Felix Naef

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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, Nouria Hernandez, 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

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Felix Naef, Jake Yeung, Jérôme Mermet

Mammals have evolved an internal timing system, the circadian clock, which synchronizes physiology and behavior to the daily light and dark cycles of the Earth. The master clock, located in the suprachiasmatic nucleus (SCN) of the brain, takes fluctuating ...

Cold Spring Harbor Lab Press, Publications Dept2017

What shapes eukaryotic transcriptional bursting?

Felix Naef, Damien Lionel Nicolas, Nicholas Edward Phillips

Isogenic cells in a common environment present a large degree of heterogeneity in gene expression. Part of this variability is attributed to transcriptional bursting: the stochastic activation and inactivation of promoters that leads to the discontinuous p ...

Royal Society of Chemistry2017

Guidelines for Genome-Scale Analysis of Biological Rhythms

Felix Naef, Frédéric Bruno Martin Gachon, Alaaddin Bulak Arpat, Han Wang, Zheng Chen, Xiaodong Li

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

Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome

Felix Naef, Carlos Canto Alvarez, Loïc Dayon, Frédéric Bruno Martin Gachon, Martin Kussmann, Daniel Alain Dominique Marie Mauvoisin, Joanna Ratajczak, Sebastiano Collino, Jingkui Wang, Florian Atger

Lysine acetylation is involved in various biological processes and is considered a key reversible post-translational modification in the regulation of gene expression, enzyme activity, and subcellular localization. This post-translational modification is t ...

Elsevier2017

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 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

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

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

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

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

CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings

Felix Naef, Benjamin Zoller, Damien Lionel Nicolas, Simon Blanchoud, Onur Tidin

Fluorescence and bioluminescence time-lapse imaging allows to investigate a vast range of cellular processes at single-cell or even subcellular resolution. In particular, time-lapse imaging can provide uniquely detailed information on the fine kinetics of ...

Academic Press Inc Elsevier Science2015

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

Felix Naef

Saeed Omidi Klishami

Oxford University Press2017

A new promoter element associated with daily time keeping in Drosophila

Felix Naef

Eric Paquet

CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings

Felix Naef, Benjamin Zoller, Damien Lionel Nicolas, Simon Blanchoud, Onur Tidin

Academic Press Inc Elsevier Science2015