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Felix Naef

Cette personne a quitté l’EPFL

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Publications associées (75)

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Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling

Françoise Gisou van der Goot Grunberg, Felix Naef, Daniel Boss, Mircea Ioan Iacovache, Mirko Bischofberger

Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their jou ...

Elsevier2016

Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells

Felix Naef, Kyle Gustafson, Cédric Gobet, Jonathan Bieler, Rosamaria Cannavo

Circadian cycles and cell cycles are two fundamental periodic processes with a period in the range of 1 day. Consequently, coupling between such cycles can lead to synchronization. Here, we estimated the mutual interactions between the two oscillators by t ...

Nature / European Molecular Biology Organization2014

Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

Felix Naef, Frédéric Bruno Martin Gachon, Cédric Gobet, Benjamin Dieter Weger, Patrick Descombes, Jingkui Wang

Diurnal oscillations of gene expression are a hallmark of rhythmic physiology across most living organisms. Such oscillations are controlled by the interplay between the circadian clock and feeding rhythms. Although rhythmic mRNA accumulation has been exte ...

National Academy of Sciences2015

Guidelines for Genome-Scale Analysis of Biological Rhythms

Felix Naef, Frédéric Bruno Martin Gachon

Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods ...

Sage Publications Inc2017

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

Sebastian Maerkl, Felix Naef, Jacques Rougemont, Nicolas Dénervaud, Philippe Jacquet

In yeast, ribosome production is controlled transcriptionally by tight coregulation of the 138 ribosomal protein genes (RPGs). RPG promoters display limited sequence homology, and the molecular basis for their coregulation remains largely unknown. Here we ...

Cold Spring Harbor Laboratory Press2014

ASSET: A robust algorithm for the automated segmentation and standardization of early Caenorhabditis elegans embryos

Felix Naef, Pierre Gönczy, Simon Blanchoud

The early Caenorhabditis elegans embryo is an attractive model to investigate evolutionarily conserved cellular mechanisms. However, there is a paucity of automated methods to gather quantitative information with subcellular precision in this system. We de ...

Wiley-Blackwell2010

Stimulus-induced modulation of transcriptional bursting in a single mammalian gene

Felix Naef, David Michael Suter, Benjamin Zoller, Rosamaria Cannavo

Mammalian genes are often transcribed discontinuously as short bursts of RNA synthesis followed by longer silent periods. However, how these "on" and "off" transitions, together with the burst sizes, are modulated in single cells to increase gene expressio ...

National Academy of Sciences2013

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

Matteo Dal Peraro, Bart Deplancke, Felix Naef, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Sunil Kumar Raghav, Irina Krier, Guillaume Rey, Alexandra Styliani Kalantzi, Jonathan Aryeh Sobel

Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles ...

Public Library of Science2017

Engineered signaling centers for the spatially controlled patterning of human pluripotent stem cells

Ambroise Roger Vuaridel, Matthias Lütolf, Felix Naef, Yoji Tabata, Eric Paquet, François Réal Rivest, Andrea Manfrin

Signaling centers, localized groups of cells that secrete morphogens, play a key role in early development and organogenesis by orchestrating spatial cell fate patterning. Here we present a microfluidic approach that exposes human pluripotent stem cell (hP ...

NATURE PUBLISHING GROUP2019

Integration of light and temperature in the regulation of circadian gene expression in Drosophila

Felix Naef

Circadian clocks are aligned to the environment via synchronizing signals, or Zeitgebers, such as daily light and temperature cycles, food availability, and social behavior. In this study, we found that genome-wide expression profiles from temperature-entr ...

Public Library of Science2007

Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp

Felix Naef

In mammals, body temperature fluctuates diurnally around a mean value of 36 degrees C-37 degrees C. Despite the small differences between minimal and maximal values, body temperature rhythms can drive robust cycles in gene expression in cultured cells and, ...

Cold Spring Harbor Laboratory2016

Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks

Felix Naef, Jacques Rougemont

Cell-autonomous and self-sustained molecular oscillators drive circadian behavior and physiology in mammals. From rhythms recorded in cultured fibroblasts we identified the dominant cause for amplitude reduction as desynchronization of self-sustained oscil ...

Nature / European Molecular Biology Organization2007

Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains

Felix Naef, Christian Antonio Pozzorini, Jonathan Bieler

Segmentation of the Drosophila melanogaster embryo results from the dynamic establishment of spatial mRNA and protein patterns. Here, we exploit recent temporal mRNA and protein expression measurements on the full surface of the blastoderm to calibrate a d ...

2011

Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

Felix Naef, Cédric Gobet, Kyle Gustafson

Background: In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles th ...

BioMed Central2014

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

Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells

Felix Naef, David Michael Suter, Torgil Elias Friman, Onur Tidin

The transduction of extracellular signals through signaling pathways that culminate in a transcriptional response is central to many biological processes. However, quantitative relationships between activities of signaling pathway components and transcript ...

Nature Research2019

Modeling an evolutionary conserved circadian cis-element

Felix Naef, Eric Paquet, Guillaume Rey

Circadian oscillator networks rely on a transcriptional activator called CLOCK/CYCLE (CLK/CYC) in insects and CLOCK/BMAL1 or NPAS2/BMAL1 in mammals. Identifying the targets of this heterodimeric basic-helix-loop-helix (bHLH) transcription factor poses chal ...

Public Library of Science2008

A new promoter element associated with daily time keeping in Drosophila

Felix Naef, Eric Paquet

Circadian clocks are autonomous daily timekeeping mechanisms that allow organisms to adapt to environmental rhythms as well as temporally organize biological functions. Clock-controlled timekeeping involves extensive regulation of rhythmic gene expression. ...

Oxford University Press2017

The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae

Felix Naef, Jacques Rougemont

Small nucleolar RNAs (snoRNAs) play a key role in ribosomal RNA biogenesis, yet factors controlling their expression are unknown. We found that the majority of Saccharomyces snoRNA promoters display an aRCCCTaa sequence motif at the upstream border of a TA ...

Elsevier2010

Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans

Felix Naef, Cédric Gobet, Lorenzo Talamanca

The circadian clock modulates human physiology. However, the organization of tissue-specific gene expression rhythms and how these depend on age and sex is not defined in humans. We combined data from the Genotype-Tissue Expression (GTEx) project with an a ...

American Association for the Advancement of Science2023