Charles G. Danko

pydreg is a Python port of dREG that improves runtime and memory efficiency while maintaining similar performance in identifying active cis-regulatory elements.

The paper introduces a model-based framework to compare promoter-proximal pausing dynamics across biological contexts, revealing kinetic and distributional variations in pausing.

The paper develops CGAP-HMM and a voting system to improve transcription unit annotation from run-on and sequencing data, showing significant performance gains over existing methods.

This study identifies new regulators of heat hormesis in C. elegans through transcriptomic and chromatin accessibility analysis, revealing tissue-specific responses and conserved factors involved in stress resilience and longevity.

The paper identifies candidate causal SNPs and target genes in CD4+ T cells for juvenile idiopathic arthritis using GWAS data, chromatin accessibility, and functional assays.

This study shows that JQ1 disrupts meiotic prophase I in male mice, leading to reversible infertility, suggesting a potential non-hormonal contraceptive strategy.

This study shows that training deep learning models on functional genomic data with matched personal genomes improves variant effect prediction.

The paper identifies disease-driving SNPs in JIA risk haplotypes using functional genomic data and genotyping, and links them to target genes through chromatin interactions.

The paper introduces CLIPNET, a deep learning model that predicts transcription initiation with single nucleotide resolution from DNA sequences, revealing core promoter motifs and non-additive interactions between activators and promoters.

This paper introduces dHICA, a deep learning framework that predicts histone modifications using chromatin accessibility and DNA sequences, outperforming existing methods and enabling downstream applications.

This study investigates enhancer-promoter contact architecture and communication, finding that RNA polymerase II and PARP1 activity stabilize these contacts.

This study identifies a GDNF-RET-EGR1 positive feedback loop that promotes tamoxifen resistance in breast cancer by upregulating cyclin D1.

This study identifies Playrr, a lncRNA that regulates Pitx2 dosage and protects against cardiac arrhythmias by modulating cardiac gene expression and atrial substrate.

The paper investigates how A-MYB and BRDT regulate RNA polymerase II pause release during meiotic prophase I, linking transcriptional bursts to chromatin changes and recombination.

This study uses genetic variation in mice to show how DNA sequence affects RNA Polymerase II positioning and transcription dynamics across the genome.

The paper shows that RNA Pol II pausing is essential for proper pluripotency transitions in mouse embryos by maintaining balance between gene expression states.

The paper examines evolutionary changes in ANTXR2 expression in humans, finding regulatory changes and recent positive selection linked to adaptation to anthrax disease.

The paper predicts enhancer activity in sea urchin embryos using chromatin accessibility, transcription, and Pol II data, finding Pol II distribution is the best predictor for promoter-overlapping elements.

The paper introduces a method to uncover transcriptionally active regions in scRNA-seq data beyond standard gene annotations, improving transcriptome coverage in understudied organisms.

The paper introduces a method to estimate RNA half-lives using PRO-seq and RNA-seq data, finding correlations between RNA stability and splicing, miRNA binding, DNA methylation, and histone modifications.

A precision run-on sequencing (PRO-seq) variant with one streptavidin bead binding and on-bead enzymatic steps yields adapter-ligated cDNA in about 10 h and libraries from 0.05–0.25 × 10^6 cells.

The paper uses machine learning to show that transcription predicts histone marks and chromatin states, and that transcription is required for maintaining active and repressive histone modifications.

The paper develops BayesPrism, a Bayesian method to infer cellular composition and gene expression from bulk RNA-seq using scRNA-seq as prior, revealing tumor-microenvironment interactions across multiple cancer types.

This study shows that chromatin conformation remains stable during heat shock-induced transcriptional changes in human and Drosophila cells.

AlleleHMM identifies allele-specific differences in genomic marks using a hidden Markov model, outperforming existing methods in simulated and real data.

The paper introduces an improved dREG implementation for identifying transcription initiation regions using PRO-seq data, showing higher accuracy, resolution, and efficiency.

This paper introduces DART-seq, a method that enables multiplexed amplicon sequencing and transcriptome profiling in single cells, applied to study viral transcripts and B cell immune repertoires.

The paper identifies a conserved DNase-I footprinting pattern across human mtDNA, suggesting a regulated protein-DNA organization involved in mtDNA transcription.