Yulia A. Medvedeva

Knockdown of the long non-coding RNA DNAAF3-AS1 activates the p53 pathway and remodels the H3K36me3 landscape

This study shows that knocking down DNAAF3-AS1 reduces gene-body H3K36me3, activates the p53 pathway, and alters promoter usage in apoptosis-related genes.

HiMoRNA and RNA-Chrom integration: Chromatin-Associated LncRNAs in Genome-Wide Epigenetic Regulation

The paper integrates HiMoRNA and RNA-Chrom resources to generate hypotheses about lncRNA epigenetic regulation mechanisms using experimentally supported RNA-chromatin interaction data.

Hobotnica: exploring molecular signature quality

Hobotnica estimates molecular signature quality by assessing their ability to stratify data and assign significance scores for comparing different groups.

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

RADICL-seq maps genome-wide RNA-chromatin interactions in intact nuclei, revealing general and cell type-specific patterns of transcript occupancy and the role of transcription in chromatin structure.

Transcriptome-Wide Prediction Of lncRNA-RNA Interactions By A Thermodynamics Algorithm

The paper introduces ASSA, a computational pipeline that predicts RNA-RNA interactions by combining sequence alignment and thermodynamics, outperforming existing tools.

CpG traffic lights are markers of regulatory regions in humans

The paper identifies CpG traffic lights as markers of regulatory regions by showing their correlation with gene expression and evolutionary conservation.