Jessica Severin

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

This study maps transcription start sites and active enhancers in Galleria mellonella larvae during fungal infection and treatment using LQ-ssCAGE.

The paper performs knockdown of 200 lncRNAs in human iPS cells, identifies 36 with growth inhibition, and finds molecular phenotypes in 29.3% of cases, with higher agreement in molecular than cell growth phenotypes across cell types.

The paper investigates somatic recombination of Alu and L1 repeat elements in human genomes, finding tissue-specific patterns and links to neurodegenerative diseases.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

This paper introduces sc-end5-seq and SCAFE to profile transcribed cis-regulatory elements in single cells, showing tCREs improve prediction of CRE interactions and disease heritability.

The paper identifies cis-interacting lncRNAs and their targets using RNA-chromatin and Hi-C data across 18 human cell types.

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

The paper investigates transcription initiation at polyT short tandem repeats (STRs) using CAGE data and develops a deep learning model to predict STR-associated transcription with high accuracy.

C1 CAGE detects transcription start sites and enhancer activity in lung cancer cells, revealing subpopulations with distinct responses to TGF-β and enhancer RNA dynamics.

The paper enhances the FANTOM5 expression atlas by associating gene-orphan promoter regions with their transcripts using CAGEscan.