Publications by Felix Naef | EPFL Graph Search

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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 ...

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 ...

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 ...

Biological cycles such as the cell cycle and circadian rhythms are fundamental cell-autonomous processes that are often obscured in single-cell RNA sequencing (scRNA-seq) data by other sources of variation, including cell-type identity, metabolic or disease-associated states. Disentangling these continuous periodic trajectories from other forms of cellular variability remains a major challenge in single-cell analysis. Here, we introduce CoPhaser, an algorithm designed to learn context-dependent periodic man

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

The cell division cycle is a ubiquitous essential process across the tree of life. Understanding cell cycle dynamics is crucial for studying biological processes such as growth, development and disease progression. While fluorescent protein reporters like the Fucci system allow live monitoring of cell cycle phases, they require genetic engineering and occupy additional fluorescence channels, limiting broader applicability in complex experiments. In this study, we conduct a comprehensive evaluation of deep l

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 ...

Biochemical reaction networks often exhibit spontaneous self-sustained oscillations. An example is the circadian oscillator that lies at the heart of daily rhythms in behavior and physiology in most organisms including humans. While the period of these oscillators evolved so that it resonates with the 24 h daily environmental cycles, the precision of the oscillator (quantified via the Q factor) is another relevant property of these cell-autonomous oscillators. Since this quantity can be measured in individu

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 ...

Felix Naef

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

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

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

CoPhaser: generic modeling of biological cycles in scRNA-seq with context-dependent periodic manifolds

Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology

Stochastic phase oscillator models for circadian clocks

The circadian oscillator analysed at the single-transcript level

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

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

Probabilistic base calling of Solexa sequencing data

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

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

Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver

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

What shapes eukaryotic transcriptional bursting?

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

Sequence models for continuous cell cycle stage prediction from brightfield images

Origins and consequences of transcriptional discontinuity

Analysis of precision in chemical oscillators: implications for circadian clocks

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