Hjörleifur Einarsson

The human RNA-DNA interactome is cell type-specific and dynamic

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.

Mapping enhancer-gene regulatory interactions from single-cell data

The paper introduces scE2G models to predict enhancer-gene regulatory interactions from single-cell data and demonstrates their performance across multiple cell types and perturbations.

Time-resolved inference of gene regulatory networks underlying human cranial neural crest development suggests novel risk genes for orofacial clefting.

Mapping active cis-regulatory elements from transcription initiation events

The paper introduces nucCAGE and PRIME to identify active cis-regulatory elements with high sensitivity and applies them to create a cell-type-resolved CRE atlas.

Genome-wide rules of transcription factor cooperativity revealed through in silico binding site ablation

The paper introduces DeepCompARE, an in silico ablation framework to analyze TF cooperativity, finding most TF motifs are independent with defined synergy and redundancy effects.

MYC enhancer invasion promotes prognostic cancer type-specific gene programs through an epigenetic switch

The paper shows MYC enhances cancer-specific gene programs by inducing an epigenetic switch that promotes RNAPII recruitment to enhancers.

Promoter sequence and architecture determine expression variability and confer robustness to genetic variants

The paper examines how promoter sequence and transcription start site architecture influence expression variability and genetic variant effects in human genes.