Publications by Fabrice David | EPFL Graph Search

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

Bart Deplancke, Fabrice David, Vincent Roland Julien Gardeux

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

Ether lipids, sphingolipids and toxic 1-deoxyceramides as hallmarks for lean and obese type 2 diabetic patients

Fabrice David

Aim: The worldwide increase in obesity and type 2 diabetes (T2D) represents a major health challenge. Chronically altered lipids induced by obesity further promote the development of T2D, and the accumulation of toxic lipid metabolites in serum and periphe ...

2021

Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms

Felix Naef, Cédric Gobet, Fabrice David, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Nicholas Edward Phillips

The circadian clock and feeding rhythms are both important regulators of rhythmic gene expression in the liver. To further dissect the respective contributions of feeding and the clock, we analyzed differential rhythmicity of liver tissue samples across se ...

National Academy of Sciences2021

Spatial tissue profiling by imaging-free molecular tomography

Fabrice David, Gioele La Manno

Several techniques are currently being developed for spatially resolved omics profiling, but each new method requires the setup of specific detection strategies or specialized instrumentation. Here we describe an imaging-free framework to localize high-thr ...

2021

ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses

Bart Deplancke, Fabrice David, Vincent Roland Julien Gardeux, Maria Litovchenko

Single-cell omics enables researchers to dissect biological systems at a resolution that was unthinkable just 10 years ago. However, this analytical revolution also triggered new demands in 'big data' management, forcing researchers to stay up to speed wit ...

2020

Identifying gene function and module connections by the integration of multispecies expression compendia

Stephan Morgenthaler, Elena Katsyuba, Kristina Schoonjans, Johan Auwerx, Fabrice David, Maroun Bou Sleiman, Daria Rukina, Andrea Komljenovic, Hao Li, Qingyao Huang, Yang Li, Changmyung Oh, Wen Gao

The functions of many eukaryotic genes are still poorly understood. Here, we developed and validated a new method, termed GeneBridge, which is based on two linked approaches to impute gene function and bridge genes with biological processes. First, Gene-Mo ...

Cold Spring Harbor Laboratory2019

Differential regulation of RNA polymerase III genes during liver regeneration

Felix Naef, Philippe Jacquet, Nicolas Jean Philippe Guex, Jonathan Aryeh Sobel, Cristian Carmeli, Olivier Martin, Irina Krier, Mauro Delorenzi, Nouria Hernandez, Bart Deplancke, Jacques Rougemont, François Mange, Laura Symul, Fabrice David, Sunil Kumar Raghav, Julien Delafontaine, Marion Leleu, Julia Catharina Cajan, Winship Herr, Kyle Gustafson, Maykel Lopes, Dominic Villeneuve, Ioannis Xenarios

Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcriptio ...

Oxford University Press (OUP)2019

Systematic lipidomic analysis of yeast protein kinase and phosphatase mutants reveals novel insights into regulation of lipid homeostasis

Howard Riezman, Fabrice David, Manuele Piccolis

The regulatory pathways required to maintain eukaryotic lipid homeostasis are largely unknown. We developed a systematic approach to uncover new players in the regulation of lipid homeostasis. Through an unbiased mass spectrometry-based lipidomic screening ...

Amer Soc Cell Biology2014

Systematic lipidomic analysis of yeast mutants reveals novel regulation of lipid homeostasis and plasma membrane/ER communication

Fabrice David

Wiley-Blackwell2012

Lipids role in COPII vesicle formation

Fabrice David

Wiley-Blackwell2012

Kinase control of lipid homeostasis in mammalian cells

Fabrice David

Wiley-Blackwell2012

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

Carine Delattre-Gubelmann, Bart Deplancke, Jacques Rougemont, Alexandre Gattiker, Fabrice David, Andreas Massouras, Frederik Decouttere

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and ...

2011