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Bart Deplancke

Cette personne a quitté l’EPFL

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Publications associées (113)

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Chromatin modules and their implication in genomic organization and gene regulation

Judith Franziska Kribelbauer, Bart Deplancke, Guido Van Mierlo

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

ELSEVIER SCIENCE LONDON2023

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

Olivier Martin, Bart Deplancke, Felix Naef, Jacques Rougemont, Mauro Delorenzi, Nicolas Jean Philippe Guex, Laura Symul

Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide, we gener ...

Public Library Science2012

Mammalian adipogenesis regulator (Areg) cells use retinoic acid signalling to be non- and anti-adipogenic in age-dependent manner

Horia Hashimi, Bart Deplancke, Daniel Alpern, Julie Marie Russeil, Maria Litovchenko, Pernille Yde Rainer, Magda Zachara, Radiana Ferrero

Adipose stem and precursor cells (ASPCs) give rise to adipocytes and determine the composition and plasticity of adipose tissue. Recently, several studies have demonstrated that ASPCs partition into at least three distinct cell subpopulations, including th ...

WILEY2022

Potential Direct Regulators of the Drosophila yellow Gene Identified by Yeast One-Hybrid and RNAi Screens

Bart Deplancke

The regulation of gene expression controls development, and changes in this regulation often contribute to phenotypic evolution. Drosophila pigmentation is a model system for studying evolutionary changes in gene regulation, with differences in expression ...

Genetics Society of America2016

Selective Retrieval of Individual Cells from Microfluidic Arrays Combining Dielectrophoretic Force and Directed Hydrodynamic Flow

Gabriele Gambardella, Bart Deplancke, Carlotta Guiducci, Jörn Pezoldt, Kevin Keim, Pierre-Emmanuel Marie Thiriet

Hydrodynamic-based microfluidic platforms enable single-cell arraying and analysis over time. Despite the advantages of established microfluidic systems, long-term analysis and proliferation of cells selected in such devices require off-chip recovery of ce ...

MDPI2020

Exhaustion of tumor-specific CD8(+) T cells in metastases from melanoma patients

Bart Deplancke, Pedro Romero, Sunil Kumar Raghav

In chronic viral infections, CD8(+) T cells become functionally deficient and display multiple molecular alterations. In contrast, only little is known of self- and tumor-specific CD8(+) T cells from mice and humans. Here we determined molecular profiles o ...

American Society for Clinical Investigation2011

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

Cross-talk between emulsion drops: how are hydrophilic reagents transported across oil phases?

Bart Deplancke, Esther Amstad, Antoine Claude Jean Vian, Marjan Biocanin, Gianluca Nicolas Etienne

Emulsion drops are frequently used as vessels, for example, to conduct biochemical reactions in small volumes or to perform screening assays at high throughputs while consuming minimal sample volumes. These applications typically require drops that do not ...

2018

Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning

Bart Deplancke, Julie Marie Russeil, Petra Catalina Schwalie

Recruitment of brite/beige cells, known as browning of white adipose tissue (WAT), is an efficient way to turn an energy-storing organ into an energy-dissipating one and may therefore be of therapeutic value in combating obesity. However, a comprehensive u ...

2019

Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip

Bart Deplancke, Esther Amstad, Riccardo Dainese, Johannes Julius Bues, Marjan Biocanin

Single-cell RNA-sequencing (scRNA-seq) has revolutionized biomedical research by enabling the in-depth analysis of cell-to-cell heterogeneity of tissues with unprecedented resolution. One of the catalyzing technologies is single cell droplet microfluidics, ...

2019

Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel

Johan Auwerx, Bart Deplancke, Adamantia Kapopoulou, Maria Litovchenko, Brian Dennis Hollis, Roel Paulus Josephus Bevers, Virginie Sandra Braman

The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along ...

2019

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

Bart Deplancke, Wouter Jozef L Saelens, Olga Pushkarev

Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the raw a ...

Nature Research2025

Tetracyclines Disturb Mitochondrial Function across Eukaryotic Models: A Call for Caution in Biomedical Research

Johan Auwerx, Bart Deplancke, Laurent Mouchiroud, Richardus Houtkooper, Evan Graehl Williams, Dongryeol Ryu, Norman Lionel Moullan, Adrienne Joëlle Laurence Mottis, Xu Wang, Michael Vincent Frochaux, Virginija Jovaisaite

In recent years, tetracyclines, such as doxycycline, have become broadly used to control gene expression by virtue of the Tet-on/Tet-off systems. However, the wide range of direct effects of tetracycline use has not been fully appreciated. We show here tha ...

Elsevier2015

LncRNA Ctcflos orchestrates transcription and alternative splicing in thermogenic adipogenesis

Bart Deplancke, Petra Catalina Schwalie

The recruitment of thermogenic brite adipocytes within white adipose tissue attenuates obesity and metabolic comorbidities, arousing interest in understanding the underlying regulatory mechanisms. The molecular network of brite adipogenesis, however, remai ...

WILEY2021

Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress

Rolf Gruetter, Maria del Carmen Sandi Perez, Bart Deplancke, Jocelin Grosse, Antoine Timothée Cherix, Daniel Alpern, Julie Marie Russeil, Meltem Weger, Sriparna Ghosal

Mitochondrial dysfunction was highlighted as a crucial vulnerability factor for the development of depression. However, systemic studies assessing stress-induced changes in mitochondria-associated genes in brain regions relevant to depression symptomatolog ...

2020

Experimental advances in the characterization of metazoan gene regulatory networks

Bart Deplancke

Gene regulatory networks (GRNs) play a vital role in metazoan development and function, and deregulation of these networks is often implicated in disease. GRNs depict the dynamic interactions between genomic and regulatory state components. The genomic com ...

2009

Tissue-specific enhancer repression through molecular integration of cell signaling inputs

Bart Deplancke

Drosophila leg morphogenesis occurs under the control of a relatively well-known genetic cascade, which mobilizes both cell signaling pathways and tissue-specific transcription factors. However, their cross-regulatory interactions, deployed to refine leg p ...

2017

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

DNA-centered approaches to characterize regulatory protein–DNA interaction complexes

Bart Deplancke, Jovan Simicevic

Gene regulation is mediated by site-specific DNA-binding proteins or transcription factors (TFs), which form protein complexes at regulatory loci either to activate or repress the expression of a target gene. The study of the dynamic properties of these re ...

Royal Society of Chemistry2010

A Comprehensive Drosophila melanogaster Transcription Factor Interactome

Sachi Iiyama Inukai, Bart Deplancke, Riccardo Dainese

Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 pr ...

2019