Publications by Felix Naef | EPFL Graph Search

Related publications (75)

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

Aims/hypothesis: Gestational diabetes mellitus (GDM) affects 14% of all pregnancies worldwide and is associated with cardiometabolic risk. We aimed to exploit high-resolution wearable device time-series data to create a fine-grained physiological character ...

2024

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

Felix Naef, Cédric Gobet, Frédéric Bruno Martin Gachon, Fabrice David, Benjamin Dieter Weger, Nicholas Edward Phillips

The circadian clock and feeding rhythms are both important regulators of rhythmic gene expression in the liver. To further dissect the respective contributions of feeding and the clock, we analyzed differential rhythmicity of liver tissue samples across se ...

National Academy of Sciences2021

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

Felix Naef, Nicholas Edward Phillips

Wearable biosensors and smartphone applications can measure physiological variables over multiple days in free-living conditions. We measure food and drink ingestion, glucose dynamics, physical activity, heart rate (HR), and heart rate variability (HRV) in ...

CELL PRESS2023

Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology

Felix Naef, Tomaz Martini

Hepatocytes are the main workers in the hepatic factory, managing metabolism of nutrients and xenobiotics, production and recycling of proteins, and glucose and lipid homeostasis. Division of labor between hepatocytes is critical to coordinate complex comp ...

ANNUAL REVIEWS2023

Stochastic phase oscillator models for circadian clocks

Felix Naef, Jacques Rougemont

Periodic environments like we experience on the surface of planet earth lead living organisms to evolve molecular anticipation devices known a circadian clocks. The word circadian refers to the period of these oscillations which last about (circa) one day ...

Springer2008

The circadian oscillator analysed at the single-transcript level

Eric Daniel Jacques Durandau, Felix Naef, Jake Yeung, Damien Lionel Nicolas

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 cloc ...

2021

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

Felix Naef, Cédric Gobet, Nagammal Neelagandan, Irene Lamberti

Protein synthesis from mRNA is an energy-intensive and tightly controlled cellular process. Translation elongation is a well-coordinated, multifactorial step in translation that undergoes dynamic regulation owing to cellular state and environmental determi ...

ROYAL SOC2020

Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico

Felix Naef, Jacques Rougemont, Mirko Bischofberger

The segmentation of Drosophila is a prime model to study spatial patterning during embryogenesis. The spatial expression of segment polarity genes results from a complex network of interacting proteins whose expression products are maintained after success ...

Elsevier2010

Probabilistic base calling of Solexa sequencing data

Felix Naef, Jacques Rougemont, Christian Iseli, Arnaud Amzallag

BACKGROUND: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput dat ...

BioMed Central2008

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays

Felix Naef

BACKGROUND: Organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arr ...

BioMed Central2009

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

Felix Naef, Jacques Rougemont, Guillaume Rey

The mammalian circadian clock uses interlocked negative feedback loops in which the heterodimeric basic helix-loop-helix transcription factor BMAL1/CLOCK is a master regulator. While there is prominent control of liver functions by the circadian clock, the ...

2011

Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver

Felix Naef, Frédéric Bruno Martin Gachon, Loïc Dayon, Daniel Alain Dominique Marie Mauvoisin, Jingkui Wang

Diurnal oscillations of gene expression controlled by the circadian clock and its connected feeding rhythm enable organisms to coordinate their physiologies with daily environmental cycles. While available techniques yielded crucial insights into regulatio ...

Cell Press2017

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

Felix Naef, Cédric Gobet

Protein synthesis is an energy consuming process characterised as a pivotal and highly regulated step in gene expression. The net protein output is dictated by a combination of translation initiation, elongation and termination rates that have remained dif ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2022

CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings

Felix Naef, Simon Blanchoud, Damien Lionel Nicolas, Benjamin Zoller, Onur Tidin

Fluorescence and bioluminescence time-lapse imaging allows to investigate a vast range of cellular processes at single-cell or even subcellular resolution. In particular, time-lapse imaging can provide uniquely detailed information on the fine kinetics of ...

Academic Press Inc Elsevier Science2015

What shapes eukaryotic transcriptional bursting?

Felix Naef, Damien Lionel Nicolas, Nicholas Edward Phillips

Isogenic cells in a common environment present a large degree of heterogeneity in gene expression. Part of this variability is attributed to transcriptional bursting: the stochastic activation and inactivation of promoters that leads to the discontinuous p ...

Royal Society of Chemistry2017

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

Olivier Martin, Bart Deplancke, Felix Naef, Jacques Rougemont, Mauro Delorenzi, Nicolas Jean Philippe Guex, Laura Symul

Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide, we gener ...

Public Library Science2012

Origins and consequences of transcriptional discontinuity

Felix Naef, David Michael Suter

In both prokaryotes and eukaryotes, transcription has been described as being temporally discontinuous, most genes being active mainly during short activity windows interspersed by silent periods. In mammalian cells, recent studies performed at the single ...

2011

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

Felix Naef, Frédéric Bruno Martin Gachon, Daniel Alain Dominique Marie Mauvoisin, Jingkui Wang

Diurnal oscillations of gene expression controlled by the circadian clock underlie rhythmic physiology across most living organisms. Although such rhythms have been extensively studied at the level of transcription and mRNA accumulation, little is known ab ...

National Academy of Sciences2014

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

Felix Naef, Cédric Gobet, Jake Yeung, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger

The circadian clock and associated feeding rhythms have a profound impact on metabolism and the gut microbiome. To what extent microbiota reciprocally affect daily rhythms of physiology in the host remains elusive. Here, we analyzed transcriptome and metab ...

Cell Press2019

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

Felix Naef, Jake Yeung, Maxime Jan

The timing and duration of sleep results from the interaction between a homeostatic sleep-wake-driven process and a periodic circadian process, and involves changes in gene regulation and expression. Unraveling the contributions of both processes and their ...

National Academy of Sciences2019