CoolBox: a flexible toolkit for visual analysis of genomics data

pyGenomeTracks: reproducible plots for multivariate genomic data sets

(2020) Lucille Lopez-Delisle et al.   BIOINFORMATICS

HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by 3D genome structure remodeling in cervical cancer

(2020) Canhui Cao et al.   Journal of Genetics and Genomics

A supervised learning framework for chromatin loop detection in genome-wide contact maps

(2020) Tarik J. Salameh et al.   Nature Communications

Cell-type-specific 3D epigenomes in the developing human cortex

(2020) Michael Song et al.   NATURE

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

(2020) M. Ryan Corces et al.   NATURE GENETICS

tagHi-C Reveals 3D Chromatin Architecture Dynamics during Mouse Hematopoiesis

(2020) Chao Zhang et al.   Cell Reports

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

Selfish: discovery of differential chromatin interactions via a self-similarity measure

(2019) Abbas Roayaei Ardakany et al.   BIOINFORMATICS

WashU Epigenome Browser update 2019

(2019) Daofeng Li et al.   NUCLEIC ACIDS RESEARCH

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps

(2017) Rajendra Kumar et al.   NUCLEIC ACIDS RESEARCH

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

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

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

ChIP-based methods for the identification of long-range chromatin interactions

(2009) Melissa J. Fullwood et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

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

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

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES