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Bart Deplancke

Cette personne a quitté l’EPFL

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Publications associées (113)

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A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks

Bart Deplancke, Sebastian Martin Waszak, Sunil Kumar Raghav, Alina Isakova, Carine Delattre-Gubelmann, Jovan Simicevic, Antonina Iagovitina

The comprehensive mapping of gene promoters and enhancers has significantly improved our understanding of how the mammalian regulatory genome is organized. An important challenge is to elucidate how these regulatory elements contribute to gene expression b ...

Nature / European Molecular Biology Organization2013

PDF Signaling Is an Integral Part of the Drosophila Circadian Molecular Oscillator

Bart Deplancke

Circadian clocks generate 24-hr rhythms in physiology and behavior. Despite numerous studies, it is still uncertain how circadian rhythms emerge from their molecular and neural constituents. Here, we demonstrate a tight connection between the molecular and ...

Elsevier2016

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 Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle

Bart Deplancke, Julie Marie Russeil, Umji Lee

Apelin (Apln) is a myokine that regulates skeletal muscle plasticity and meta-bolism and declines during aging. Through a yeast one-hybrid transcription factor binding screen, we identified the TEA domain transcription factor 1 (Tead1) as a novel regulator ...

CELL PRESS2022

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

Enteric infection induces Lark-mediated intron retention at the 5 ' end of Drosophila genes

Bart Deplancke, Maroun Bou Sleiman, Dani Osman, Michael Vincent Frochaux

Background RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study ...

2020

Global and stage specific patterns of krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells

Yoann Mouscaz, Didier Trono, Bart Deplancke, Adamantia Kapopoulou, Michaël Imbeault, Carine Delattre-Gubelmann, Andrea Corsinotti

Highly coordinated transcription networks orchestrate the self-renewal of pluripotent stem cell and the earliest steps of mammalian development. KRAB-containing zinc finger proteins represent the largest group of transcription factors encoded by the genome ...

Public Library of Science2013

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

Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution

Bart Deplancke

Adipose tissue (AT) is a complex connective tissue with a high relative proportion of adipocytes, which are specialized cells with the ability to store lipids in large droplets. AT is found in multiple discrete depots throughout the body, where it serves a ...

Springer Science and Business Media LLC2025

WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data

Bart Deplancke, Andreas Massouras

High-throughput sequencing (HTS) is revolutionizing our ability to obtain cheap, fast and reliable sequence information. Many experimental approaches are expected to benefit from the incorporation of such sequencing features in their pipeline. Consequently ...

Oxford University Press2010

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression

Bart Deplancke, Daniel Alpern, Julie Marie Russeil

Skeletal muscles are composed of gigantic cells called muscle fibers, packed with force-producing myofibrils. During development, the size of individual muscle fibers must dramatically enlarge to match with skeletal growth. How muscle growth is coordinated ...

2021

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Dariia Gudkova, Bart Deplancke, Daniel Migliozzi, Riccardo Dainese, Hüseyin Baris Atakan, Daniel Alpern, Mustafa Demir

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Springer2024

A systems perspective on brown adipogenesis and metabolic activation

Bart Deplancke, Magda Zachara, Rachana Narendra Pradhan

Brown adipocytes regulate energy expenditure via mitochondrial uncoupling. This makes these fat cells attractive therapeutic targets to tackle the burgeoning issue of obesity, which itself is coupled to insulin resistance, type 2 diabetes, cardiovascular a ...

Wiley-Blackwell2017

Topology and dynamics of the zebrafish segmentation clock core circuit

Bart Deplancke, Sebastian Maerkl, Andrew Charles Oates, Alina Isakova, Daniele Soroldoni

During vertebrate embryogenesis, the rhythmic and sequential segmentation of the body axis is regulated by an oscillating genetic network termed the segmentation clock. We describe a new dynamic model for the core pace-making circuit of the zebrafish segme ...

2012

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

Multilevel regulation of the glass locus during Drosophila eye development

Bart Deplancke, Michael Vincent Frochaux

Development of eye tissue is initiated by a conserved set of transcription factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to contr ...

2019

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

Cross-Tissue Identification of Somatic Stem and Progenitor Cells Using a Single-Cell RNA-Sequencing Derived Gene Signature

Bart Deplancke, Jörg Hülsken, Petra Catalina Schwalie

A long-standing question in biology is whether multipotent somatic stem and progenitor cells (SSPCs) feature molecular properties that could guide their system-independent identification. Population-based transcriptomic studies have so far not been able to ...

Wiley2017