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Felix Naef

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Publications associées (80)

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

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

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

Felix Naef, Simon Blanchoud, Pierre Gönczy, Yemima Suryani Budirahardja

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

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

Felix Naef, Jacques Rougemont, Enrico Guarnera

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

Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico

Felix Naef, Mirko Bischofberger, Jacques Rougemont

The segmentation of Drosophila is a prime model to study spatial patterning during embryogenesis. The spatial expression of segment polarity genes results from a complex network of interacting proteins whose expression products are maintained after success ...

Elsevier2010

Network inference by combining biologically motivated regulatory constraints with penalized regression

Felix Naef

2009

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays

Felix Naef

BACKGROUND: Organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arr ...

BioMed Central2009

Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors

Felix Naef, Mauro Delorenzi

BACKGROUND: To understand cancer-related modifications to transcriptional programs requires detailed knowledge about the activation of signal-transduction pathways and gene expression programs. To investigate the mechanisms of target gene regulation by hum ...

BioMed Central2009

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

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

Genotypic features of lentivirus transgenic mice

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

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

Probabilistic base calling of Solexa sequencing data

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

Modeling an evolutionary conserved circadian cis-element

Felix Naef, Guillaume Rey, Eric Paquet

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

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

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

Stochastic phase oscillators and circadian bioluminescence recordings

Felix Naef, Jacques Rougemont

2007

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

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

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 properties of quasi one-dimensional correlated electrons

Felix Naef

EPFL2000

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