Felix Naef

Related publications (104)

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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

Analysis of precision in chemical oscillators: implications for circadian clocks

Felix Naef, Alessandro De Simone, Thomas d'Eysmond

Biochemical reaction networks often exhibit spontaneous self-sustained oscillations. An example is the circadian oscillator that lies at the heart of daily rhythms in behavior and physiology in most organisms including humans. While the period of these osc ...

Institute of Physics2013

A chemostat array enables the spatio-temporal analysis of the yeast proteome

Michaël Unser, Felix Naef, Sebastian Maerkl, Ricard Delgado Gonzalo, Nicolas Dénervaud, Arun Stephen Rajkumar, Johannes Becker

Observing cellular responses to perturbations is central to generating and testing hypotheses in biology. We developed a massively parallel microchemostat array capable of growing and observing 1,152 yeast-GFP strains on the single-cell level with 20 min t ...

National Academy of Sciences2013

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

Olivier Martin, Bart Deplancke, Felix Naef, Jacques Rougemont, Nicolas Jean Philippe Guex, Winship Herr, Mauro Delorenzi, Nouria Hernandez, Laura Symul

Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide, we gener ...

Public Library Science2012

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

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

Analysis of the dynamics of limb transcriptomes during mouse development

Denis Duboule, Felix Naef, István Gyurján

ABSTRACT: BACKGROUND: The development of vertebrate limbs has been a traditional system to study fundamental processes at work during ontogenesis, such as the establishment of spatial cellular coordinates, the effect of diffusible morphogenetic molecules o ...

BioMed Central2011

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

Felix Naef, Jacques Rougemont, Guillaume Rey

The mammalian circadian clock uses interlocked negative feedback loops in which the heterodimeric basic helix-loop-helix transcription factor BMAL1/CLOCK is a master regulator. While there is prominent control of liver functions by the circadian clock, the ...

2011

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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

Origins and consequences of transcriptional discontinuity

Felix Naef, David Michael Suter

In both prokaryotes and eukaryotes, transcription has been described as being temporally discontinuous, most genes being active mainly during short activity windows interspersed by silent periods. In mammalian cells, recent studies performed at the single ...

2011