Felix Naef

Publications associées (104)

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 ...

2009

Genotypic features of lentivirus transgenic mice

Didier Trono, Denis Duboule, Felix Naef, Frédéric Schütz, Marc-Olivier Sauvain

Lentivector-mediated transgenesis is increasingly used, whether for basic studies as an alternative to pronuclear injection of naked DNA or to test candidate gene therapy vectors. In an effort to characterize the genetic features of this approach, we first ...

American Society for Microbiology2008

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

Probabilistic base calling of Solexa sequencing data

Felix Naef, Jacques Rougemont, Christian Iseli, Arnaud Amzallag, Ioannis Xenarios

BACKGROUND: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput dat ...

BioMed Central2008

Stochastic phase oscillator models for circadian clocks

Felix Naef, Jacques Rougemont

Periodic environments like we experience on the surface of planet earth lead living organisms to evolve molecular anticipation devices known a circadian clocks. The word circadian refers to the period of these oscillations which last about (circa) one day ...

Springer2008

Identifying synergistic regulation involving c-Myc and sp1 in human tissues

Felix Naef

Combinatorial gene regulation largely contributes to phenotypic versatility in higher eukaryotes. Genome-wide chromatin immuno-precipitation (ChIP) combined with expression profiling can dissect regulatory circuits around transcriptional regulators. Here, ...

Oxford University Press2007

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

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

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

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