Publications by Vincent Roland Julien Gardeux

Related publications (28)

Live-seq enables temporal transcriptomic recording of single cells

Orane Josiane Guillaume-Gentil, Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Wouter Jozef L Saelens, Pernille Yde Rainer, Wanze Chen, Magda Zachara

Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity(1). However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Liv ...

NATURE PORTFOLIO2022

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

Bart Deplancke, Vincent Roland Julien Gardeux, Michael Vincent Frochaux

Background The evolution of embryological development has long been characterized by deep conservation. In animal development, the phylotypic stage in mid-embryogenesis is more conserved than either early or late stages among species within the same phylum ...

2020

Transcriptomic profiling of murine GnRH neurons reveals developmental trajectories linked to human reproduction and infertility

Bart Deplancke, Vincent Roland Julien Gardeux, Daniel Alpern, Julie Marie Russeil

Rationale: Neurons producing Gonadotropin-Releasing Hormone (GnRH) are essential for human reproduction and have to migrate from nose to brain during prenatal life. Impaired GnRH neuron biology results in alterations of the reproductive axis, including del ...

2025

Extensive tissue-specific expression variation and novel regulators underlying circadian behavior

Matteo Dal Peraro, Bart Deplancke, Vincent Roland Julien Gardeux, Julie Marie Russeil, Alessio Prunotto, Maria Litovchenko, Michael Vincent Frochaux, Antonio Carlos Alves Meireles Filho, Brian Dennis Hollis, Roel Paulus Josephus Bevers, Virginie Sandra Braman

Natural genetic variation affects circadian rhythms across the evolutionary tree, but the underlying molecular mechanisms are poorly understood. We investigated population-level, molecular circadian clock variation by generating >700 tissue-specific transc ...

2021

Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

Bart Deplancke, Vincent Roland Julien Gardeux, Guido Van Mierlo, Wouter Jozef L Saelens, Olga Pushkarev, Judith Franziska Kribelbauer

Background: Interactions among cis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been developed to map these interactions genome-wide, including those relying on interindividual epigenomic variation to identify ...

2024

A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation

Freddy Radtke, Bart Deplancke, Ute Koch, Vincent Roland Julien Gardeux, Riccardo Dainese, Daniel Alpern, Jörn Pezoldt, Julie Marie Russeil, Maria Litovchenko, Gerard Llimos Aubach, Judith Franziska Kribelbauer

Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of h ...

Nature Portfolio2022

DGRPool, a web tool leveraging harmonized Drosophila Genetic Reference Panel phenotyping data for the study of complex traits

Romain Guy Daniel Rochepeau, Emily Rosschaert, Bart Deplancke, Vincent Roland Julien Gardeux

Genome-wide association studies have advanced our understanding of complex traits, but studying how a GWAS variant can affect a specific trait in the human population remains challenging due to environmental variability. Drosophila melanogaster is in this ...

2024

Dissecting the brown adipogenic regulatory network using integrative genomics

Bart Deplancke, Vincent Roland Julien Gardeux, Daniel Alpern, Sunil Kumar Raghav, Petra Catalina Schwalie, Julie Marie Russeil, Wanze Chen, Johannes Julius Bues, Rachana Narendra Pradhan

Brown adipocytes regulate energy expenditure via mitochondrial uncoupling, which makes them attractive therapeutic targets to tackle obesity. However, the regulatory mechanisms underlying brown adipogenesis are still poorly understood. To address this, we ...

Springer Nature2017

ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data

Bart Deplancke, Vincent Roland Julien Gardeux, Petra Catalina Schwalie, Adrian Shajkofci

Motivation: Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research gr ...

Oxford University Press2017

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle

Bart Deplancke, David Michael Suter, Vincent Roland Julien Gardeux, Cédric Deluz, Torgil Elias Friman, Antonio Carlos Alves Meireles Filho, Subashika Govindan

The pioneer activity of transcription factors allows for opening of inaccessible regulatory elements and has been extensively studied in the context of cellular differentiation and reprogramming. In contrast, the function of pioneer activity in self-renewi ...

2019

A human omentum-specific mesothelial-like stromal population inhibits adipogenesis through IGFBP2 secretion

Marie Denise Rumpler, Bart Deplancke, Vincent Roland Julien Gardeux, Daniel Alpern, Jörn Pezoldt, Julie Marie Russeil, Guido Van Mierlo, Wouter Jozef L Saelens, Pernille Yde Rainer, Magda Zachara, Radiana Ferrero

Although several mouse and human adipose SVF cellular subpopulations have by now been identified, we still lack an understanding of the cellular and functional variability of adipose stem and progenitor cell (ASPC) populations across human fat depots. To a ...

Cell Press2024

Postnatal expansion of mesenteric lymph node stromal cells towards reticular and CD34(+) stromal cell subsets

Bart Deplancke, Vincent Roland Julien Gardeux, Julie Marie Russeil, Maria Litovchenko, Guido Van Mierlo, Wanze Chen, Jörn Pezoldt, Marjan Biocanin

Gut-draining mesenteric lymph nodes (LN) provide the framework to shape intestinal adaptive immune responses. Based on the transcriptional signatures established by our previous work, the composition and immunomodulatory function of LN stromal cells (SC) v ...

Nature Portfolio2022

The Genetics of Transcription Factor DNA Binding Variation

Bart Deplancke, Vincent Roland Julien Gardeux, Daniel Alpern

Most complex trait-associated variants are located in non-coding regulatory regions of the genome, where they have been shown to disrupt transcription factor (TF)-DNA binding motifs. Variable TF-DNA interactions are therefore increasingly considered as key ...

Elsevier2016

Predicting standardized uptake value of brown adipose tissue from CT scans using convolutional neural networks

Bart Deplancke, Vincent Roland Julien Gardeux

The standard method for identifying active Brown Adipose Tissue (BAT) is [18F]-Fluorodeoxyglucose ([18F]-FDG) PET/CT imaging, which is costly and exposes patients to radiation, making it impractical for population studies. These issues can be addressed wit ...

Nature Research2024

Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly

Bart Deplancke, Vincent Roland Julien Gardeux, Fabrice David, Wouter Jozef L Saelens

For more than 100 years, the fruit fly Drosophila melanogaster has been one of the most studied model organisms. Here, we present a single-cell atlas of the adult fly, Tabula Drosophilae, that includes 580,000 nuclei from 15 individually dissected sexed ti ...

American Association for the Advancement of Science2022

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

Bart Deplancke, Maroun Bou Sleiman, Vincent Roland Julien Gardeux, Riccardo Dainese, Maria Litovchenko, Michael Vincent Frochaux, Dani Osman, Brian Dennis Hollis, Virginie Sandra Braman

Background: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understan ...

2020

Sex-dependent and sex-independent regulatory systems of size variation in natural populations

Bart Deplancke, Vincent Roland Julien Gardeux, Ernst Hafen

Size of organs/organisms is a polygenic trait. Many of the growth-regulatory genes constitute conserved growth signaling pathways. However, how these multiple genes are orchestrated at the systems level to attain the natural variation in size including sex ...

2019

Profiling of Single-Cell Transcriptomes

Bart Deplancke, Vincent Roland Julien Gardeux, Wanze Chen, Antonio Carlos Alves Meireles Filho

Complex biological systems are composed of multiple cell types whose transcriptional activity can vary due to differences in cell state, environmental stimulation or intrinsic programs. Conventional bulk analysis methods capture the average transcriptional ...

2017

Epigenomic landscape defines immuno-modulatory properties across lymph node stromal cell subsets

Bart Deplancke, Vincent Roland Julien Gardeux, Maria Litovchenko, Jörn Pezoldt

WILEY2019

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Daniel Alpern, Antonio Carlos Alves Meireles Filho, Gerard Llimos Aubach

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molec ...

National Academy of Sciences2020