Identification of Replication Timing Domains Using DNN-HMM

Transcription Factor Highly Occupied Target (HOT) Regions of 145 Cell Lines

CpG island mediated linear and spatial gene partitioning (other data sets)

Implications of CpG islands on chromosomal architectures and modes of global gene regulation

Compute the Significant Interactions of Hi-C data through HOMER

The repressive genome compartment is established early in the cell cycle before forming the lamina associated domains II (re-analysis)

The landscape of A-to-I RNA editome from 462 individuals human genomes

Transcriptional responses to RTS,S induced vaccination in controlled human malaria infection studies

The landscape of A-to-I RNA editome in mouse embryonic development

Epigenomic and Topological Mechanisms Regulate Transcriptional Programs in Hepatocellular Carcinoma Cells

Hi-C ES and neocortex from Bonev et al. 2017

DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS [HiC reanalysis]

Annotation- and Batch Effect Correction in TCGA IsomiR Expression Data [Third-party re-analysis]

PLK1 inhibition selectively induces apoptosis in ARID1A deficient cells through uncoupling of oxygen consumption from ATP production -- DATA HAVE BEEN MOVED TO GSE193942

Induction of broadly reactive influenza antibodies increases susceptibility to autoimmunity

DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain

Hi-C ES and neocortex from Bonev et al. 2017 on mm39

K562 and human brain transcriptomes, and various epigenomes from K562 and human/mouse brain curated from public databases and re-analyzed for comparison with the single-stranded DNA open-chromatin detected by CHEX-seq

Twins: A deep learning method for replicate-based conformation contact map analysis.

hictk: blazing fast toolkit to work with .hic and .cool files