Article-Journal

FreeHi-C Spike-in Simulations for Benchmarking Differential Chromatin Interaction Detection

High-throughput genome-wide chromatin conformation capture assay (Hi-C) is routinely used to profile long-range genomic interactions …

Zheng Y , Zhou P, Keleş S

Single-cell CUTTag analysis of chromatin modifications in differentiation and tumor progression

Methods for quantifying gene expression1 and chromatin accessibility2 in single cells are well established, but single-cell analysis of …

Wu S, Furlan S, Mihalas A, Kaya-Okur H, Feroze H, Emerson S, Zheng Y , Carson K, Cimino P, Keene C, Holland E, Sarthy J, Gottardo R, Ahmad K, Henikoff S, Patel A

Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder

Recent advances in consortium-scale genome-wide association studies (GWAS) have highlighted the involvement of common genetic variants …

Huang K, Wu Y, Shin J, Zheng Y , Siahpirani A, Lin Y, Ni Z, Chen J, You J, Keleş S, Wang D, Roy S, Lu Q

Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naïve diffuse midline glioma models

Background: Diffuse midline gliomas (DMGs), including diffuse intrinsic pontine gliomas (DIPGs), have a dismal prognosis, with less …

Vitanza N, Biery M, Myers C, Ferguson E, Zheng Y , Girard E, Przystal J, Park G, Noll A, Pakiam F, Winter C, Morris S, Sarthy J, Cole B, Leary S, Crane C, Lieberman N, Mueller S, Nazarian J, Gottardo R, Brusniak M, Mhyre A, Olson J

Discovering How Heme Controls Genome Function Through Heme-omics

Protein ensembles control genome function by establishing, maintaining, and deconstructing cell-type-specific chromosomal landscapes. A …

Liao R, Zheng Y , Liu X, Zhang Y, Seim G, Tanimura N, Wilson G, Hematti P, Coon J, Fan J, Xu J, Keleş S, Bresnick E

Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context …

The ENCODE Project Consortium, Admin

Perspectives on ENCODE

The ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ

CUTTag Data Processing and Analysis Tutorial

A comprehensive tutorial for processing and analyzing CUT&Tag data, with detailed protocols and best practices. This protocol has …

Zheng Y , Ahmad K, Henikoff K

FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation

The ability to simulate high-throughput chromatin conformation (Hi-C) data is foundational for benchmarking Hi-C data analysis methods. …

Zheng Y , Keleş S

Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies

Current Hi-C analysis approaches are unable to account for reads that align to multiple locations, and hence underestimate biological …

Zheng Y , Ay F, Keleş S