Naef lab – UPNAE Laboratory of Computational and Systems Biology

Our lab is interested in quantitative, systems biology, and more generally the link between physics and biology. We work on various problems including circadian rhythms, transcriptional bursting, developmental patterning, gene regulation, and single cell imaging. To study these systems we combine theoretical, computational and experimental methods.

Current Research Areas

> Circadian gene regulatory networks in mammals > Chronobiology of the liver > Circadian oscillators in single cells > Interactions of circadian oscilators and cell cycle > Transcriptional bursting and noise in mammalian gene transcription

Would you like to join us for your PhD or Post-doc? See Openings.

Please contact [email protected]

The latest news



Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver


Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and transfer RNA (tRNA) profiling to investigate the relations between translation elongation rates, (aminoacyl-) tRNA levels, and codon usage in mammals. We modeled codon-specific (…)

Modulation of transcriptional burst frequency by histone acetylation


Many mammalian genes are transcribed during short bursts of variable frequencies and sizes that substantially contribute to cell-to-cell variability. However, which molecular mechanisms determine bursting properties remains unclear. To probe putative mechanisms, we combined temporal analysis of transcription along the circadian cycle with multiple genomic reporter integrations, using both short-lived luciferase live microscopy and single-molecule (…)

Clock-dependent chromatin topology modulates circadian transcription and behavior


The circadian clock in animals orchestrates widespread oscillatory gene expression programs, which underlie 24-h rhythms in behavior and physiology. Several studies have shown the possible roles of transcription factors and chromatin marks in controlling cyclic gene expression. However, how daily active enhancers modulate rhythmic gene transcription in mammalian tissues is not known. Using circular chromosome (…)

See all our previous Research Highlights


Laboratory of Computational and Systems Biology

Monday to Friday: 08.00 – 16.00

Head of laboratory: Prof. Felix Naef
♦ Office AAB 040
♦ Phone:  +41 21 693 16 21

♦ Email: [email protected]

Administrative Assistant: Sophie Barret
♦ Office AAB 038
♦ Phone:  +41 21 693 83 58
♦ Email: [email protected]

Mailing Address:

Prof. Felix Naef
AAB 040
Station 15
CH-1015 Lausanne