High-resolution TADs reveal DNA sequences underlying genome organization in flies

Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts

(2017) Pau Pascual-Garcia et al.   MOLECULAR CELL

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach

(2017) Raphaël Mourad et al.   PLoS Computational Biology

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture

(2016) Caelin Cubeñas-Potts et al.   NUCLEIC ACIDS RESEARCH

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

A CTCF Code for 3D Genome Architecture

(2015) Michael H. Nichols et al.   CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

Interaction between TBP and Condensin Drives the Organization and Faithful Segregation of Mitotic Chromosomes

(2015) Osamu Iwasaki et al.   MOLECULAR CELL

High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila

(2015) Fidel Ramírez et al.   MOLECULAR CELL

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments

(2015) Dhawal Jain et al.   NUCLEIC ACIDS RESEARCH

Standardizing chromatin research: a simple and universal method for ChIP-seq

(2015) Laura Arrigoni et al.   NUCLEIC ACIDS RESEARCH

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

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

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

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

(2014) Suhas S.P. Rao et al.   CELL

Ibf1 and Ibf2 are novel CP190-interacting proteins required for insulator function

(2014) S. Cuartero et al.   EMBO JOURNAL

Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin

(2014) Oksana Maksimenko et al.   GENOME RESEARCH

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

(2014) Muhammad A. Zabidi et al.   NATURE

Motif-based analysis of large nucleotide data sets using MEME-ChIP

(2014) Wenxiu Ma et al.   Nature Protocols

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Insulator function and topological domain border strength scale with architectural protein occupancy

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle

(2013) B Gurudatta et al.   CELL CYCLE

Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor

(2013) Jian Li et al.   EMBO JOURNAL

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Nature and function of insulator protein binding sites in the Drosophila genome

(2012) Y. B. Schwartz et al.   GENOME RESEARCH

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

(2012) K. Van Bortle et al.   GENOME RESEARCH

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

(2012) S. G. Landt et al.   GENOME RESEARCH

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

(2012) Maxim Imakaev et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Self-organization of domain structures by DNA-loop-extruding enzymes

(2012) E. Alipour et al.   NUCLEIC ACIDS RESEARCH

The NSL Complex Regulates Housekeeping Genes in Drosophila

(2012) Kin Chung Lam et al.   PLoS Genetics

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Regulation of Chromatin Organization and Inducible Gene Expression by a Drosophila Insulator

(2011) Ashley M. Wood et al.   MOLECULAR CELL

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

(2011) Morgane Thomas-Chollier et al.   Nature Protocols

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset

(2011) Christian Feller et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

(2008) S. Cuddapah et al.   GENOME RESEARCH

BEAF Regulates Cell-Cycle Genes through the Controlled Deposition of H3K9 Methylation Marks into Its Conserved Dual-Core Binding Sites

(2008) Eldon Emberly et al.   PLOS BIOLOGY