Mark Gerstein

Research interests

Publications

• GENCODE: reference annotation for the human and mouse genomes in 2023

  Nucleic Acids Research · 2022 · 10.1093/nar/gkac1071

• High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

  Cell · 2022 · https://doi.org/10.1016/j.cell.2022.08.004

• Haplotype-resolved diverse human genomes and integrated analysis of structural variation

  Science · 2021 · https://doi.org/10.1126/science.abf7117

• GENCODE 2021

  Nucleic Acids Research · 2020 · https://doi.org/10.1093/nar/gkaa1087

• Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

  Nature Genetics · 2020 · https://doi.org/10.1038/s41588-019-0562-0

• Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

  Nature Genetics · 2020 · https://doi.org/10.1038/s41588-019-0576-7

• Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

  Nature Communications · 2019 · 10.1038/s41467-019-13036-1

• Multi-platform discovery of haplotype-resolved structural variation in human genomes

  Nature Communications · 2019 · 10.1038/s41467-018-08148-z

• Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap

  Science · 2018 · 10.1126/science.aad6469

• GENCODE reference annotation for the human and mouse genomes

  Nucleic Acids Research · 2018 · https://doi.org/10.1093/nar/gky955

• Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

  Science · 2018 · 10.1126/science.aat8127

• KBase: The United States Department of Energy Systems Biology Knowledgebase

  Nature Biotechnology · 2018 · 10.1038/nbt.4163

• The Molecular Taxonomy of Primary Prostate Cancer

  Cell · 2015 · 10.1016/j.cell.2015.10.025

• An integrated map of structural variation in 2,504 human genomes

  Nature · 2015 · 10.1038/nature15394

• Transcriptional landscape of the prenatal human brain

  Nature · 2014 · 10.1038/nature13185

• Guidelines for investigating causality of sequence variants in human disease

  Nature · 2014 · 10.1038/nature13127

• Defining functional DNA elements in the human genome

  Proceedings of the National Academy of Sciences · 2014 · 10.1073/pnas.1318948111

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

  Genome Research · 2012 · 10.1101/gr.136184.111

• GENCODE: The reference human genome annotation for The ENCODE Project

  Genome Research · 2012 · https://doi.org/10.1101/gr.135350.111

• A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

  Science · 2012 · 10.1126/science.1215040

• Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

  Cell · 2012 · 10.1016/j.cell.2011.12.014

• Landscape of transcription in human cells

  Nature · 2012 · https://doi.org/10.1038/nature11233

• Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

  Cell · 2012 · 10.1016/j.cell.2012.02.009

• Architecture of the human regulatory network derived from ENCODE data

  Nature · 2012 · 10.1038/nature11245

• An integrated encyclopedia of DNA elements in the human genome

  The Journal of the American Medical Association (JAMA) Network (American Medical Association) · 2012

• Mapping copy number variation by population-scale genome sequencing

  Nature · 2011 · 10.1038/nature09708

• The genomic complexity of primary human prostate cancer

  Nature · 2011 · 10.1038/nature09744

• CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

  Genome Research · 2011 · 10.1101/gr.114876.110

• Molecular Characterization of Neuroendocrine Prostate Cancer and Identification of New Drug Targets

  Cancer Discovery · 2011 · 10.1158/2159-8290.cd-11-0130

• Unlocking the secrets of the genome

  Nature · 2009 · 10.1038/459927a

• The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

  Science · 2008 · 10.1126/science.1158441

• RNA-Seq: a revolutionary tool for transcriptomics

  Nature Reviews Genetics · 2008 · https://doi.org/10.1038/nrg2484

• Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome

  Science · 2007 · 10.1126/science.1149504

• Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

  Nature · 2006 · 10.1038/nature04670

• Structure and evolution of transcriptional regulatory networks

  Current Opinion in Structural Biology · 2004 · 10.1016/j.sbi.2004.05.004

• A Map of the Interactome Network of the Metazoan C. elegans

  Science · 2004 · 10.1126/science.1091403

• Genomic analysis of regulatory network dynamics reveals large topological changes

  Nature · 2004 · 10.1038/nature02782

• Comparing protein abundance and mRNA expression levels on a genomic scale.

  Genome biology · 2003 · 10.1186/gb-2003-4-9-117

• A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data

  Science · 2003 · 10.1126/science.1087361

• Functional profiling of the Saccharomyces cerevisiae genome

  Nature · 2002 · https://doi.org/10.1038/nature00935

• Global Analysis of Protein Activities Using Proteome Chips

  Science · 2001 · 10.1126/science.1062191

Current projects

No projects listed.