Sarah Djebali

The paper studies the evolution of regulatory chromatin contacts in duplicated genes using Hi-C data, finding faster divergence in chromatin contacts compared to expression patterns.

The paper identifies stage-specific regulatory variants in pig skeletal muscle by analyzing chromatin accessibility, molecular QTLs, and GWAS data across prenatal and postnatal stages.

The paper integrates tissue-specific epigenetic annotations into genomic predictions of gene expression in three pig breeds, improving eQTL mapping interpretability but facing challenges in cross-breed predictions.

The paper profiles RNA-seq from porcine intestinal organoids and tissues to assess their retention of regional identity and animal-specific molecular signatures.

This paper discusses the adoption of Nextflow and nf-core frameworks to standardize bioinformatics pipelines, improving collaboration and interoperability across research communities.

The paper analyzes single-cell transcriptomic and epigenomic data from porcine blastocysts to identify gene regulatory dynamics in embryonic and extra-embryonic lineages during development.

This study assesses the progress and limitations of polygenic risk score prediction accuracy for common diseases, showing diminishing returns from recent GWAS and highlighting the need for broader variant coverage.

This study shows that high-fiber maternal diets alter gene expression and chromatin accessibility in fetuses and piglets, improving metabolic health and immune tolerance.

The paper introduces tools to efficiently index and query annotations in pangenome graphs using GAF format, demonstrating applications on human pangenome data.

The paper evaluates two functional link methods for identifying enhancer/gene relationships using benchmark data and finds neither performs best, highlighting the need for reliable genome-wide reference data.

The paper identifies five major cell types based on transcriptional programs in human tissues and shows their composition correlates with tissue morphology and disease.

The paper annotates transcriptomes and chromatin structures in liver and T cells from four livestock species using RNA-seq, ATAC-seq, and Hi-C, revealing conserved regulatory elements and genome organization patterns.

This study compares the epigenomes of neutrophils and monocytes to identify regulatory elements and chromatin states, revealing differences in enhancer activity and DNA methylation.

ChimPipe identifies chimeric transcripts from RNA-seq data with high accuracy, detecting both fusion genes and transcription-induced chimeras with better sensitivity and precision than existing tools.

The paper analyzes RNA-seq data from multiple mouse tissues to identify genes with conserved expression patterns across species and cell types, revealing evolutionary constraints in gene expression.