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

© 2022 EPFL

Felix Naef and Li Tang Win SNSF Sinergia Grants

— Felix Naef and Li Tang, both Professors at the EPFL's Institute of Bioengineering (IBI), have been awarded major collaborative Sinergia grants by the Swiss National Science Foundation (SNSF).

iStock photos (credit: magicmine)

How the circadian clock regulates liver genes in time and space

— EPFL scientists have carried out the first comprehensive study of how genes in the liver perform their metabolic functions in both space and time of day. Monitoring almost 5000 genes at the level of the individual cell across a 24-hour period, the researchers have modelled how the circadian clock and liver functions crosstalk throughout the day in sync with the feeding-fasting cycle.

Felix Naef. Credit: Alain Herzog (EPFL)

Felix Naef elected EMBO Member

— The European Molecular Biology Organization (EMBO) has elected 63 new life scientists to membership, joining more than 1800 of the best researchers in Europe and the world. Among the new members is Professor Felix Naef at EPFL’s Institute of Bioengineering.

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HIGHLIGHTS

Space-time logic of liver gene expression at sub-lobular scale

31-03-2022

The mammalian liver is a central hub for systemic metabolic homeostasis. Liver tissue is spatially structured, with hepatocytes operating in repeating lobules, and sub-lobule zones performing distinct functions. The liver is also subject to extensive temporal regulation, orchestrated by the interplay of the circadian clock, systemic signals and feeding rhythms. However, liver zonation has previously (…)

The circadian oscillator analysed at the single-transcript level

31-03-2022

The circadian clock is an endogenous and self-sustained oscillator that anticipates daily environmental cycles. While rhythmic gene expression of circadian genes is well-described in populations of cells, the single-cell mRNA dynamics of multiple core clock genes remain largely unknown. Here we use single-molecule fluorescence in situ hybridisation (smFISH) at multiple time points to measure pairs (…)

Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle

31-03-2022

The circadian clock drives extensive temporal gene expression programs controlling daily changes in behavior and physiology. In mouse liver, transcription factors dynamics, chromatin modifications, and RNA Polymerase II (PolII) activity oscillate throughout the 24-hour (24h) day, regulating the rhythmic synthesis of thousands of transcripts. Also, 24h rhythms in gene promoter-enhancer chromatin looping accompany rhythmic mRNA (…)

See all our previous Research Highlights

Contact


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:

EPFL SV IBI UPNAE
Prof. Felix Naef
AAB 040
Station 15
CH-1015 Lausanne