Jesse R. Dixon

Escape from replicative crisis and immortalization precedes complex genome evolution

The paper shows that escaping replicative crisis and achieving immortality precedes complex genome evolution in cancer cells.

Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation

The paper maps 3D genome organization and DNA methylation across 86,689 single nuclei from 16 human tissues, revealing cell-type-specific variations and discrepancies between methylation and chromatin structure.

Genome-wide in vivo dynamics of cohesin-mediated loop extrusion and its role in transcription activation

This study investigates cohesin-mediated loop extrusion dynamics and its role in transcription activation by depleting NIPBL in vivo.

Oncogenic drivers shape the tumor microenvironment in human gliomas

This study investigates how oncogenic mutations in gliomas influence the tumor microenvironment through integrative multiomic and spatial transcriptomic analysis of glioma samples.

A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis

This study identifies a STAG2-PAXIP1/PAGR1 tumor-suppressive axis in lung cancer by showing their combined role in suppressing oncogenic KRAS-driven tumorigenesis.

Heterogeneity in chromatin structure drives core regulatory pathways in B-cell Acute Lymphoblastic Leukemia

This study identifies how chromatin structure heterogeneity in B-ALL correlates with transcriptional subtypes and developmental stages, revealing its role in disease progression.

Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain

The paper generates a single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain, identifying methylation patterns and regulatory networks across cell types and brain regions.

Epigenomic and chromosomal architectural reconfiguration in developing human frontal cortex and hippocampus

The paper investigates epigenomic and 3D chromatin conformation changes in human frontal cortex and hippocampus development using sn-m3C-seq, finding distinct chromatin conformations in neurons and glial cells and linking risk variants to regulatory regions.

Deciphering the Evolutionary History of Complex Rearrangements in Head and Neck Cancer Patients Using Multi-Omic Approach

This study uses a multi-omic approach to analyze complex genomic rearrangements in head and neck cancers, identifying HPV-mediated instability and enhancer hijacking as drivers of oncogene overexpression.

Single nucleus multi-omics links human cortical cell regulatory genome diversity to disease risk variants

The paper develops a multi-omic single-nucleus sequencing method and framework to analyze regulatory genome diversity in human cortical cells and link it to disease risk variants.

DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution

The paper constructs a DNA methylation atlas of the mouse brain at single-cell resolution, revealing epigenetic diversity and spatial organization of neuronal subtypes.

Incorporation of a nucleoside analog maps genome repair sites in post-mitotic human neurons

The paper identifies DNA repair hotspots in post-mitotic human neurons linked to genes essential for their identity and function.

Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells

This study shows that chromatin organization remains largely intact in mouse embryonic stem cells after acute CTCF depletion, despite reduced cell growth and changes in chromatin loop interactions and cohesin occupancy.

CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells

This study shows that CTCF depletion in mESCs weakens TAD boundaries and INs but only affects a small subset of enhancer-promoter contacts, highlighting CTCF's role in promoting long-range gene regulation.

Spatial Genome Organization as a Framework for Somatic Alterations in Human Cancer

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

cis-Regulatory Chromatin Contacts in Neural Cells Reveal Contributions of Genetic Variants to Complex Neurological Disorders

The paper identifies cis-regulatory chromatin contacts in neural cells and links them to genetic variants associated with complex neurological disorders.

Comparing 3D genome organization in multiple species using Phylo-HMRF

This paper introduces Phylo-HMRF, a probabilistic model to analyze 3D genome organization across species using Hi-C data, revealing evolutionary patterns in chromatin structure.

HiCluster: A Robust Single-Cell Hi-C Clustering Method Based on Convolution and Random Walk

HiCluster improves clustering of low coverage single-cell Hi-C data by imputing using linear convolution and random walk, revealing TAD-like structures consistent with bulk data.

Single-cell multi-omic profiling of chromatin conformation and DNA methylome

The paper develops sn-m3C-seq to profile chromatin conformation and DNA methylation in single nuclei, enabling high-resolution cell-type classification and chromatin map reconstruction in mice.

Process-specific somatic mutation distributions vary with three-dimensional genome structure

The paper examines how somatic mutation distributions vary across chromatin folding domains in cancer genomes, revealing distinct patterns associated with different mutational processes.

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.