List of works - John Stamatoyannopoulos

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

scientific article (publication date: 9 October 2009)

The accessible chromatin landscape of the human genome

scientific article

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

scientific article

Mapping and sequencing of structural variation from eight human genomes

scientific article

Quantifying similarity between motifs

scientific article

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

scientific article

A comparative encyclopedia of DNA elements in the mouse genome

scientific article

Dynamic DNA methylation across diverse human cell lines and tissues

scientific article published on 16 January 2013

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

scientific article published on 22 March 2009

Topologically associating domains are stable units of replication-timing regulation

scientific article

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

scientific article

The human mitochondrial transcriptome

scientific article

Defining functional DNA elements in the human genome

scientific article

Resolving the complexity of the human genome using single-molecule sequencing

scientific article

An encyclopedia of mouse DNA elements (Mouse ENCODE).

scientific article

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

scientific article published on July 8, 2011

BEDOPS: high-performance genomic feature operations

scientific article

Circuitry and dynamics of human transcription factor regulatory networks

scientific article published on 5 September 2012

Human mutation rate associated with DNA replication timing

scientific article published on 15 March 2009

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

scientific article published in July 2006

Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification

scientific article

Interaction of the glucocorticoid receptor with the chromatin landscape

scientific article

Nucleosome positioning signals in genomic DNA

scientific article published on 9 July 2007

A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development

scientific article published on 11 September 2012

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes

scientific article published on August 2013

Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing transcription of the gene encoding interferon-gamma

scientific article

Exonic transcription factor binding directs codon choice and affects protein evolution

scientific article published on December 2013

Power of deep, all-exon resequencing for discovery of human trait genes

scholarly article

Domains of genome-wide gene expression dysregulation in Down's syndrome

scientific article published in April 2014

Contribution of inherited mutations in the BRCA2-interacting protein PALB2 to familial breast cancer

scientific article

Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis

scientific article

Conservation of trans-acting circuitry during mammalian regulatory evolution

scientific article

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA.

scientific article

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

scientific article published on 7 April 2011

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

scientific article published on March 14, 2013

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

scientific article

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

scientific article published on 12 March 2013

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

scientific article

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

scientific article published on 11 May 2011

Discovery of functional noncoding elements by digital analysis of chromatin structure

scholarly article

Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development

scientific article

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

scientific article published on 10 December 2012

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana

scientific article published on 15 September 2014

Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries

scientific article

Role of DNA Methylation in Modulating Transcription Factor Occupancy

scientific article published on August 6, 2015

Identification of higher-order functional domains in the human ENCODE regions

scientific article published on June 2007

CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus

scientific article

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

scientific article

High-throughput localization of functional elements by quantitative chromatin profiling

scientific article

List of works by John Stamatoyannopoulos

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Comprehensive mapping of long-range interactions reveals folding principles of the human genome

The accessible chromatin landscape of the human genome

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

Mapping and sequencing of structural variation from eight human genomes

Quantifying similarity between motifs

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

A comparative encyclopedia of DNA elements in the mouse genome

Dynamic DNA methylation across diverse human cell lines and tissues

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

Topologically associating domains are stable units of replication-timing regulation

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

The human mitochondrial transcriptome

Defining functional DNA elements in the human genome

Resolving the complexity of the human genome using single-molecule sequencing

An encyclopedia of mouse DNA elements (Mouse ENCODE).

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

BEDOPS: high-performance genomic feature operations

Circuitry and dynamics of human transcription factor regulatory networks

Human mutation rate associated with DNA replication timing

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification

Interaction of the glucocorticoid receptor with the chromatin landscape

Nucleosome positioning signals in genomic DNA

A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development

Developmental fate and cellular maturity encoded in human regulatory DNA landscapes

Comprehensive epigenetic profiling identifies multiple distal regulatory elements directing transcription of the gene encoding interferon-gamma

Exonic transcription factor binding directs codon choice and affects protein evolution

Power of deep, all-exon resequencing for discovery of human trait genes

Domains of genome-wide gene expression dysregulation in Down's syndrome

Contribution of inherited mutations in the BRCA2-interacting protein PALB2 to familial breast cancer

Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis

Conservation of trans-acting circuitry during mammalian regulatory evolution

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA.

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

Discovery of functional noncoding elements by digital analysis of chromatin structure

Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana

Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries

Role of DNA Methylation in Modulating Transcription Factor Occupancy

Identification of higher-order functional domains in the human ENCODE regions

CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

High-throughput localization of functional elements by quantitative chromatin profiling