Jonas Ibn-Salem

The paper introduces k4neo, a tool that computes tumor specificity of transcript variants by k-mer indexing of healthy tissue RNA-seq data, identifying tumor-specific antigens across multiple cancer cohorts.

This paper introduces splice2neo, a tool to identify tumor-specific splice junctions from somatic mutations, which can generate neoantigen candidates for immunotherapy.

This study analyzes the transcriptome of Lytechinus variegatus during embryonic and larval development, identifying four temporally distinct phases of gene expression.

The paper introduces 7C, a method using ChIP-seq data to predict chromatin loops with high resolution and applies it to identify loop-associated genes and candidate factors.

The paper investigates the evolutionary conservation of TADs and finds that TAD boundaries are enriched with rearrangement breakpoints, while TADs show conserved gene expression patterns.