Catherine Do

A developmentally regulated long-range enhancer-promoter contact mediates human neural development

The paper identifies a developmentally regulated long-range enhancer-promoter contact that is critical for SOX2 expression and neuroectodermal differentiation in human neural development.

Persistent chromatin alterations and gene expression reprogramming follow widespread DNA damage in glioblastoma

This study shows that DNA damage in glioblastoma cells leads to long-term chromatin changes and gene expression reprogramming, affecting cellular function and tumor outcomes.

R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription

The paper maps R-loop landscapes in the developing human brain and shows their role in neural differentiation and gene expression programs.

Chromatin architecture and physical constriction cooperate in phenotype switching and cancer cell dissemination

This study shows that chromatin architecture and physical constriction together drive phenotype switching and metastasis in melanoma by altering CTCF positioning and heterochromatin structure.

A targetable developmental program co-regulates angiogenesis and immune evasion

This study identifies HOXD13 as a driver of a developmental program in melanoma that promotes angiogenesis and suppresses T-cell infiltration through a gene regulatory axis involving VEGFA, SEMA3A, and CD73.

Phasing single-molecule nano-NOMe-seq reveals chromatin state heterogeneity in the context of transcription and long-range interactions

The paper uses nano-NOMe-seq to phase single-molecule chromatin states and link them to transcriptional activity, revealing heterogeneity in enhancer-promoter interactions.

mtgRNA-db: An annotated database of multi-target CRISPR-Cas9 guide-RNAs in the human genome

The paper creates a database of multi-target CRISPR-Cas9 guide-RNAs with on- and off-target scores and provides a web tool for selecting these guide-RNAs.

Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation

The paper investigates how CTCF mutations affect chromatin accessibility, cohesin binding, and gene regulation through multivariate modeling and mutant perturbations.

The coordination between CTCF, cohesin and TFs impacts nucleosome repositioning and chromatin insulation to define state specific 3D chromatin folding

The paper investigates how CTCF, cohesin, and TFs influence nucleosome repositioning and chromatin insulation across cell states using mouse and human data.

Epigenetic changes regulating the epithelial-mesenchymal transition in human trophoblast differentiation

The paper identifies an epithelial-mesenchymal transition (EMT) mechanism in human trophoblast differentiation, linking DNA methylation changes to gene expression and invasion capacity.

Genetic Ethnicity and Hypertension Epistatic Interaction Underlying Racial Disparities in US Multiple Myeloma Susceptibility

The paper identifies an epistatic interaction between genetic ethnicity and hypertension that explains racial disparities in multiple myeloma risk among Black and mixed-ancestry individuals.

Improving allele-specific epigenomic signal coverage by 10-fold using Hidden Markov Modeling and Machine Learning

This paper improves allele-specific epigenomic signal coverage by 10-fold using variational hidden Markov modeling and machine learning, demonstrating it on DNA methylation data.

Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs

The paper maps allele-specific DNA methylation in normal and cancer tissues, identifying disease-associated regulatory SNPs that are missed by other methods.

CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation

CloudASM provides an efficient cloud-based pipeline for quantifying allele-specific DNA methylation by leveraging Google Cloud Computing infrastructure.

Genetic variants influence on the placenta regulatory landscape

The paper investigates how genetic variants affect gene expression and DNA methylation in human placentas, revealing interaction profiles and providing a reference for future studies.