Olivier Harismendy

Multi-omic QTL mapping in early developmental tissues reveals phenotypic and temporal complexity of regulatory variants underlying GWAS loci

The paper identifies multi-omic QTLs in early developmental tissues and shows that GWAS loci often involve complex regulatory variants not captured by eQTLs alone.

Analysis of regulatory network modules in hundreds of human stem cell lines reveals complex epigenetic and genetic factors contribute to pluripotency state differences between subpopulations

The paper identifies regulatory network modules in human stem cells, showing epigenetic and genetic factors influence pluripotency state differences.

eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk

The paper maps eQTLs in fetal-like pancreatic progenitor cells, identifying regulatory variants that influence diabetes risk by affecting gene expression and splicing in early development.

Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease

This study identifies causal genetic variants for cardiac traits by integrating spatiotemporal eQTL analysis with GWAS data, showing stage- and tissue-specific effects.

The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ

The paper creates a breast pre-cancer atlas by analyzing multiple micro-dissected regions from DCIS cases, revealing molecular and micro-environmental diversity and immune states associated with progression risk.

Prevalence of cancer susceptibility variants in patients with multiple Lynch syndrome related cancers

The paper identifies pathogenic variants in Lynch Syndrome genes in patients with multiple cancers and finds higher prevalence of non-LS gene variants in early-onset cases.

Mutational profiling of micro-dissected pre-malignant lesions from archived specimens

This paper develops a method to improve mutational profiling of pre-malignant lesions using degraded FFPE DNA, achieving better coverage and variant calling accuracy.

Ad-Seq, a genome-wide DNA-adduct profiling assay

Ad-Seq maps DNA-adduct locations genome-wide at single-nucleotide resolution, confirming known adduct specificities and showing cisplatin adducts are depleted in active chromatin.

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens

PinAPL-Py provides a user-friendly web application for analyzing CRISPR/Cas9 screening data, offering comprehensive tools and workflows for sequence analysis and gene ranking.

Sharing genetic admixture and diversity of public biomedical datasets

The paper proposes a framework to enrich public biomedical datasets with admixture information and diversity scores, using The Cancer Genome Atlas data to demonstrate its utility.

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.

Pan-Cancer Analysis Reveals Technical Artifacts in The Cancer Genome Atlas (TCGA) Germline Variant Calls

This study identifies technical artifacts in TCGA germline variant calls, showing how batch effects from DNA amplification confound germline-tumor type associations and recommends removing amplified DNA samples.