Felix Naef

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Full Professor

felix.naef@epfl.ch +41 21 693 16 21

Citizenship: swiss

EPFL SV IBI-SV UPNAE
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Biography

Felix Naef studied theoretical physics at the ETHZ and obtained his PhD from the EPFL in 2000. He then received postdoctoral training at the Center for Studies in Physics and Biology at the Rockefeller University (NYC) under the guidance of Prof. Magnasco. His research focuses on the modeling and interpretation of high-throughput functional data and the study of biomolecular oscillators. He joined ISREC as an associate scientist in early 2004 and is currently Associate Professor in the Institute of Bioengineering (IBI).

Publications

Infoscience publications

Infoscience

Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates

I. Lamberti; J. A. Chao; C. Gobet; F. Naef

2025

Felix Naef

Full Professor

Biography

Publications

Infoscience publications

Infoscience

Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates

Conditional Deep Learning Model Reveals Translation Elongation Determinants during Amino Acid Deprivation

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

The metabolic and circadian signatures of gestational diabetes in the postpartum period characterised using multiple wearable devices

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Characterisation of EIF5A perturbations on ribosome dynamics with single-molecule imaging

Uncovering personalized glucose responses and circadian rhythms from multiple wearable biosensors with Bayesian dynamical modeling

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

Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology

Statistical physics of periodic biological processes

V-ATPase/TORC1-mediated ATFS-1 translation directs mitochondrial UPR activation in C. elegans

Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver

Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

Comment on "Circadian rhythms in the absence of the clock gene Bmal1"

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

The circadian oscillator analysed at the single-transcript level

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

Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms

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

Circadian dynamics of RNA localisation in the mammalian liver

What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis

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

Inference methods for the study of interacting biological oscillators in single-cells

Sleep-wake-driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex

Low-dimensional dynamics of two coupled biological oscillators

Organization of temporal gene expression: from circadian clocks to promoter cycles and back

Engineered signaling centers for the spatially controlled patterning of human pluripotent stem cells

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

Differential regulation of RNA polymerase III genes during liver regeneration

The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism

Tissue-specific circadian transcriptional regulation

Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior

Cross-regulatory circuits linking inflammation, high-fat diet, and the circadian clock

Single Live Cell Monitoring of Protein Turnover Reveals Intercellular Variability and Cell-Cycle Dependence of Degradation Rates

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

Circadian clock- and feeding-dependent regulation of translation initiation and elongation in the liver

Quantitative single cell dynamics of signaling and transcriptional response in mammalian cells

A new promoter element associated with daily time keeping in Drosophila

Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome

Ribosome profiling and dynamic regulation of translation in mammals

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver

Rhythmic and clock-dependent chromatin loops regulate circadian gene expression

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

What shapes eukaryotic transcriptional bursting?

Rhythmic modulation of transcriptional burst frequency in circadian gene promoters

Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp

Circadian rhythm and cell cycle : two synchronized processes

Phase specific transcriptional regulation of circadian clock and metabolism in mouse liver

Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling

Mechanisms of centrosome separation in C. elegans

Quantitative single-cell analysis of S. cerevisiae using a microfluidic live-cell imaging platform

Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver

Structure of silent transcription intervals and noise characteristics of mammalian genes

Context-specific regulation of BMAL1 target genes during the circadian rhythm in mouse

Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver

Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

Spatio-temporal synchronization of biological oscillators

Modeling of transcription mechanisms in mammals from kinetic measurements in single cells

Non-Circadian Expression Masking Clock-Driven Weak Transcription Rhythms in U2OS Cells

Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

Kinetic Analysis of Transcriptional and Post-Transcriptional Processes During Circadian Cycles

A microfluidic live-cell imaging platform to study large collections of microbial genotypes

The Circadian Clock Coordinates Ribosome Biogenesis

Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics

Quantitative analysis and mathematical modeling of polarity establishment in C. elegans embryos

A chemostat array enables the spatio-temporal analysis of the yeast proteome

Stimulus-induced modulation of transcriptional bursting in a single mammalian gene

Analysis of precision in chemical oscillators: implications for circadian clocks

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

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

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

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver