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

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, +530

Nature

A comparative encyclopedia of DNA elements in the mouse genome

Feng Yue, Yong Cheng, Alessandra Breschi, +134

Nature

DnaGeneticsGenomic MechanismMolecular BiologyGenomics +22

A map of the cis-regulatory sequences in the mouse genome

Yin Shen, Feng Yue, David McCleary, +8

Nature

Cis-regulatory SequencesTranscriptional RegulationGeneticsGenomic MechanismGene Regulation +8

Topologically associating domains are stable units of replication-timing regulation

Benjamin D. Pope, Tyrone Ryba, Vishnu Dileep, +18

Nature

GeneticsMolecular BiologyGene Regulatory NetworkStable UnitsSynchronization Protocol +19

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Tao Yang, Feipeng Zhang, Galip Gürkan Yardımcı, +5

Genome Research

EngineeringGeneticsStratum-adjusted Correlation CoefficientData PreparationMolecular Biology +26

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions

Yanli Wang, Fan Song, Bo Zhang, +10

Genome biology

GeneticsMolecular BiologyGenomicsBioinformatics DatabaseEpigenetics +21

Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome

Wei Xie, Cathy L. Barr, Audrey Kim, +5

Cell

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

Gary C. Hon, Nisha Rajagopal, Yin Shen, +4

Nature Genetics

Epigenetic MemoryChromatinAdult Mouse TissuesDevelopmental BiologyChromatin Remodeling +10

An encyclopedia of mouse DNA elements (Mouse ENCODE)

J Stamatoyannopoulos, M Snyder, Ross C. Hardison, +83

Genome biology