Publications by Felix Naef | EPFL Graph Search

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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 ...

The transduction of extracellular signals through signaling pathways that culminate in a transcriptional response is central to many biological processes. However, quantitative relationships between activities of signaling pathway components and transcript ...

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 ...

Circadian clocks are autonomous daily timekeeping mechanisms that allow organisms to adapt to environmental rhythms as well as temporally organize biological functions. Clock-controlled timekeeping involves extensive regulation of rhythmic gene expression. ...

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 ...

The circadian clock modulates human physiology. However, the organization of tissue-specific gene expression rhythms and how these depend on age and sex is not defined in humans. We combined data from the Genotype-Tissue Expression (GTEx) project with an a ...

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 ...

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 ...

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 ...

Across biological systems, cells undergo coordinated changes in gene expression, resulting in transcriptome dynamics that unfold within a low-dimensional manifold. While low-dimensional dynamics can be extracted using RNA velocity, these algorithms can be ...

Weight loss is key to controlling the increasing prevalence of metabolic syndrome (MS) and its components, i.e., central obesity, hypertension, prediabetes and dyslipidaemia. The goals of our study were two-fold. First, we characterised the relationships b ...

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 ...

Protein synthesis is an energy-demanding cellular process. Consequently, a well-timed, fine-tuned and plastic regulation of translation is needed to adjust and maintain cell states under dynamically changing environments. Genome-wide monitoring of translat ...

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 ...

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 ...

As Molecular Systems Biology marks its 20th anniversary, we take this moment to reflect on two decades of discovery and innovation. Since its launch, the journal has stood at the forefront of integrating quantitative biology, computational modeling, and systems science—helping to shape how we understand complex biological systems.

Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcriptio ...

Felix Naef

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Stochastic phase oscillators and circadian bioluminescence recordings

Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells

Modeling an evolutionary conserved circadian cis-element

A new promoter element associated with daily time keeping in Drosophila

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

Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans

A self-regulatory system of interlinked signaling feedback loops controls mouse limb patterning

Stochastic phase oscillators and circadian bioluminescence recordings

Computational analysis of protein-DNA interactions from ChIP-seq data

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

Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations

The Effects of Time-Restricted Eating versus Standard Dietary Advice on Weight, Metabolic Health and the Consumption of Processed Food: A Pragmatic Randomised Controlled Trial in Community-Based Adults

Cold-Inducible RNA-Binding Protein Modulates Circadian Gene Expression Posttranscriptionally

Ribosome profiling and dynamic regulation of translation in mammals

Circadian Dbp Transcription Relies on Highly Dynamic BMAL1-CLOCK Interaction with E Boxes and Requires the Proteasome

Dynamical properties of quasi one-dimensional correlated electrons

Representing perturbed dynamics in biological network models

Long- and short-term molecular consequences of sleep loss in mice

Molecular Systems Biology at 20: reflecting on the past, envisioning the future

Differential regulation of RNA polymerase III genes during liver regeneration