Ryan Dale

The paper identifies sRNA candidates in B. burgdorferi and maps their regulatory interactions across growth phases, revealing a dynamic RNA-RNA interactome.

The paper identifies ATF2 phosphorylation as a key driver of neuron apoptosis and shows that inhibiting ATF2 protects neurons in culture and in vivo.

This study identifies and validates serum protein biomarkers for Niemann-Pick disease, type C1, showing correlations with disease severity and response to therapy.

This study shows that reducing H3K4 methylation in specific brain regions causes neurodevelopmental disorder-like phenotypes, including seizures, growth issues, and behavioral deficits.

This study identifies and characterizes specialized endothelial cells in zebrafish gills that resemble mammalian lung aerocytes, using single-cell RNA sequencing and advanced imaging techniques.

The paper uses RIL-seq to show that Hfq's rim face is critical for sRNA-mRNA pairing in vivo, while distal and proximal faces have less impact.

The paper analyzes young KRAB-zinc finger gene clusters in mice, showing ERVs drive genetic heterogeneity through recombination and duplication mechanisms.

The paper shows that disrupting chromatin domain boundaries with multiple developmental regulators can cause severe gene dysregulation and developmental defects in mice.

The paper introduces an EpiTag zebrafish transgenic reporter to visualize epigenetic silencing/activation and identifies tissue-specific epigenetic regulatory genes through mutagenesis screening.

The paper uses a novel transgenic reporter to study epigenetic reprogramming during zebrafish fin regeneration, identifying early chromatin remodeling events and key factors required for regeneration.

This paper characterizes the zebrafish meninges using single-cell transcriptomics, identifying a novel cell type essential for brain development.

The paper introduces a zebrafish transgenic line to profile endothelial cell translatomes in vivo, revealing novel genes and expression signatures across adult organs.

This study shows LEDGF is recruited to promoters by MLL1 and recruits RNA Pol II, facilitating HIV-1 integration across gene bodies.

This study shows that loss of Ezh2 in the medial ganglionic eminence (MGE) leads to changes in interneuron fate, morphology, and gene expression.

The paper uses integrated bulk, single-cell, and spatial RNA-seq to uncover the timeline of osteogenic transcriptional programming in embryonic palate development, identifying novel genes and spatial expression patterns involved in palatal fusion.

The paper shows that high affinity enhancer-promoter interactions can bypass CTCF/cohesin insulation and maintain gene expression in some tissues but not others.

The paper shows GATA6 and NANOG bind shared regulatory elements to drive divergent cell fates in mouse blastocysts by modulating chromatin accessibility and transcriptional activation.

The paper characterizes the epigenomic landscape of embryonic mouse forebrain neural progenitors using snATAC-Seq and integrates multi-omics data to reveal region-specific regulatory mechanisms.

This study identifies Grin1 as a key regulator of subtype-specific gene expression in MGE-derived interneurons, linking NMDAR signaling to neurodevelopmental disorders like schizophrenia.

The paper introduces TIARS, a method to detect precise CRISPR/Cas9 edits using restriction-fragment length polymorphisms, and validates it in zebrafish for atp7a gene mutations.

This study identifies OTUD5 as essential for chromatin remodeling during development, showing its role in preventing degradation of chromatin regulators and maintaining proper gene expression networks.

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

The paper presents technologies that make computational reproducibility practical by integrating package management, containerization, and workflow systems.

The paper shows that the LDB1 complex uses CTCF to create specific long-range enhancer interactions in erythroid cells, activating genes like Car2.