Jelena M. Telenius

The paper shows that super-enhancers function directionally and orientation-dependently, unlike regular enhancers, by analyzing the β-globin super-enhancer.

The paper identifies Wnt-responsive cis-regulatory elements that coordinate Paupar-Pax6 expression in neuronal cells through chromatin interactions.

The paper examines how dynamic chromatin boundaries around the Runx1 gene influence its expression during hematopoietic development in mice.

DeepC predicts chromatin interactions from DNA sequence using deep learning and transfer learning, generalizing across cell types and resolutions.

The paper shows that actively transcribed genes can function as chromatin boundary elements, similar to CTCF-bound sites, by stalling chromatin loop extrusion.

The paper studies chromatin architecture changes during mouse erythroid differentiation using Tiled-C and shows enhancer-promoter interactions form during differentiation, not before gene expression.

The paper introduces a new method, NuTi Capture-C, that improves high-resolution chromosome conformation capture by reducing noise and increasing sequencing content, enabling reproducible genome-wide interaction profiles.

CaptureCompendium provides software tools to simplify the design, analysis, and visualization of 3C experiments, addressing the need for specialized bioinformatics skills in genome folding studies.

The paper develops a platform combining ATAC-seq, DNaseI footprints, NG Capture-C, and machine learning to identify causal variants and genes for polygenic human traits.

The paper investigates promoter competition in the -globin domain using chromatin interaction data, finding that promoters interact simultaneously with a super-enhancer rather than competing.

This study shows that enhancers primarily regulate gene expression by promoting transcription initiation rather than by affecting RNA polymerase II pausing.

The paper reconstructs the global neural crest gene regulatory network in vivo using epigenomic and single-cell transcriptome data combined with genome engineering.

The paper identifies a distinct class of enhancers in leukemia cells that depend on H3K79 methylation and shows that DOT1L inhibition disrupts their function.

The paper develops Tri-C, a single-cell 3C method, to reveal dynamic chromatin interactions and regulatory hubs in mammalian cells.

NGseqBasic is a single-command tool for processing and visualizing ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data, providing quality control and UCSC data hub integration.