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Felix Naef

Cette personne a quitté l’EPFL

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Publications associées (75)

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A self-regulatory system of interlinked signaling feedback loops controls mouse limb patterning

Felix Naef, Mirko Bischofberger

Embryogenesis depends on self-regulatory interactions between spatially separated signaling centers, but few of these are well understood. Limb development is regulated by epithelial-mesenchymal (e-m) feedback loops between sonic hedgehog (SHH) and fibrobl ...

American Association for the Advancement of Science2009

Stochastic phase oscillators and circadian bioluminescence recordings

Felix Naef, Jacques Rougemont

Cultured circadian oscillators from peripheral tissues were recently shown to be both cell-autonomous and self-sustained. Therefore, the dominant cause for amplitude reduction observed in bioluminescence recordings of cultured fibroblasts is desynchronizat ...

2007

Computational analysis of protein-DNA interactions from ChIP-seq data

Felix Naef, Jacques Rougemont

Chromatin immunoprecipitation experiments followed by ultra-high-throughput sequencing (ChIP-seq) is becoming the method of choice to identify transcription factor binding sites in prokaryotes and eukaryotes in vivo. Here, we review the computational steps ...

2011

Circadian gene expression is resilient to large fluctuations in overall transcription rates

Felix Naef, Michaël Unser, Daniel Sage, Thomas d'Eysmond

Mammalian circadian oscillators are considered to rely on transcription/translation feedback loops in clock gene expression. The major and essential loop involves the autorepression of cryptochrome (Cry1, Cry2) and period (Per1, Per2) genes. The rhythm-gen ...

Nature Publishing Group2009

Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations

Felix Naef, Maxine Leonardi, Colas Noé Droin, Lorenzo Talamanca, Gioele La Manno, Alex Russell Lederer, Irina Khven, Antonio Herrera Camacho, Albert Dominguez Mantes, Alessandro Valente

Across biological systems, cells undergo coordinated changes in gene expression, resulting in transcriptome dynamics that unfold within a low-dimensional manifold. While low-dimensional dynamics can be extracted using RNA velocity, these algorithms can be ...

Nature Publishing Group2024

The Effects of Time-Restricted Eating versus Standard Dietary Advice on Weight, Metabolic Health and the Consumption of Processed Food: A Pragmatic Randomised Controlled Trial in Community-Based Adults

Felix Naef, Nicholas Edward Phillips

Weight loss is key to controlling the increasing prevalence of metabolic syndrome (MS) and its components, i.e., central obesity, hypertension, prediabetes and dyslipidaemia. The goals of our study were two-fold. First, we characterised the relationships b ...

2021

Cold-Inducible RNA-Binding Protein Modulates Circadian Gene Expression Posttranscriptionally

Felix Naef, Guillaume Rey

In mammalian tissues, circadian gene expression can be driven by local oscillators or systemic signals controlled by the master pacemaker in the suprachiasmatic nucleus. We show that simulated body temperature cycles, but not peripheral oscillators, contro ...

American Association for the Advancement of Science2012

Ribosome profiling and dynamic regulation of translation in mammals

Felix Naef, Cédric Gobet

Protein synthesis is an energy-demanding cellular process. Consequently, a well-timed, fine-tuned and plastic regulation of translation is needed to adjust and maintain cell states under dynamically changing environments. Genome-wide monitoring of translat ...

Elsevier2017

Circadian Dbp Transcription Relies on Highly Dynamic BMAL1-CLOCK Interaction with E Boxes and Requires the Proteasome

Felix Naef, David Michael Suter

The transcription factors BMAL1 and CLOCK drive the circadian transcription of clock and clock-controlled genes, such as Dbp. To investigate the kinetics of BMAL1 binding to target genes in real time, we generated a cell line harboring tandem arrays of Dbp ...

Elsevier2012

Dynamical properties of quasi one-dimensional correlated electrons

Felix Naef

EPFL2000

Representing perturbed dynamics in biological network models

Felix Naef, Jacques Rougemont

We study the dynamics of gene activities in relatively small size biological networks (up to a few tens of nodes), e.g., the activities of cell-cycle proteins during the mitotic cell-cycle progression. Using the framework of deterministic discrete dynamica ...

American Physical Society2007

Long- and short-term molecular consequences of sleep loss in mice

Felix Naef, Jake Yeung

WILEY2018

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, Bart Deplancke, Jacques Rougemont, Laura Symul, Fabrice David, Sunil Kumar Raghav, Marion Leleu, Julia Catharina Cajan, Kyle Gustafson, Dominic Villeneuve

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

Organization of temporal gene expression: from circadian clocks to promoter cycles and back

Felix Naef

WILEY2019

Comment on "Circadian rhythms in the absence of the clock gene Bmal1"

Felix Naef, Cédric Gobet

Ray et al. (Reports, 14 February 2020, p. 800) recently claimed temperature-compensated, free-running mRNA oscillations in Bmal1(-/-) liver slices and skin fibroblasts. We reanalyzed these data and found far fewer reproducible mRNA oscillations in this gen ...

American Association for the Advancement of Science2021