Nawaf Alomran

The paper shows that TAD hierarchy restricts LTR activation, and its loss in cancer allows LTRs to act as alternative promoters, driving oncogene activation and transcriptional diversity.

SCReadCounts estimates cell-level SNVs from scRNA-seq data, enabling mutation analysis and downstream applications in cancer and other studies.

scReQTL correlates SNVs to gene expression in single-cell RNA-seq data by using variant allele fraction instead of population genotypes, enabling analysis of rare variants.

GeTallele estimates and compares variant read probabilities in DNA and RNA sequencing data to assess allele asymmetries and genomic events.

The paper estimates allele-specific expression from 10x Genomics scRNA-seq data and finds that most SNVs are bi-allelic at higher read thresholds, with intronic SNVs showing more monoallelic expression.

RsQTL identifies splicing quantitative trait loci by correlating variant allele fractions with splicing patterns in RNA-seq data from human tissues.

The paper introduces ReQTL, an eQTL analysis method using RNA genetic variation instead of DNA genotypes, showing high performance in identifying molecular associations from RNA-sequencing data.