Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg

Nature Methods

Long-read SequencingSequence AssemblyNatural SciencesComputational BiologyMolecular Biology +5

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang, Tao Liu, Clifford A. Meyer, +8

Genome biology

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

Suhas S.P. Rao, Miriam Huntley, Neva C. Durand, +8

Cell

ChromatinFunctional GenomicsChromatin StructureChromatin RemodelingNatural Sciences +12

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

Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams, +16

Science

Structural BioinformaticsGeneticsGenomic MechanismMolecular BiologyGenomics +19

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

Fidel Ramírez, Devon Ryan, Björn Grüning, +6

Nucleic Acids Research

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Jesse R. Dixon, Siddarth Selvaraj, Feng Yue, +6

Nature

ChromatinFunctional GenomicsChromatin StructureChromatin RemodelingChromatin Interactions +13

The MEME Suite

Timothy L. Bailey, James Johnson, Charles E. Grant, +1

Nucleic Acids Research

EngineeringGeneticsMolecular BiologyGenerative ArtGenomics +19

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

Elphège P. Nora, Bryan R. Lajoie, Edda G. Schulz, +12

Nature

BiologySystems BiologyDevelopmental BiologyCell DivisionSpatial Partitioning +5

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

Darío G. Lupiáñez, Katerina Kraft, Verena Heinrich, +19

Cell

ChromatinChromatin StructureChromatin RemodelingNatural SciencesEpigenetic Change +9

Formation of Chromosomal Domains by Loop Extrusion

Geoffrey Fudenberg, Maxim Imakaev, Carolyn Lu, +3

Cell Reports