H3K9 trimethylation in active chromatin restricts the usage of functional CTCF sites in SINE B2 repeats

Genome folding through loop extrusion by SMC complexes

(2021) Iain F. Davidson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A first exon termination checkpoint preferentially suppresses extragenic transcription

(2021) Liv M. I. Austenaa et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Complete loss of H3K9 methylation dissolves mouse heterochromatin organization

(2021) Thomas Montavon et al.   Nature Communications

The Histone Methyltransferase SETDB1 Controls T Helper Cell Lineage Integrity by Repressing Endogenous Retroviruses

(2019) Véronique Adoue et al.   IMMUNITY

HiChIRP reveals RNA-associated chromosome conformation

(2019) Maxwell R. Mumbach et al.   NATURE METHODS

Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells

(2019) Federico Comoglio et al.   GENES & DEVELOPMENT

Roles and regulation of histone methylation in animal development

(2019) Ashwini Jambhekar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Accurate loop calling for 3D genomic data with cLoops

(2019) Yaqiang Cao et al.   BIOINFORMATICS

The ChAHP Complex Counteracts Chromatin Looping at CTCF Sites that Emerged from SINE Expansions in Mouse

(2019) Lucas J.T. Kaaij et al.   CELL

Epigenome editing strategies for the functional annotation of CTCF insulators

(2019) Daniel R. Tarjan et al.   Nature Communications

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

(2018) Verena M. Link et al.   CELL

Co-optation of Tandem DNA Repeats for the Maintenance of Mesenchymal Identity

(2018) Chiara Balestrieri et al.   CELL

A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing

(2018) Masaki Kato et al.   Nature Communications

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Activity-dependent neuroprotective protein recruits HP1 and CHD4 to control lineage-specifying genes

(2018) Veronika Ostapcuk et al.   NATURE

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation

(2018) Sergi Cuartero et al.   NATURE IMMUNOLOGY

High constitutive activity of a broad panel of housekeeping and tissue-specificcis-regulatory elements depends on a subset of ETS proteins

(2017) Alessia Curina et al.   GENES & DEVELOPMENT

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain

(2017) Yan Jiang et al.   NATURE GENETICS

CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation

(2016) Matthias Merkenschlager et al.   Annual Review of Genomics and Human Genetics

Setdb1 maintains hematopoietic stem and progenitor cells by restricting the ectopic activation of nonhematopoietic genes

(2016) S. Koide et al.   BLOOD

SRF Co-factors Control the Balance between Cell Proliferation and Contractility

(2016) Francesco Gualdrini et al.   MOLECULAR CELL

Molecular control of activation and priming in macrophages

(2016) Christopher K Glass et al.   NATURE IMMUNOLOGY

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Improved Placement of Multi-mapping Small RNAs

(2016) Nathan R. Johnson et al.   G3-Genes Genomes Genetics

regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests

(2015) Bernat Gel et al.   BIOINFORMATICS

The histone methyltransferase SETDB1 represses endogenous and exogenous retroviruses in B lymphocytes

(2015) Patrick L. Collins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Type I Interferon Induced Epigenetic Regulation of Macrophages Suppresses Innate and Adaptive Immunity in Acute Respiratory Viral Infection

(2015) Danielle N. Kroetz et al.   PLoS Pathogens

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Setdb1is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells

(2014) Sheng Liu et al.   GENES & DEVELOPMENT

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

(2014) Iros Barozzi et al.   MOLECULAR CELL

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

The methyltransferase Setdb2 mediates virus-induced susceptibility to bacterial superinfection

(2014) Christopher Schliehe et al.   NATURE IMMUNOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

CATCH: a randomised clinical trial comparing long-term tinzaparin versus warfarin for treatment of acute venous thromboembolism in cancer patients

(2013) Agnes YY Lee et al.   BMC CANCER

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

(2011) Mohammad M. Karimi et al.   Cell Stem Cell

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Identification and Characterization of Enhancers Controlling the Inflammatory Gene Expression Program in Macrophages

(2010) Serena Ghisletti et al.   IMMUNITY

CLLD8/KMT1F Is a Lysine Methyltransferase That Is Important for Chromosome Segregation

(2010) Claire Falandry et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Embryonic stem cells use ZFP809 to silence retroviral DNAs

(2009) Daniel Wolf et al.   NATURE

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

(2009) E. Lieberman-Aiden et al.   SCIENCE

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

(2008) Vania Parelho et al.   CELL

Endogenous retroviruses

(2008) C. Stocking et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY