum number of types necessary to represent the sizes of protein atoms.
Bioinformatics, 2001

An XML Application For Genomic Data Interoperation.
Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering, 2001

Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence.
Bioinformatics, 1998

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

Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures.
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

Using a measure of structural variation to define a core for the globins.
Computer Applications in the Biosciences, 1995

Finding an Average Core Structure: Application to the Globins.
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994