Olivier Poirion

Mapping the genetic landscape establishing a tumor immune microenvironment favorable for anti-PD-1 response in mice and humans

The paper identifies host genetic factors influencing anti-PD-1 response in mice and humans by mapping QTLs and finding a core gene network with prognostic value in human tumors.

Enhlink infers distal and context-specific enhancer-promoter linkages

Enhlink infers enhancer-promoter linkages using scATAC-seq data and outperforms existing methods, revealing a super-enhancer regulating striatal neuron markers.

A comparative atlas of single-cell chromatin accessibility in the human brain

The paper constructs a single-cell chromatin accessibility atlas of the human brain, identifies cell-type-specific regulatory elements, and develops models to predict regulatory function of disease risk variants.

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

The paper identifies gene-CRE pairs in mouse brain cells by integrating single-cell transcriptomes and epigenomes, controlling for gene co-expression.

A cell atlas of chromatin accessibility across 25 adult human tissues

The paper creates a chromatin accessibility atlas across 25 adult human tissues, identifying over 750,000 cis-regulatory elements and linking them to gene regulatory programs and disease-associated variants.

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

The paper compares cellular diversity in the primary motor cortex across human, marmoset, and mouse using single-nucleus transcriptomics and epigenomics, finding conserved cell types and species-specific adaptations.

An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum

The paper identifies 491,818 candidate cis regulatory elements in adult mouse brain sub-types and links them to target genes and transcriptional regulators involved in various pathways.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

The paper creates a comprehensive atlas of mouse primary motor cortex cell types using integrated transcriptomic and epigenomic data from over 600,000 samples.

DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution

The paper constructs a DNA methylation atlas of the mouse brain at single-cell resolution, revealing epigenetic diversity and spatial organization of neuronal subtypes.

DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data

DeepProg predicts patient survival subtypes using multi-omics data, identifying two optimal subtypes and improving risk-stratification across multiple cancers.

Gene regulatory networks underlying human microglia maturation

This study defines age-specific brain environmental factors driving microglia phenotypes through transcriptomic and epigenomic analysis of human fetal and postnatal microglia.

GranatumX: A community engaging, modularized and flexible webtool for single-cell analysis

GranatumX provides a web-based platform for single-cell RNA sequencing analysis, enabling biologists to use bioinformatics tools through a graphical interface and allowing developers to integrate their own tools into customizable pipelines.

Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association

The paper defines cardiac cell type-specific cis-regulatory elements and links disease risk variants to these elements in human hearts.

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Across 1,176,683 airway and lung cells from 22 datasets, ACE2 rises with age, in males and in smokers' multiciliated cells, and is lowest in young children.

Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection

The paper uses single nucleus ATAC-seq and RNA-seq to show age-related changes in chromatin accessibility and gene expression linked to SARS-CoV-2 entry genes in human lung cells.

DeepImpute: an accurate, fast and scalable deep neural network method to impute single-cell RNA-Seq data

DeepImpute is a deep neural network method for imputing single-cell RNA-seq data, showing better accuracy and scalability than existing methods.

Single-cell chromatin accessibility analysis of mammary gland development reveals cell state transcriptional regulators and cellular lineage relationships

Using Single Nucleotide Variations in Single-Cell RNA-Seq to Identify Subpopulations and Genotype-phenotype Linkage

The paper introduces SSrGE, a method using SNVs from scRNA-seq to identify subpopulations and link genotype-phenotype relationships, showing better accuracy than gene expression.

Neo-formation of chromosomes in bacteria

The paper distinguishes bacterial replicons into chromosomes, plasmids, and neochromosomes, showing neochromosomes arise from fission of multi-replicon molecules.

Multi-modal meta-analysis of 1494 hepatocellular carcinoma samples reveals vast impacts of consensus driver genes on phenotypes

This study identifies 10 consensus driver genes in HCC across six cohorts and shows their associations with mRNA transcriptomes, patient survival, and demographic factors.

Deep Learning based multi-omics integration robustly predicts survival in liver cancer

This paper develops a deep learning model integrating multi-omics data to predict survival in liver cancer, identifying two patient subgroups with significant survival differences.