Latifa Karim

A near telomere-to-telomere phased reference assembly for the male mountain gorilla

The paper presents a high-quality, near telomere-to-telomere, haplotype-phased reference genome for a male mountain gorilla using long-read sequencing technologies.

Integrated cell type-specific analysis of blood and gut identifies matching eQTL for 140 IBD risk loci and entrectinib as possible repurposing candidate.

The paper identifies 140 IBD risk loci with matching eQTL in blood and gut tissues and suggests entrectinib as a potential repurposing drug.

Benchmarking phasing software with a whole-genome sequenced cattle pedigree

This paper benchmarks phasing software using a whole-genome sequenced cattle pedigree, finding ShapeIT4.1 and Beagle5.2 to be the most accurate for long haplotype segments.

A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle

The paper identifies a 12 kb multi-allelic CNV associated with mastitis resistance in dairy cattle by linking it to increased GC expression and a cis-regulatory enhancer.

SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole genome sequencing of tank milk.

The paper presents a SNP-based method to deconvolute biological mixtures using whole genome sequencing, applied to detect subclinical mastitis in cows via tank milk analysis.

Combined analysis of single cell RNA-Seq and ATAC-Seq data reveals putative regulatory toggles operating in native and iPS-derived retina.

The paper analyzes single-cell RNA-Seq and ATAC-Seq data from native and iPSC-derived murine retina to identify regulatory toggles involved in differentiation.

Transcriptome wide analysis of natural antisense transcripts shows their potential role in breast cancer.

The paper analyzes natural antisense transcripts (NATs) in breast cancer using RNA sequencing to identify their potential role in gene regulation and survival outcomes.

Frequency of mosaicism points towards mutation-prone early cleavage cell divisions.

Cattle pedigrees indicate up to ~30% of de novo mutations in male gametes and ~50% in female gametes arise during early cleavage divisions, leaving parental mosaicism and sibling sharing.