Elias T. Friman

The paper identifies severe COVID-19 risk variants that modulate enhancer activity in lung cells using functional assays and deep learning.

The paper shows that loop extrusion and enhancer cooperativity independently affect enhancer-driven transcription through synthetic gene activation experiments.

This study benchmarks deconvolution methods for inferring tissue and cell type-of-origin from plasma cfRNA, showing method and reference variability impact performance.

The paper identifies H3K115ac enrichment at fragile nucleosomes in promoters and enhancers, suggesting its role in nucleosome destabilization and regulatory element identification.

The paper shows that disease-associated variants in alternative protein isoforms can cause structural mutations, emphasizing the need to consider tissue-specific expression and full-length transcripts in variant interpretation.

The paper investigates how estrogen receptor activation affects enhancer-promoter contact frequencies and spatial proximity, finding they change independently during gene activation.

The paper identifies functional non-coding genetic variants by combining DNase footprints and enhancer RNAs, introducing a framework called FINDER to prioritize variants for functional validation.

The paper identifies ultra-long-range chromatin interactions between active regulatory elements in vertebrate and invertebrate genomes, showing they are driven by three distinct mechanisms independent of RNA polymerase II and some cofactors.

The paper shows that disrupting PRC1 condensates with 1,6-hexandiol reversibly disrupts polycomb chromatin domains and loops in mouse embryonic stem cells.

The paper investigates oncogene expression from extrachromosomal DNA in glioblastoma and finds that copy number amplification, not spatial clustering, drives high transcriptional output.

This study investigates how OCT4 and SOX2 regulate chromatin accessibility in mouse embryonic stem cells across the cell cycle, showing their independent and cooperative roles in maintaining pluripotency.

The paper shows that fluctuations in OCT4 and SOX2 levels influence cell fate decisions by affecting chromatin accessibility at differentiation enhancers.

The paper quantifies how SMAD4 and SMAD2 dynamics relate to ctgf gene activation kinetics in single cells using live imaging and temporal analysis.

The paper shows that mitotic chromosome binding of transcription factors correlates with their interphase properties and impact on chromatin accessibility.