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Bart Deplancke

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Related publications (115)

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

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

WILEY2019

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

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

Commensal Gut Bacteria Buffer the Impact of Host Genetic Variants on Drosophila Developmental Traits under Nutritional Stress

Michael Vincent Frochaux, Bart Deplancke, Maroun Bou Sleiman, Virginie Sandra Braman, Maria Litovchenko

Eukaryotic genomes encode several buffering mechanisms that robustly maintain invariant phenotypic outcome despite fluctuating environmental conditions. Here we show that the Drosophila gut-associated commensals, represented by a single facultative symbion ...

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

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

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

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

Engineered Multivalent Sensors to Detect Coexisting Histone Modifications in Living Stem Cells

Horst Pick, Cédric Deluz, Bart Deplancke, Aurore Marie-France Delachat, Nora Guidotti, Beat Fierz, David Michael Suter, Antonio Carlos Alves Meireles Filho, Carolin Christine Lechner, Andreas Linus Bachmann

2018

A stromal cell population that inhibits adipogenesis in mammalian fat depots

Bart Deplancke, Petra Catalina Schwalie, Julie Marie Russeil, Magda Zachara, Daniel Alpern

2018

Reversible De-differentiation of Mature White Adipocytes into Preadipocyte-like Precursors during Lactation

Bart Deplancke, Petra Catalina Schwalie, Wanze Chen, Fei Zhang

Cell Press2018

The NAD plus Salvage Pathway Potently Stimulates Hematopoiesis through Increased Mitochondrial Clearance and Asymmetric Division

Matthias Lütolf, Yannick Lionel Yersin, Bart Deplancke, Nicola Vannini, Carlos Canto Alvarez, Martin Ehrbar, Mukul Girotra, Aurélien Laurent Jean-Charles Oggier, Dongryeol Ryu, Eija Riitta Pirinen, Olaia Maria Naveiras Torres-Quiroga, Pernille Yde Rainer, Gennady Nikitin, Vasco Ledebur de Antas de Campos, Joanna Ratajczak, Loïc Tauzin, Josefine Catharina Pedersen Tratwal, Federico Sizzano, George Coukos, Sonja Giger, Shanti Rojas-Sutterlin, Yang Li, Simone Ragusa

AMER SOC HEMATOLOGY2018

Device for high throughput single-cell studies

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

The present invention concerns a microfluidic device or chip including at least one inlet for introducing at least one object into the device; an oil inlet for introducing an oil that supports droplet formation into the device or a droplet forming substanc ...

2018

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

Philipp Bucher, Didier Trono, Giovanna Ambrosini, Bart Deplancke, Romain Fernand Pietro Groux, Alina Isakova, Pernille Yde Rainer, Michaël Imbeault, Riccardo Dainese, Daniel Alpern

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand ...

Nature Publishing Group2017

Hippo, TGF-beta, and Src-MAPK pathways regulate transcription of the upd3 cytokine in Drosophila enterocytes upon bacterial infection

Bart Deplancke, Yu-Chen Tsai

Cytokine signaling is responsible for coordinating conserved epithelial regeneration and immune responses in the digestive tract. In the Drosophila midgut, Upd3 is a major cytokine, which is induced in enterocytes (EC) and enteroblasts (EB) upon oral infec ...

Public Library of Science2017

GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms

Bart Deplancke, Jacques Rougemont

GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing geneand transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification o ...

Oxford University Press2017

Dissecting the brown adipogenic regulatory network using integrative genomics

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

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

Transcription factor proteomics - Tools, applications, and challenges

Jovan Simicevic, Bart Deplancke

Transcription factors (TFs) are a family of DNA-binding proteins whose gene regulatory capabilities are of vital importance in defining the molecular state of a cell. Despite their biological significance, our understanding of TF behavior and function is s ...

Wiley-Blackwell2017

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

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

Jörg Hülsken, Bart Deplancke, Paloma Ordonez Moran, 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

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

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

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

A systems perspective on brown adipogenesis and metabolic activation

Bart Deplancke, Rachana Narendra Pradhan, Magda Zachara

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

Gene regulatory mechanisms underlying the intestinal innate immune response

Bart Deplancke, Antonio Carlos Alves Meireles Filho

In the mammalian gastrointestinal tract, distinct types of cells, including epithelial cells and macrophages, collaborate to eliminate ingested pathogens while striving to preserve the commensal microbiota. The underlying innate immune response is driven b ...

Elsevier2017

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