Ross C. Hardison

RETROFIT: REFERENCE-FREE DECONVOLUTION OF CELL-TYPE MIXTURES IN SPATIAL TRANSCRIPTOMICS

RETROFIT deconvolves cell-type mixtures in spatial transcriptomics without requiring references, outperforming existing methods and matching reference-based approaches when references are imperfect.

LDB1-dependent enhancer connectivity defines T-cell leukemia identities and masks metabolic vulnerabilities

The paper identifies LDB1-dependent enhancer connectivity as critical for T-cell leukemia subtypes and reveals a metabolic vulnerability exploitable by statins.

Dissecting polycomb complexes for enhanced fetal hemoglobin production

This study uses CRISPR-Cas9 to identify EZH2 mutations that reactivate fetal hemoglobin without compromising cell fitness, showing potential for treating sickle cell disease and beta-thalassemia.

Single-stranded DNA binding proteins are essential components of the architectural LDB1 protein complex

This study shows SSBP3 is essential for LDB1-mediated chromatin looping and transcription, and stabilizes LDB1 homodimers.

Divergence between transcriptomes and chromatin accessibility during differentiation from a bipotential progenitor cell population to erythroblasts and megakaryocytes

The paper compares transcriptomes and chromatin accessibility in MEP, ERY, and MEG cells to reveal divergence in gene regulation during differentiation.

LDB1 establishes multi-enhancer networks to regulate gene expression

This study shows LDB1 directly promotes enhancer-promoter loops and organizes multi-enhancer networks to activate transcription, independent of CTCF, cohesin, or YY1.

JOnTADS: a unified caller for TADs and stripes in Hi-C data

JOnTADS identifies TADs and stripes in Hi-C data across different experimental contexts, improving robustness and computational efficiency.

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

This study identifies conserved and species-specific cis-regulatory elements in human and mouse blood cells using integrative epigenomic analysis and clustering.

Genome folding principles revealed in condensin-depleted mitotic chromosomes

This study investigates genome folding in condensin-depleted mitotic chromosomes, revealing compartmentalization mechanisms distinct from interphase.

Domain adaptive neural networks improvecross-species prediction of transcription factor binding

This study improves cross-species prediction of transcription factor binding by addressing domain shifts caused by species-specific repeats using domain adaptive neural networks.

CTCF blocks anti-sense transcription initiation at divergent gene promoters

The paper shows CTCF suppresses antisense transcription at divergent promoters without affecting sense transcription, using a combination of genetic and molecular techniques.

CTCF and transcription influence chromatin structure re-configuration after mitosis

This study investigates how CTCF and transcription influence chromatin structure reconfiguration after mitosis, revealing their distinct roles in boundary formation and gene domain establishment.

Effects of sheared chromatin length on ChIP-seq quality and sensitivity

This study investigates how chromatin shearing affects ChIP-seq quality and shows that sonication levels significantly impact signal quality and specificity for different transcription factors.

S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types

S3V2-IDEAS normalizes, denoises, and integrates epigenomic data across cell types to identify epigenetic states and signal intensity patterns.

High-dimensional association detection in large scale genomic data

This paper introduces CLIMB, a statistical method for detecting high-dimensional associations in genomic data, showing improved precision and biological relevance in hematopoietic datasets.

ZNF410 uniquely activates the NuRD component CHD4 to silence fetal hemoglobin expression

The paper identifies ZNF410 as a highly specific transcriptional activator in erythroid cells that regulates CHD4 and fetal hemoglobin expression.

Detecting local changes in chromatin architecture with false discovery control

The paper introduces a spatial modeling approach for detecting differentially interacting genomic regions in Hi-C data with false discovery control, demonstrating its ability to reveal biologically meaningful changes in chromatin architecture.

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

The paper quantifies the mouse embryo transcriptome from E10.5 to birth using whole-tissue and single-cell RNA-seq, identifying key gene expression patterns and cell types.

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

The paper integrates epigenomic and transcriptomic data from mouse hematopoiesis to identify regulatory elements and their dynamics across cell types.

S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data

S3norm improves normalization of epigenomic data by simultaneously adjusting sequencing depth and signal-to-noise ratio, enhancing the detection of biological variation.

Hierarchical Domain Structure Reveals the Divergence of Activity among TADs and Boundaries

OnTAD identifies hierarchical TAD structures from Hi-C data with improved accuracy and speed, revealing new insights into TAD organization and gene regulation.

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of mouse hematopoietic cells

The paper integrates GATA transcription factors and epigenomes in mouse hematopoietic cells using IDEAS to map regulatory landscapes and identify candidate cis-regulatory elements.

Re-configuration of Chromatin Structure During the Mitosis-G1 Phase Transition

The paper examines how chromatin structures re-establish after mitosis using Hi-C, showing rapid compartment formation and dynamics of CTCF and cohesin binding.

Snapshot: clustering and visualizing epigenetic history during cell differentiation

Snapshot generates hierarchical visualizations of epigenetic features along cell differentiation hierarchies using epigenomic data from the VISION project.

Transcriptional burst initiation and polymerase pause release are key control points of transcriptional regulation

The paper develops a framework to link Pol II ChIP-seq and single-cell data to transcriptional step rates, showing burst initiation and pause release are key regulated steps, while polymerase binding is not.

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

The paper introduces a web-based browser for visualizing 3D genome organization and chromatin interactions, enabling integration with other omics data to study gene regulation.

An Integrative Framework For Detecting Structural Variations In Cancer Genomes

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

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

HiCRep assesses Hi-C data reproducibility using a stratum-adjusted correlation coefficient, improving accuracy over existing methods.

Accurate and Reproducible Functional Maps in 127 Human Cell Types via 2D Genome Segmentation

This paper presents an improved functional annotation map for 127 human cell types using the IDEAS method, showing higher accuracy than the Roadmap Epigenomics consortium's map.

A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition

The paper tracks Pol II occupancy genome-wide during mitosis-G1 transition and finds a transcriptional spike at the mitosis-G1 transition that exceeds later G1 levels.