J. Stamatoyannopoulos

发表

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

Mark J. P. Chaisson, Peter H. Sudmant, E. Eichler, 2014, Nature.

Mapping and sequencing of structural variation from eight human genomes

Joshua M. Korn, Nancy F. Hansen, D. Altshuler, 2008, Nature.

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

William Stafford Noble, Nancy R. Zhang, Stephen C. J. Parker, 2007, Nature.

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Shane J. Neph, Fidencio J. Neri, Alex P. Reynolds, 2012, Science.

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

Shane J. Neph, Alex P. Reynolds, R. Sandstrom, 2012, Cell.

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

I. Amit, A. Gnirke, E. Lander, 2011 .

Comprehensive analysis of the chromatin landscape in Drosophila

Lovelace J. Luquette, Manolis Kellis, R. Sandstrom, 2010, Nature.

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

Shane J. Neph, Alex P. Reynolds, R. Sandstrom, 2014, Cell reports.

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

Marc D. Perry, James B. Brown, Timothy E. Reddy, 2012, Genome research.

The NIH Roadmap Epigenomics Mapping Consortium

T. Mikkelsen, E. Lander, Manolis Kellis, 2010, Nature Biotechnology.

The accessible chromatin landscape of the human genome

Nathan C. Sheffield, Shane J. Neph, Matthew T. Maurano, 2012, Nature.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

The ENCODE (ENCyclopedia Of DNA Elements) Project

Paul T. Groth, William Stafford Noble, Colin N. Dewey, 2004, Science.

eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data

Andrew E. Teschendorff, Shane J. Neph, John A. Stamatoyannopoulos, 2019, Bioinform..

Quantifying similarity between motifs

William Stafford Noble, J. Stamatoyannopoulos, T. Bailey, 2007, Genome Biology.

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

Alex P. Reynolds, J. Stamatoyannopoulos, E. Haugen, 2013, Science.

Probing DNA shape and methylation state on a genomic scale with DNase I

R. Sandstrom, J. Stamatoyannopoulos, Tianyin Zhou, 2013, Proceedings of the National Academy of Sciences.

Integrative analysis of 111 reference human epigenomes

Michael Q. Zhang, Nicholas A. Sinnott-Armstrong, Michael T. McManus, 2015, Nature.

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

William Stafford Noble, Shane J. Neph, Alex P. Reynolds, 2009, Nature Methods.

APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions.

Steven A. Roberts, J. Stamatoyannopoulos, S. Sunyaev, 2015, Cell reports.

Automated mapping of large-scale chromatin structure in ENCODE

William Stafford Noble, Heng Lian, Robert E. Thurman, 2008, Bioinform..

Discovery of functional noncoding elements by digital analysis of chromatin structure.

J. Stamatoyannopoulos, M. Hawrylycz, M. Dorschner, 2004, Proceedings of the National Academy of Sciences of the United States of America.

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

William Stafford Noble, J. Stamatoyannopoulos, R. Thurman, 2007, Genome research.

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

William Stafford Noble, J. Stamatoyannopoulos, M. Hawrylycz, 2006, Nature Methods.

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

J. Stamatoyannopoulos, M. Hawrylycz, M. Dorschner, 2004, Proceedings of the National Academy of Sciences of the United States of America.

High-throughput localization of functional elements by quantitative chromatin profiling

J. Stamatoyannopoulos, M. Hawrylycz, J. Goldy, 2004, Nature Methods.

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

J. Stamatoyannopoulos, M. Eisen, P. Sabo, 2011, Genome Biology.

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

James B. Brown, P. Bickel, J. Stamatoyannopoulos, 2012, Proceedings of the National Academy of Sciences.

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

R. Sandstrom, J. Stamatoyannopoulos, S. Celniker, 2011, Genome Biology.

Defining functional DNA elements in the human genome

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

J. Stamatoyannopoulos, M. Eisen, P. Sabo, 2011, PLoS genetics.

Nucleosome positioning signals in genomic DNA.

William Stafford Noble, Z. Weng, J. Stamatoyannopoulos, 2007, Genome research.

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2011, PLoS biology.

An expansive human regulatory lexicon encoded in transcription factor footprints

Shane J. Neph, Matthew T. Maurano, Alex P. Reynolds, 2012, Nature.

DNA methylation status predicts cell type‐specific enhancer activity

J. Stamatoyannopoulos, R. Thurman, P. Sabo, 2011, The EMBO journal.

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

Alex P. Reynolds, R. Sandstrom, J. Stamatoyannopoulos, 2015, Cell.

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

Matthew T. Maurano, J. Stamatoyannopoulos, M. Maurano, 2012, PLoS genetics.

A Quantitative Proteome Map of the Human Body

Christopher D. Brown, Katherine H. Huang, Christopher M. Lee, 2019, Cell.

Integrative detection and analysis of structural variation in cancer genomes

William Stafford Noble, Jesse R. Dixon, Royden A. Clark, 2018, Nature Genetics.

An encyclopedia of mouse DNA elements (Mouse ENCODE)

Philip Cayting, Katrina Learned, Daniel Blankenberg, 2012, Genome Biology.

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

Paz Polak, John A. Stamatoyannopoulos, Shamil R. Sunyaev, 2015, Nature.

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

J. Stamatoyannopoulos, R. Thurman, P. Sabo, 2011, Nature Genetics.

Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding.

Myong-Hee Sung, Saskia Trump, J. Stamatoyannopoulos, 2011, Molecular cell.

Genetic origins of the Minoans and Mycenaeans

J. Stamatoyannopoulos, D. Reich, N. Patterson, 2017, Nature.

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

Stylianos E. Antonarakis, Laurent Farinelli, Richard S. Sandstrom, 2014, Nature.

A comparative encyclopedia of DNA elements in the mouse genome

Shane J. Neph, Dmitri D. Pervouchine, Matthew D. Rasmussen, 2014, Nature.

DNase I hypersensitivity mapping, genomic footprinting, and transcription factor networks in plants

R. Sandstrom, J. Stamatoyannopoulos, Alessandra M. Sullivan, 2015 .

Human mutation rate associated with DNA replication timing

J. Stamatoyannopoulos, R. Thurman, I. Adzhubei, 2009, Nature Genetics.

Personal and population genomics of human regulatory variation

Shane J. Neph, Matthew T. Maurano, Benjamin Vernot, 2012, Genome research.

Dynamic DNA methylation across diverse human cell lines and tissues

Timothy E. Reddy, D. Absher, J. Stamatoyannopoulos, 2013, Genome research.

An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level

Matthew C. Canver, J. Stamatoyannopoulos, S. Orkin, 2013, Science.

Functional footprinting of regulatory DNA

Yuri R. Bendaña, J. Stamatoyannopoulos, S. Orkin, 2015, Nature Methods.

Index and biological spectrum of human DNase I hypersensitive sites

Fidencio J. Neri, Alex P. Reynolds, R. Sandstrom, 2020, Nature.

Index and biological spectrum of accessible DNA elements in the human genome

Alex P. Reynolds, R. Sandstrom, J. Stamatoyannopoulos, 2019, bioRxiv.

Integrative Meta-Analysis of Differential Gene Expression in Acute Myeloid Leukemia

J. Stamatoyannopoulos, B. Miller, 2010, PloS one.

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

C. Baker, E. Eichler, John Huddleston, 2016, American journal of human genetics.

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair

J. Stamatoyannopoulos, G. Getz, M. Lawrence, 2013, Nature Biotechnology.

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Jonathan M. Mudge, J. Harrow, A. Frankish, 2012, PloS one.

Widespread plasticity in CTCF occupancy linked to DNA methylation

Matthew T. Maurano, R. Sandstrom, J. Stamatoyannopoulos, 2012, Genome research.

Role of DNA Methylation in Modulating Transcription Factor Occupancy.

Matthew T. Maurano, J. Stamatoyannopoulos, A. Shafer, 2015, Cell reports.

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

J. Stamatoyannopoulos, S. Sunyaev, G. Kryukov, 2009, Proceedings of the National Academy of Sciences.

The Human Mitochondrial Transcriptome

Tim R. Mercer, Shane J. Neph, John A. Stamatoyannopoulos, 2011, Cell.

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

Shane J. Neph, Robert E. Thurman, John A. Stamatoyannopoulos, 2013, Cell.

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

Thomas Cremer, Volker J. Schmid, Felix Kraus, 2017, Epigenetics & Chromatin.

Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells.

Michael O. Dorschner, John A. Stamatoyannopoulos, Stuart H. Orkin, 2008, Genes & development.

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

Boris Lenhard, Nathan C. Sheffield, Nathan C Sheffield, 2013, Genome research.

Genome-scale mapping of DNase I hypersensitivity.

Alex P. Reynolds, Jeff Vierstra, J. Stamatoyannopoulos, 2013, Current protocols in molecular biology.

What does our genome encode?

J. Stamatoyannopoulos, 2012, Genome research.

Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells

Shane J. Neph, A. Reymond, J. Stamatoyannopoulos, 2008, Genome Biology.

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

William Stafford Noble, J. Stamatoyannopoulos, R. Thurman, 2007 .

Identification of cellular context sensitive regulatory variation in mouse genomes

Matthew T. Maurano, J. Stamatoyannopoulos, M. Groudine, 2020, bioRxiv.

Mapping the Functional Genome

J. Stamatoyannopoulos, Hao Wang, S. John, 2013 .

Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

J. Stamatoyannopoulos, M. Creyghton, Seung-Min Yang, 2015, Genome Biology.

Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding

J. Stamatoyannopoulos, H. Bravo, R. Chatterjee, 2013, BMC Genomics.

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene

John A. Stamatoyannopoulos, Ian Dunham, Job Dekker, 2010, Nucleic acids research.

NF‐E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta‐globin locus control region.

J. Stamatoyannopoulos, C. Lowrey, T. Joyce, 1995, The EMBO journal.

Global reference mapping and dynamics of human transcription factor footprints

Fidencio J. Neri, Alex P. Reynolds, R. Sandstrom, 2020, bioRxiv.

52 Genetic Loci Influencing Myocardial Mass.

Christian Gieger, Thomas Meitinger, Manolis Kellis, 2016, Journal of the American College of Cardiology.

Leveraging pleiotropy to discover and interpret GWAS results for sleep-associated traits

Sina A. Gharib, J. Stamatoyannopoulos, S. Sunyaev, 2019, bioRxiv.

A vast resource of allelic expression data spanning human tissues

Christopher M. Lee, Helen M. Moore, Bryan M. Gillard, 2020, Genome Biology.

DNA methylation modulates transcription factor occupancy chiefly at sites of high intrinsic cell-type variability

J. Stamatoyannopoulos, A. Shafer, Hao Wang, 2014, bioRxiv.

2p15-p16.1 microdeletions encompassing and proximal to BCL11A are associated with elevated HbF in addition to neurologic impairment.

J. Stamatoyannopoulos, A. Migliaccio, P. Prontera, 2015, Blood.

Challenges and Approaches to Genotyping Repetitive DNA

J. Stamatoyannopoulos, C. Queitsch, R. Waterston, 2019, G3: Genes, Genomes, Genetics.

Epigenetic Modifications and Chromosome Conformations of the Beta Globin Locus throughout Development

J. Stamatoyannopoulos, Hao Wang, Xiangdong Fang, 2013, Stem Cell Reviews and Reports.

A Genome-wide Map of Aav-mediated Human Gene Targeting Hhs Public Access

R. Sandstrom, J. Stamatoyannopoulos, Chia-Lin Wei, 2022 .

Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome.

Reid F. Thompson, Kevin W. Lau, R. Sandstrom, 2011, Genome research.

The diverse genetic origins of a Classical period Greek army

J. Stamatoyannopoulos, D. Reich, N. Patterson, 2022, Proceedings of the National Academy of Sciences of the United States of America.

Integrative analysis of 111 reference human epigenomes Open

David Haussler, Michael Q. Zhang, Gerald T. Quon, 2015, Nat..

Epigenomics at the tipping point. Foreword.

J. Stamatoyannopoulos, I. Dunham, 2008, Pharmacogenomics.

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing

Michael O Dorschner, R. Sandstrom, J. Stamatoyannopoulos, 2009, Proceedings of the National Academy of Sciences.

Patterns of Growth and Decline in Lung Function in Persistent Childhood Asthma.

D. Postma, J. Stamatoyannopoulos, E. Silverman, 2016, The New England journal of medicine.

Method Quantifying similarity between motifs

William Stafford Noble, J. Stamatoyannopoulos, T. Bailey, 2007 .

Epigenetic Modifications and Chromosome Conformations of the Beta Globin Locus throughout Development

J. Stamatoyannopoulos, Xiangdong Fang, H. Cao, 2013, Stem Cell Reviews and Reports.

Position independence and proper developmental control of gamma-globin gene expression require both a 5' locus control region and a downstream sequence element

J. Stamatoyannopoulos, Qiliang Li, Q. Li, 1994, Molecular and cellular biology.

Genetic history of the population of Crete

J. Stamatoyannopoulos, K. Kidd, P. Paschou, 2019, Annals of human genetics.

Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks

J. Stamatoyannopoulos, K. Kidd, P. Paschou, 2017, European Journal of Human Genetics.

Genomic footprinting

Jeff Vierstra, J. Stamatoyannopoulos, John A Stamatoyannopoulos, 2016, Nature Methods.

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

Ty C. Voss, John A. Stamatoyannopoulos, Paul M. Yen, 2011, Cell.

Maritime route of colonization of Europe

J. Stamatoyannopoulos, K. Kidd, P. Paschou, 2014, Proceedings of the National Academy of Sciences.

A European population in Minoan Bronze Age Crete

J. Stamatoyannopoulos, P. Paschou, P. Navas, 2013, Nature Communications.

Topologically associating domains are stable units of replication-timing regulation

Yanli Wang, Tamer Kahveci, Yong Cheng, 2014, Nature.

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

Nicola J. Rinaldi, Emily K. Tsang, Ellen T. Gelfand, 2017, Nature Genetics.

The genomics of gene expression.

J. Stamatoyannopoulos, John A Stamatoyannopoulos, 2004, Genomics.

Tissue context determines the penetrance of regulatory DNA variation

Matthew T. Maurano, J. Stamatoyannopoulos, M. Groudine, 2021, Nature Communications.

Therapeutic approaches to hemoglobin switching in treatment of hemoglobinopathies.

J. Stamatoyannopoulos, A. Nienhuis, J A Stamatoyannopoulos, 1992, Annual review of medicine.

Mapping and Dynamics of Regulatory DNA in Maturing Arabidopsis thaliana Siliques

Shane J. Neph, R. Sandstrom, J. Stamatoyannopoulos, 2019, Front. Plant Sci..

Mapping and dynamics of regulatory DNA in maturing seeds

Shane J. Neph, R. Sandstrom, J. Stamatoyannopoulos, 2018, bioRxiv.

Chromatin dynamics during hematopoiesis reveal discrete regulatory modules instructing differentiation

J. Stamatoyannopoulos, M. Yiangou, M. Iwata, 2020, bioRxiv.

Regions Bound by 119 Human Transcription Factors Sequence Features and Chromatin Structure around the Genomic Material Supplemental

William Stafford Noble, Nathan C. Sheffield, Eurie L. Hong, 2012 .

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

Fidencio J. Neri, E. Eichler, R. Sandstrom, 2014, Science.

The impact of rare variation on gene expression across tissues

Gao Wang, Mary Goldman, Brian Craft, 2016, Nature.

Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

J. Stamatoyannopoulos, P. Meltzer, S. Davis, 2008, Molecular cell.

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

J. Stamatoyannopoulos, R. Thurman, P. Sabo, 2011, Genome research.

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

Ty C. Voss, Peter J. Sabo, Robert E. Thurman, 2011 .

Analysis of Sequence Conservation at Nucleotide Resolution

Mikhail A. Roytberg, John A. Stamatoyannopoulos, Shamil R. Sunyaev, 2007, PLoS Comput. Biol..

Guidelines for investigating causality of sequence variants in human disease

D. G. MacArthur, T. A. Manolio, D. P. Dimmock, 2014, Nature.

Erez Lieberman-Aiden Principles of the Human Genome Comprehensive Mapping of Long-Range Interactions Reveals Folding

I. Amit, A. Gnirke, E. Lander, 2012 .

Human Genome Interactions Reveals Folding Principles of the Comprehensive Mapping of Long-Range

I. Amit, A. Gnirke, E. Lander, 2009 .

Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

Christopher D. Brown, Katherine H. Huang, Christopher M. Lee, 2021, Cell.

Comprehensive characterization of erythroid-specific enhancers in the genomic regions of human Krüppel-like factors

R. Sandstrom, J. Stamatoyannopoulos, P. Sabo, 2013, BMC Genomics.

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

Luca Pinello, Guo-Cheng Yuan, Zhen Shao, 2012, Developmental cell.

Predicting the in vivo signature of human gene regulatory sequence

William Stafford Noble, Robert E. Thurman, John A. Stamatoyannopoulos, 2005, ISMB.

Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults

T. Lumley, J. Stamatoyannopoulos, P. Kwok, 2015, PLoS genetics.

BEDOPS: high-performance genomic feature operations

Richard S. Sandstrom, Shane J. Neph, Robert E. Thurman, 2012, Bioinform..

Predicting Human Nucleosome Occupancy from Primary Sequence

William Stafford Noble, Jonathan H. Dennis, Robert E. Thurman, 2008, PLoS Comput. Biol..

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

Eric Haugen, Matthew T. Maurano, Jeff Vierstra, 2015, Nature Genetics.

Global reference mapping of human transcription factor footprints

Fidencio J. Neri, Alex P. Reynolds, R. Sandstrom, 2020, Nature.

Global Regulatory DNA Potentiation by SMARCA4 Propagates to Selective Gene Expression Programs via Domain-Level Remodeling.

Fidencio J. Neri, R. Sandstrom, J. Stamatoyannopoulos, 2020, Cell reports.

Widely distributed noncoding purifying selection in the human genome

William Stafford Noble, Charles E Grant, William S Noble, 2007, Proceedings of the National Academy of Sciences.

DNA methylation alone does not cause most cell-type selective transcription factor binding

J. Stamatoyannopoulos, A. Shafer, M. Maurano, 2013, Epigenetics & Chromatin.

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

Michael O Dorschner, J. Stamatoyannopoulos, M. Dorschner, 2007, Nature Immunology.

Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

J. Stamatoyannopoulos, M. Creyghton, Seung-Min Yang, 2015, Genome Biology.

Conservation of trans-acting circuitry during mammalian regulatory evolution

Elhanan Borenstein, R. Scott Hansen, Peter J. Sabo, 2014, Nature.

Inflammation-induced repression of chromatin bound by the transcription factor Foxp3 in regulatory T cells

J. Stamatoyannopoulos, A. Rudensky, R. Samstein, 2014, Nature Immunology.

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

Wei Xie, Yan Li, Manolis Kellis, 2013, PLoS Comput. Biol..

A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

Sean Thomas, Gordon Keller, Charles E. Murry, 2012, Cell.

A microbial profiling method for the human microbiota using high-throughput sequencing.

W. L. Ruzzo, R. Sandstrom, J. Stamatoyannopoulos, 2013, Metagenomics.

Taking Stock of Regulatory Variation.

J. Stamatoyannopoulos, M. Maurano, 2015, Cell systems.

locus in ES cells Oct 4 dependence of chromatin structure within the extended Nanog

J. Stamatoyannopoulos, M. Dorschner, S. Orkin, 2007 .

Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification

Shane J. Neph, Alex P. Reynolds, R. Sandstrom, 2012, Cell.

ClampFISH detects individual nucleic-acid molecules using click chemistry based amplification

J. Stamatoyannopoulos, A. Raj, Alessandra M. Sullivan, 2018, Nature Biotechnology.

Integrative detection and analysis of structural variation in cancer genomes

William Stafford Noble, Jesse R. Dixon, Royden A. Clark, 2018, Nature Genetics.

An Integrative Framework for Detecting Structural Variations in Cancer Genomes

William Stafford Noble, Feng Yue, Jesse R. Dixon, 2017, bioRxiv.

DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements

Shane J. Neph, Yijun Ruan, John S Mattick, 2013, Nature Genetics.

Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma.

D. Postma, J. Stamatoyannopoulos, E. Silverman, 2016, American journal of respiratory and critical care medicine.

Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing

J. Stamatoyannopoulos, A. Coulon, C. Chow, 2015, Genome research.

Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution

G. J. Ray, J. Stamatoyannopoulos, D. Tillo, 2015, Genome biology and evolution.

Quantitative dialing of gene expression via precision targeting of KRAB repressor

Alexander J. Federation, R. Sandstrom, J. Stamatoyannopoulos, 2020, bioRxiv.

Single-molecule regulatory architectures captured by chromatin fiber sequencing

J. Stamatoyannopoulos, E. Haugen, A. Stergachis, 2020, Science.

Rapid empirical discovery of optimal peptides for targeted proteomics

Brendan MacLean, Michael J. MacCoss, John A. Stamatoyannopoulos, 2011, Nature Methods.

Atlas and developmental dynamics of mouse DNase I hypersensitive sites

Fidencio J. Neri, Alex P. Reynolds, R. Sandstrom, 2020, bioRxiv.

Myasthenia gravis genome-wide association study implicates AGRN as a risk locus

J. Stamatoyannopoulos, P. Paschou, E. Maltezos, 2021, Journal of Medical Genetics.

Stamatoyannopoulos What does our genome encode ?

J. Stamatoyannopoulos, 2012 .

Transcriptional environment and chromatin architecture interplay dictates globin expression patterns of heterospecific hybrids derived from undifferentiated human embryonic stem cells or from their erythroid progeny.

J. Stamatoyannopoulos, H. Qu, Xiangdong Fang, 2013, Experimental hematology.

Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH

Jeff Vierstra, R. Sandstrom, J. Stamatoyannopoulos, 2013, Nature Methods.

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements

Kyle T. Siebenthall, R. Sandstrom, J. Stamatoyannopoulos, 2015, Epigenetics & Chromatin.

Genome-wide Association Study identifies two novel loci for Gilles de la Tourette Syndrome

H. Stefánsson, J. Stamatoyannopoulos, Y. Worbe, 2021, medRxiv.

Inaccessible LCG Promoters Act as Safeguards to Restrict T Cell Development to Appropriate Notch Signaling Environments

R. Sandstrom, J. Stamatoyannopoulos, I. Bernstein, 2021, Stem cell reports.

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

T. Walsh, M. King, J. Stamatoyannopoulos, 2011, Cancer research.

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

James B. Brown, Timothy E. Reddy, P. Bickel, 2012 .

The fecal microbiome in diverticulitis and asymptomatic diverticulosis: A case-control study in the US

R. Sandstrom, J. Stamatoyannopoulos, L. Strate, 2019 .

Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR.

R. Sandstrom, J. Stamatoyannopoulos, L. Zon, 2012, Developmental biology.

Positively selected enhancer elements endow osteosarcoma cells with metastatic competence

James J. Morrow, J. Stamatoyannopoulos, P. Meltzer, 2017, Nature Medicine.

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

R. Sandstrom, J. Stamatoyannopoulos, M. Dorschner, 2009, Immunity.

Genetic association of long-chain acyl-CoA synthetase 1 variants with fasting glucose, diabetes, and subclinical atherosclerosis[S]

Kyle T. Siebenthall, J. Stamatoyannopoulos, I. Borecki, 2016, Journal of Lipid Research.

Genomic discovery of potent chromatin insulators for human gene therapy

J. Stamatoyannopoulos, P. Navas, G. Stamatoyannopoulos, 2015, Nature Biotechnology.

Gammaretroviral vector integration occurs overwhelmingly within and near DNase hypersensitive sites.

C. L. Li, J. Stamatoyannopoulos, M. Dorschner, 2012, Human gene therapy.

Sheltering of gamma-globin expression from position effects requires both an upstream locus control region and a regulatory element 3' to the A gamma-globin gene

J. Stamatoyannopoulos, Qiliang Li, C. Clegg, 1997, Molecular and cellular biology.

Q Li 3 ' to the A gamma-globin gene . locus control region and a regulatory element position effects requires both an upstream Sheltering of gamma-globin expression from

J. Stamatoyannopoulos, C. Clegg, L. Q, 1996 .

Differences in nanoscale organization of DNase I hypersensitive and insensitive chromatin in single human cells

J. Stamatoyannopoulos, E. Haugen, Eric Rynes, 2021, bioRxiv.

Unsupervised segmentation of continuous genomic data

William Stafford Noble, Robert E. Thurman, John A. Stamatoyannopoulos, 2007, Bioinform..

Inflammation-induced Repression of Foxp3-bound Chromatin in Regulatory T Cells Hhs Public Access Prc2 Represses Foxp3-bound Chromatin during Inflammation On-line Methods Gene Expression Profiling Processing of Raw Sequencing Data Supplementary Material

J. Stamatoyannopoulos, A. Rudensky, R. Samstein, 2022 .

Highly Parallel Quantification and Compartment Localization of Transcription Factors and Nuclear Proteins.

Alexander J. Federation, Gennifer E. Merrihew, Ying S. Ting, 2020, Cell reports.

Quantification of nuclear protein dynamics reveals chromatin remodeling during acute protein degradation

Alexander J. Federation, Gennifer E. Merrihew, Ying S. Ting, 2018, bioRxiv.

Functionally and phenotypically distinct subpopulations of marrow stromal cells are fibroblast in origin and induce different fates in peripheral blood monocytes.

R. Sandstrom, J. Stamatoyannopoulos, J. Delrow, 2014, Stem cells and development.

Positively Selected Enhancer Elements Endow Tumor Cells with Metastatic Competence

James J. Morrow, J. Stamatoyannopoulos, P. Meltzer, 2017, bioRxiv.

Collaborative Regulation of Development but Independent Control of Metabolism by Two Epidermis-specific Transcription Factors in Caenorhabditis elegans*

Hao Wang, Jiaofang Shao, Zhongying Zhao, 2013, The Journal of Biological Chemistry.

De novo design of protein logic gates

Michael C. Jewett, Galen Dods, Hana El-Samad, 2020, Science.

Regulatory DNA keyholes enable specific and persistent multi-gene expression programs in primary T cells without genome modification

David Baker, John A. Stamatoyannopoulos, Zibo Chen, 2020 .

Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease

Nicola J. Rinaldi, Emily K. Tsang, Ellen T. Gelfand, 2017, Nature Genetics.

Polygenic risk scores based on European GWAS correlate to disease prevalence differences around the world

Myson C. Burch, J. Stamatoyannopoulos, P. Paschou, 2021, medRxiv.

A single nucleotide polymorphism of cyclin‐dependent kinase inhibitor 1B (p27Kip1) associated with human vein graft failure affects growth of human venous adventitial cells but not smooth muscle cells

J. Stamatoyannopoulos, E. Wijelath, A. Stergachis, 2018, Journal of vascular surgery.

Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study

J. Stamatoyannopoulos, D. Nickerson, E. Haugen, 2021, medRxiv.

Dielectrophoretic enrichment of low-abundance nanoparticles using a nanotip-concentrator for nanoengineered medicine and biology

Adrian M. Kopacz, Wing Kam Liu, J. Stamatoyannopoulos, 2011 .

Highly sensitive and specific microtip-immunofluorescence sensor for rapid TB diagnosis

J. Stamatoyannopoulos, J. Riley, W. Yeo, 2011 .

Operating on Genomic Ranges Using BEDOPS

Shane J. Neph, John A. Stamatoyannopoulos, Alex P. Reynolds, 2016, Statistical Genomics.

Cross-Platform DNA Encoding for Single-Cell Imaging of Gene Expression.

J. Stamatoyannopoulos, L. True, Xiaohu Gao, 2016, Angewandte Chemie.

Contribution of InheritedMutations in the BRCA 2-Interacting Protein PALB 2 to Familial Breast Cancer

T. Walsh, M. King, J. Stamatoyannopoulos, 2011 .

A thermodynamic approach to PCR primer design

William Stafford Noble, Michael Dorschner, Richard Humbert, 2008, Nucleic acids research.

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters

Volker J Schmid, J. Stamatoyannopoulos, I. Hellmann, 2017, Epigenetics & Chromatin.

Automated validation of polymerase chain reactions using amplicon melting curves

William Stafford Noble, John A. Stamatoyannopoulos, Tobias P. Mann, 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

A Myasthenia Gravis genomewide association study of three cohorts identifies Agrin as a novel risk locus.

J. Stamatoyannopoulos, P. Paschou, E. Maltezos, 2020, medRxiv.

Contribution of InheritedMutations in the BRCA2-Interacting Protein PALB2 to Familial Breast Cancer

T. Walsh, M. King, J. Stamatoyannopoulos, 2011 .

Nucleosome positioning signals in genomic DNA data

William Stafford Noble, Z. Weng, J. Stamatoyannopoulos, 2007 .

Correction: Corrigendum: Positively selected enhancer elements endow osteosarcoma cells with metastatic competence

James J. Morrow, J. Stamatoyannopoulos, P. Meltzer, 2018, Nature Medicine.

Collaborative regulation of development but independent control of metabolism by two epidermis specific transcription factors in C. elegans

J. Stamatoyannopoulos, Zhongying Zhao, Xiaoliang Ren, 2020 .

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

I. Amit, A. Gnirke, E. Lander, 2009, Science.

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

I. Amit, A. Gnirke, E. Lander, 2009, Science.

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Jonathan M. Mudge, J. Harrow, A. Frankish, 2012, PloS one.

Connecting the regulatory genome

J. Stamatoyannopoulos, 2016, Nature Genetics.

Unsupervised segmentation of continuous genomic data

William Stafford Noble, J. Stamatoyannopoulos, B. Schmidt, 2007, Bioinform..

Multi-Scale Correlations in Continuous Genomic Data

William Stafford Noble, Robert E. Thurman, John A. Stamatoyannopoulos, 2007, Pacific Symposium on Biocomputing.

Positively Selected Enhancer Elements Endow Tumor Cells with Metastatic Competence

James J. Morrow, J. Stamatoyannopoulos, P. Meltzer, 2017, bioRxiv.

Patterns of Growth and Decline in Lung Function in Persistent Childhood Asthma.

D. Postma, J. Stamatoyannopoulos, E. Silverman, 2016, The New England journal of medicine.

Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification

Shane J. Neph, Alex P. Reynolds, R. Sandstrom, 2012, Cell.

The NIH Roadmap Epigenomics Mapping Consortium

T. Mikkelsen, E. Lander, Manolis Kellis, 2010, Nature Biotechnology.

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Shane J. Neph, Matthew T. Maurano, Fidencio J. Neri, 2012, Science.

Inflammation-induced repression of Foxp3-bound chromatin in regulatory T cells

J. Stamatoyannopoulos, A. Rudensky, R. Samstein, 2014, Nature Immunology.

DNase I–hypersensitive exons colocalize with promoters and distal regulatory elements

Shane J. Neph, R. Sandstrom, J. Stamatoyannopoulos, 2013, Nature Genetics.

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

Fidencio J. Neri, E. Eichler, R. Sandstrom, 2014, Science.

A comparative encyclopedia of DNA elements in the mouse genome

Mukul S. Bansal, Shane J. Neph, Dmitri D. Pervouchine, 2014, Nature.

Human mutation rate associated with DNA replication timing

J. Stamatoyannopoulos, R. Thurman, I. Adzhubei, 2009, Nature Genetics.

Probing DNA shape and methylation state on a genomic scale with DNase I

R. Sandstrom, J. Stamatoyannopoulos, Tianyin Zhou, 2013, Proceedings of the National Academy of Sciences.

Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR.

R. Sandstrom, J. Stamatoyannopoulos, L. Zon, 2012, Developmental biology.

Genetic association of long-chain acyl-CoA synthetase 1 variants with fasting glucose, diabetes, and subclinical atherosclerosis[S]

Kyle T. Siebenthall, J. Stamatoyannopoulos, I. Borecki, 2016, Journal of Lipid Research.

Genomic discovery of potent chromatin insulators for human gene therapy

Matthew T. Maurano, J. Stamatoyannopoulos, P. Navas, 2015, Nature Biotechnology.

Defining functional DNA elements in the human genome

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

Supporting Online Material Materials and Methods Som Text Comprehensive Mapping of Long-range Interactions Reveals Folding Principles of the Human Genome

I. Amit, A. Gnirke, E. Lander, 2022 .

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome.

Reid F. Thompson, Kevin W. Lau, R. Sandstrom, 2011, Genome research.

ClampFISH detects individual nucleic-acid molecules using click chemistry based amplification

J. Stamatoyannopoulos, A. Raj, Alessandra M. Sullivan, 2018, Nature Biotechnology.