Felix Naef

Publications associées (104)

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In prokaryotes and eukaryotes, most genes appear to be transcribed during short periods called transcriptional bursts, interspersed by silent intervals. We describe how such bursts generate gene-specific temporal patterns of messenger RNA (mRNA) synthesis ...

2011

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

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

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

Pierre Gönczy, Felix Naef, Simon Blanchoud, 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

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

Felix Naef, Jacques Rougemont, Mirko Bischofberger

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

Information processing in cells and tissues (IPCAT'2009): from small scale dynamics to understanding systems behavior

Felix Naef

Elsevier2010

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

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

Circadian gene expression is resilient to large fluctuations in overall transcription rates

Michaël Unser, Felix Naef, 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