Gerstein Lab Publications

[ review ] All Review Papers
[ informatics-research-article ] Informatics research article lead by the Gerstein Lab
[ expt-collab ] Research articles driven by another lab in collaboration with Gerstein Lab
[ otherpub ] Other Publications
[ preprint ] Preprints in advance of formal peer review and publication in a peer-reviewed journal
[ student ] Undergraduate Publications

[ LLM ] Large language model
[ deeplearning ] Deep Learning
[ 1kgphase3 ] 1000 Genomes Project Phase 3
[ 1000genomes ] Papers Related to the 1000 Genomes Pilot Project
[ cancer ] Papers Related to Cancer
[ epublishing ] E-publishing and scientific communication
[ interactions ] Biological Networks
[ intro-cs ] Intro. to Lab with a very CS focus
[ intro-to-lab ] Introduction to the Lab
[ mining ] Systematic Datamining and Biological Database Design
[ motions ] Macromolecular Motions
[ pseudogenes ] Pseudogenes
[ rnaseq ] Papers related to transcription and RNA-seq
[ strgen ] Structural Genomics
[ sv ] Structural Variation
[ resources ] Lab Software and Web Servers
[ modencoderollout ] Papers Related to Dec 2014 modENCODE rollout
[ variation ] Analysis of Human Sequence Variation
[ volumes ] Macromolecular Packing
[ ngtools ] Tools for Processing Next-Generation Sequencing Data
[ coretools ] Tools that are actively maintained by the lab.
[ formalism ] Bioinformatics Formalism or Approach but Not as Developed Software Program
[ encode-nc ] ENCODE and non-coding annotation
[ CNVpre1KG ] Paper related to CNV discovery prior to 1000 Genomes Project
[ privacy ] Papers Related to Genomic Privacy
[ privacy-tools ] Papers which develop genomic privacy tools.
[ modencode ] Papers Related to Dec 2010 modENCODE rollout
[ encoderollout ] Papers Related to Sept 2012 ENCODE rollout (core papers)
[ encode3rollout ] Papers Related to ENCODE 3 rollout (core papers)
[ otherencodepapers ] Additiional Papers Related to Sept 2012 ENCODE rollout
[ statmodels ] Papers on Statistical Models of Gene Expression
[ bookreview ] Papers on Book Review
[ pecrollout ] PsychENCODE
[ neurogenomics ] Neurogenomics
[ conference ] Conference Papers
[ pcawg ] PCAWG rollout and related papers
[ encode-channel ] BioRxiv ENCODE Channel
[ quantumcomputing ] Quantum computing
[ culturomics ] Omic of culture
[ sciofsci ] Science of science

[ best ] Best Papers
[ best122020 ] Best Papers (as of the end of 2020)
[ best2006 ] Best from 1997 to 2006
[ best-revs ] Best Reviews and Other Contributions
[ fav0312 ] 5 Favorites as of March 2012
[ fav0214 ] 5 Favorites as of Feb 2014
[ recentpaper ] Some Highlighted Recent Papers
[ best2014 ] Best papers (as of the end of 2014)
[ almostbest ] Group of papers that are 'Almost Best'
[ withnobelists ] Papers with Nobel prize winners
[ fav0819 ] Favorites as of August 2019
[ best062020 ] Best Papers (as of June 2020)

[ expression ] Analysis of Expression Datasets (including Tiling Arrays)
[ evolution ] Evolution
[ interrelate ] Inter-relating Functional Genomics Features
[ intro-to-lab-old ] Introduction to the Lab (old, see new one)
[ microarray ] Microarray experiments and analysis
[ persgenomics ] Personal Genomics
[ regnet ] Regulatory Networks
[ opinion-review ] Lists of Opinion and Review Pieces
[ cs-dml ] Datamining & Machine Learning
[ cs-network ] Network Analysis
[ cs-other ] Other
[ cs-semweb ] Semantic Web and Knowledge Representation
[ singlecell ] Single Cell
[ wearables ] Wearables
[ netanalogy ] Listing of lab network papers making analogies between biological and non-biological networks
[ microbiome ] Microbiome
[ textmining ] Text Mining
[ gencode ] GENCODE
[ deeplearning ] Deep Learning

[ cegs ] CEGS grant
[ don ] Dongahue Young Investigator
[ encode ] Transcriptional and Regulatory Elements in the ENCODE Region
[ encode-pgenes ] ENCODE Pseudogene
[ forgetppg ] Molecular Basis of Myelopoiesis
[ hpc ] High Performance Computing
[ keck ] Keck Foundation grant
[ mem ] NIH membranes grant
[ nbc ] NIH Northeast Biodefense Center
[ nesg ] NESG grant
[ NIDA ] Yale/NIDA Neuroproteomics Research Center
[ nih-tn ] Global Analysis of Transcription Regulatory Networks
[ nsfdbi ] NSF Database Activities Program
[ nsfg1s ] Modeling G1/S Transition During Yeast Cell Cycle
[ nsfymd ] Microarray Database Design
[ onrrec ] Navy Young Investigator
[ phrma ] PhRMA grant
[ pilotctr ] Planning a Biomedical Computing Center of Excellence
[ proteomicsctr ] Yale/NHLBI Proteomics Center
[ ricearray ] NSF grant
[ ycemh ] Yale Center of Excellence in Molecular Hematology
[ encodecore ] mod/ENCODE "Rollout" publications
[ grant-lof ] LOST-OF-FUNCTION VARIANTS IN THE 1000 GENOMES DATA SET AND IMPLICATIONS TO GWAS
[ bbsrc ] ABI Innov.: Graph-Based Approach for the Genome-Wide Prediction of Conditionally Essential Genes
[ 4dac ] EDAC: ENCODE Data Analysis Center
[ prR01 ] Enhancing Open Data Sharing For Functional Genomics Experiments: Measures To Quantify Genomic Information Leakage And File Formats For Privacy Preservation
[ ggK99 ] ggK99
[ bd2kpr ] Methods and Software to Enhance Genomic Privacy and Sharing of RNA-Seq Data
[ hivbigdat ] A Big Data Approach to Identify Epigenetic, Transcriptomic, and Network Dynamics as Immune Dysfunction Drivers Associated with HIV Infection and Substance Use Disorder
[ u24sv ] Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human Genomes
[ psychdac ] Discovery and validation of neuronal enhancers associated with the development of psychiatric disorders
[ wormfly2 ] Creating Comprehensive Maps of Worm and Fly Transcription Factor Binding Sites
[ ncvarg ] Prioritizing rare variants associated with cancer using non-coding annotation
[ scorchum1 ] The Y-SCORCH Data Generation Center at Yale for Single-Cell Opioid Responses in the Context of HIV
[ scorchum2 ] M-SCORCH: Methamphetamine use disorder data generation center for Single Cell Opioid Responses in the Context of HIV
[ x57gbig ] Integrative analysis of genomics and imaging data from the BRAIN Initiative and other public data sources
[ u24pg2 ] u24pg2
[ psychdac2 ] PsychENCODE Data Analysis and Coordination Center
[ Ucix57g ] Interpretable Deep Learning Methods to Investigate Genetics and Epigenetics of Alzheimer's Disease at a Single-Cell Resolution
[ G0schmidt ] Schmidt Futures