Imad Abugessaisa

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 evaluates the impact of different Cell Ranger versions on single-cell gene expression data, finding significant variations in cell barcode processing, gene expression, and clustering results.

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

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

The paper uses single-cell RNA sequencing and C1 CAGE to identify distinct phases of pluripotency during the naive-to-primed transition in mice.

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

The paper introduces SkewC, a method to identify poor quality cells in scRNA-seq by analyzing gene coverage skewness, and validates it across 37,993 cells from 15 protocols.

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.

The paper generates a single-cell RNA-seq dataset of HeLa cells labeled with Fucci reporters and provides an open workflow for data processing and quality control.