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Felix Naef

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Circadian clocks go in vitro: purely post-translational oscillators in cyanobacteria

Felix Naef

Recent findings about the core of the circadian oscillator in cyanobacteria are challenging the dogma that such clocks are driven through transcriptional-translational feedback regulation. Instead, the master pacemaker is independent of both transcription ...

Nature / European Molecular Biology Organization2005

Molecular and statistical tools for circadian transcript profiling

Felix Naef

This article describes methods used to evaluate mRNA expression patterns on microarrays and their application in circadian biology. With the intention of complementing rather than duplicating the existing literature, particular emphasis is placed on experi ...

Elsevier2005

Freedom and rules: the acquisition and reprogramming of a bird's learned song

Felix Naef

Canary song is hierarchically structured: Short stereotyped syllables are repeated to form phrases, which in turn are arranged to form songs. This structure occurs even in the songs of young isolates, which suggests that innate rules govern canary song dev ...

2005

Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells

Felix Naef, Thierry Laroche

The mammalian circadian timing system is composed of a central pacemaker in the suprachiasmatic nucleus (SCN) of the brain and subsidiary oscillators in most peripheral cell types. While oscillators in SCN neurons are known to function in a self-sustained ...

2004

A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations

Felix Naef

MOTIVATION: Despite the success and popularity of oligonucleotide arrays as a high-throughput technique for measuring mRNA expression levels, quantitative calibration studies have until now been limited. The main reason is that suitable data was not availa ...

2003

Production of ribosome components in effector CD4+ T cells is accelerated by TCR stimulation and coordinated by ERK-MAPK

Felix Naef

Effector CD4+ T cells rapidly activate high-level cytokine expression following TCR stimulation. Consistent with accelerated protein production in these cells, global mRNA profiles revealed that, after cytokines, the most impressive cluster of activated ge ...

Elsevier2003

Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays

Felix Naef

Oligonucleotide microarrays are based on the hybridization of labeled mRNA molecules to short length oligonucleotide probes on a glass surface. Two effects have been shown to affect the raw data: the sequence dependence of the probe hybridization propertie ...

Oxford University Press2003

Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays

Felix Naef

RNA binding to high-density oligonucleotide arrays has shown tantalizing differences with solution experiments. We analyze here its sequence specificity, fitting binding affinities to sequence composition in large datasets. Our results suggest that the flu ...

American Physical Society2003

Molecular signature of human embryonic stem cells and its comparison with the mouse

Felix Naef

The molecular mechanism underlying pluripotency is largely unknown. Here, we provide the first global transcriptional profile of the state of "stemness" in human embryonic stem cells (HESCs). We have identified a set of 918 genes enriched in undifferentiat ...

Elsevier2003

Genomic and expression analysis of the 12p11-p12 amplicon using EST arrays identifies two novel amplified and overexpressed genes

Felix Naef

We performed parallel array comparative genomic hybridization and array expression analysis of the 12p11-p12 amplicon in human testicular seminomas and an ovarian carcinoma cell line using an expressed sequence tags (ESTs) array spotted with 8254 ESTs. The ...

American Association for Cancer Research2002

Circadian clocks go in vitro: purely post-translational oscillators in cyanobacteria

Felix Naef

Nature / European Molecular Biology Organization2005

Freedom and rules: the acquisition and reprogramming of a bird's learned song

Felix Naef

2005

Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells

Felix Naef, Thierry Laroche

2004

A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations

Felix Naef

2003

Production of ribosome components in effector CD4+ T cells is accelerated by TCR stimulation and coordinated by ERK-MAPK

Felix Naef

Elsevier2003

Genomic and expression analysis of the 12p11-p12 amplicon using EST arrays identifies two novel amplified and overexpressed genes

Felix Naef

American Association for Cancer Research2002