Mark Gerstein
Orcid: 0000-0002-9746-3719Affiliations:
- Yale University
According to our database1,
Mark Gerstein
authored at least 137 papers
between 1994 and 2024.
Collaborative distances:
Collaborative distances:
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Bibliography
2024
A Survey of Generative AI for De Novo Drug Design: New Frontiers in Molecule and Protein Generation.
CoRR, 2024
2023
Binding peptide generation for MHC Class I proteins with deep reinforcement learning.
Bioinform., February, 2023
FAVOR: functional annotation of variants online resource and annotator for variation across the human genome.
Nucleic Acids Res., January, 2023
Nucleic Acids Res., January, 2023
Bioinform., January, 2023
Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes.
PLoS Comput. Biol., 2023
Igniting Language Intelligence: The Hitchhiker's Guide From Chain-of-Thought Reasoning to Language Agents.
CoRR, 2023
CoRR, 2023
ML-Bench: Large Language Models Leverage Open-source Libraries for Machine Learning Tasks.
CoRR, 2023
CoRR, 2023
CoRR, 2023
Struc-Bench: Are Large Language Models Really Good at Generating Complex Structured Data?
CoRR, 2023
BioCoder: A Benchmark for Bioinformatics Code Generation with Contextual Pragmatic Knowledge.
CoRR, 2023
CoRR, 2023
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
GersteinLab at MEDIQA-Chat 2023: Clinical Note Summarization from Doctor-Patient Conversations through Fine-tuning and In-context Learning.
Proceedings of the 5th Clinical Natural Language Processing Workshop, 2023
Aligning Factual Consistency for Clinical Studies Summarization through Reinforcement Learning.
Proceedings of the 5th Clinical Natural Language Processing Workshop, 2023
2022
Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data.
PLoS Comput. Biol., October, 2022
CoRR, 2022
Higher-Order Generalization Bounds: Learning Deep Probabilistic Programs via PAC-Bayes Objectives.
CoRR, 2022
Privacy-preserving Model Training for Disease Prediction Using Federated Learning with Differential Privacy.
Proceedings of the 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society, 2022
2021
Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions.
PLoS Comput. Biol., 2021
Forest Fire Clustering: Cluster-oriented Label Propagation Clustering and Monte Carlo Verification Inspired by Forest Fire Dynamics.
CoRR, 2021
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization.
Bioinform., 2021
DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays.
Bioinform., 2021
Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption.
IEEE Access, 2021
2020
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks.
PLoS Comput. Biol., 2020
PLoS Comput. Biol., 2020
NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis.
BMC Bioinform., 2020
DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring.
BMC Bioinform., 2020
The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data.
BMC Bioinform., 2020
Origins and characterization of variants shared between databases of somatic and germline human mutations.
BMC Bioinform., 2020
Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients.
BMC Bioinform., 2020
Bioinform., 2020
Shaping the nebulous enhancer in the era of high-throughput assays and genome editing.
Briefings Bioinform., 2020
2019
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements.
PLoS Comput. Biol., 2019
Nucleic Acids Res., 2019
2018
Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018
MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool.
Bioinform., 2018
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.
Bioinform., 2018
2017
PLoS Comput. Biol., 2017
MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.
PLoS Comput. Biol., 2017
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.
Bioinform., 2017
2016
DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks.
PLoS Comput. Biol., 2016
Extending gene ontology in the context of extracellular RNA and vesicle communication.
J. Biomed. Semant., 2016
2015
PLoS Comput. Biol., 2015
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications.
Bioinform., 2015
MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.
Bioinform., 2015
Bioinform., 2015
2014
Comparative analysis of regulatory information and circuits across distant species Open.
Nat., 2014
Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, 2014
2013
PLoS Comput. Biol., 2013
BMC Syst. Biol., 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
2012
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.
Bioinform., 2012
2011
PLoS Comput. Biol., 2011
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data.
PLoS Comput. Biol., 2011
BMC Bioinform., 2011
BMC Bioinform., 2011
Bioinform., 2011
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
Bioinform., 2011
TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles.
Bioinform., 2011
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision.
Bioinform., 2011
2010
Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis.
PLoS Comput. Biol., 2010
Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets.
PLoS Comput. Biol., 2010
Nucleic Acids Res., 2010
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model.
BMC Bioinform., 2010
BMC Bioinform., 2010
Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique.
BMC Bioinform., 2010
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
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010
2009
PLoS Comput. Biol., 2009
PLoS Comput. Biol., 2009
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants.
PLoS Comput. Biol., 2009
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels.
BMC Bioinform., 2009
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions.
Bioinform., 2009
2008
2007
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics.
PLoS Comput. Biol., 2007
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.
Nucleic Acids Res., 2007
An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective.
J. Biomed. Informatics, 2007
BMC Bioinform., 2007
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.
BMC Bioinform., 2007
BMC Bioinform., 2007
BMC Bioinform., 2007
BMC Bioinform., 2007
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.
Bioinform., 2007
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
Bioinform., 2007
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.
Bioinform., 2007
Assessing the need for sequence-based normalization in tiling microarray experiments.
Bioinform., 2007
2006
An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits.
PLoS Comput. Biol., 2006
Nucleic Acids Res., 2006
Bioinform., 2006
A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.
Bioinform., 2006
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.
Bioinform., 2006
Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research.
Proceedings of the 40th Annual Conference on Information Sciences and Systems, 2006
2005
Case Report: A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies.
J. Am. Medical Informatics Assoc., 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
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005
Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis.
Proceedings of the Data Analysis and Visualization in Genomics and Proteomics, 2005
2004
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search.
J. Comput. Biol., 2004
BMC Bioinform., 2004
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.
BMC Bioinform., 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
2003
Nucleic Acids Res., 2003
MolMovDB: analysis and visualization of conformational change and structural flexibility.
Nucleic Acids Res., 2003
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
Bioinform., 2003
Computational Proteomics: Genome-scale Analysis of Protein Structure, Function, & Evolution(Invited Talk).
Proceedings of the German Conference on Bioinformatics, 2003
2002
Toward a systematic definition of protein function that scales to the genome level: defining function in terms of interactions.
Proc. IEEE, 2002
Bioinform., 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.
Bioinform., 2002
Proceedings of the AMIA 2002, 2002
2001
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.
Nucleic Acids Res., 2001
Determining the minimum number of types necessary to represent the sizes of protein atoms.
Bioinform., 2001
Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering, 2001
1998
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence.
Bioinform., 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
1996
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
1995
Comput. Appl. Biosci., 1995
1994
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994