Felix Naef
Nationality: swiss
EPFL SV IBI-SV UPNAE
AAB 2 48 (Bâtiment AAB)
Station 19
1015 Lausanne
+41 21 693 16 21
+41 21 693 83 58
Office:
AAB 2 48
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Website: https://naef-lab.epfl.ch
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Website: https://go.epfl.ch/phd-edcb
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).
Awards
Leenaards Prize
2012
Membership to European Molecular Biology Organization (EMBO)
2020
Infoscience
Cell-cycle inhibition preserves robust development but rebalances lineages in mouse gastruloids
2026CoPhaser: generic modeling of biological cycles in scRNA-seq with context-dependent periodic manifolds
2025Conditional Deep Learning Model Reveals Translation Elongation Determinants during Amino Acid Deprivation
Communications Biology. 2025. DOI : 10.1038/s42003-025-09092-7.Chrono-atlas of cell-type specific daily gene expression rhythms in the regenerating colon
2025Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation
Genome Biology. 2025. DOI : 10.1186/s13059-025-03800-6.Daily liver rhythms: Coupling morphological and molecular oscillations
Proceedings of the National Academy of Sciences. 2025. DOI : 10.1073/pnas.2517648122.Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates
2025Molecular Systems Biology at 20: reflecting on the past, envisioning the future
Molecular systems biology. 2025. DOI : 10.1038/s44320-025-00170-w.Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations
Nature methods. 2024. DOI : 10.1038/s41592-024-02471-8.Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations
2024. 19th Machine Learning in Computational Biology meeting, Seattle, WA, USA, 2024-09-05 - 2024-09-06.The metabolic and circadian signatures of gestational diabetes in the postpartum period characterised using multiple wearable devices
Diabetologia. 2024. DOI : 10.1007/s00125-024-06318-x.Characterisation of EIF5A perturbations on ribosome dynamics with single-molecule imaging
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10511.Uncovering personalized glucose responses and circadian rhythms from multiple wearable biosensors with Bayesian dynamical modeling
Cell Reports Methods. 2023. DOI : 10.1016/j.crmeth.2023.100545.Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans
Science. 2023. DOI : 10.1126/science.add0846.Statistical physics of periodic biological processes
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-9772.Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology
Annual Review Of Pathology-Mechanisms Of Disease. 2023. DOI : 10.1146/annurev-pathmechdis-031521-024831.V-ATPase/TORC1-mediated ATFS-1 translation directs mitochondrial UPR activation in C. elegans
Journal of Cell Biology (JCB). 2022. DOI : 10.1083/jcb.202205045.Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver
Plos Genetics. 2022. DOI : 10.1371/journal.pgen.1009903.Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data
Methods. 2022. DOI : 10.1016/j.ymeth.2021.10.004.Comment on "Circadian rhythms in the absence of the clock gene Bmal1"
Science. 2021. DOI : 10.1126/science.abf0922.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
Nutrients. 2021. DOI : 10.3390/nu13031042.The circadian oscillator analysed at the single-transcript level
Molecular Systems Biology. 2021. DOI : 10.15252/msb.202010135.Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle
PLOS Genetics. 2021. DOI : 10.1371/journal.pgen.1009350.Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2021. DOI : 10.1073/pnas.2015803118.Space-time logic of liver gene expression at sub-lobular scale
Nature Metabolism. 2021. DOI : 10.1038/s42255-020-00323-1.Circadian dynamics of RNA localisation in the mammalian liver
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8104.What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis
Open Biology. 2020. DOI : 10.1098/rsob.200292.Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2020. DOI : 10.1073/pnas.1918145117.Inference methods for the study of interacting biological oscillators in single-cells
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-8364.Sleep-wake-driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2019. DOI : 10.1073/pnas.1910590116.Low-dimensional dynamics of two coupled biological oscillators
Nature Physics. 2019. DOI : 10.1038/s41567-019-0598-1.Organization of temporal gene expression: from circadian clocks to promoter cycles and back
2019. p. 49 - 49.Engineered signaling centers for the spatially controlled patterning of human pluripotent stem cells
Nature Methods. 2019. DOI : 10.1038/s41592-019-0455-2.Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells
Scientific Reports. 2019. DOI : 10.1038/s41598-019-41870-2.Differential regulation of RNA polymerase III genes during liver regeneration
Nucleic Acids Research. 2019. DOI : 10.1093/nar/gky1282.The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism
Cell Metabolism. 2019. DOI : 10.1016/j.cmet.2018.09.023.Tissue-specific circadian transcriptional regulation
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-8893.Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior
Trends In Genetics. 2018. DOI : 10.1016/j.tig.2018.09.005.Cross-regulatory circuits linking inflammation, high-fat diet, and the circadian clock
Genes & Development. 2018. DOI : 10.1101/gad.320911.118.Single Live Cell Monitoring of Protein Turnover Reveals Intercellular Variability and Cell-Cycle Dependence of Degradation Rates
Molecular Cell. 2018. DOI : 10.1016/j.molcel.2018.07.023.Long- and short-term molecular consequences of sleep loss in mice
2018. 24th Congress of the European-Sleep-Research-Society (ESRS), Basel, SWITZERLAND, Sep 25-28, 2018.Quantitative single cell dynamics of signaling and transcriptional response in mammalian cells
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8629.Circadian clock- and feeding-dependent regulation of translation initiation and elongation in the liver
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8900.Ribosome profiling and dynamic regulation of translation in mammals
Current Opinion In Genetics & Development. 2017. DOI : 10.1016/j.gde.2017.03.005.A new promoter element associated with daily time keeping in Drosophila
Nucleic Acids Research. 2017. DOI : 10.1093/nar/gkx268.Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome
Cell Reports. 2017. DOI : 10.1016/j.celrep.2017.07.065.Transcriptional regulatory logic of the diurnal cycle in the mouse liver
PLoS Biology. 2017. DOI : 10.1371/journal.pbio.2001069.Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World
Cold Spring Harbor Perspectives In Biology. 2017. DOI : 10.1101/cshperspect.a028720.Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver
Cell Metabolism. 2017. DOI : 10.1016/j.cmet.2016.10.003.Rhythmic and clock-dependent chromatin loops regulate circadian gene expression
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7485.Rhythmic modulation of transcriptional burst frequency in circadian gene promoters
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-8016.What shapes eukaryotic transcriptional bursting?
Molecular Biosystems. 2017. DOI : 10.1039/c7mb00154a.Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp
Genes & Development. 2016. DOI : 10.1101/gad.287094.116.Circadian rhythm and cell cycle : two synchronized processes
Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-6902.Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling
Biophysical Journal. 2016. DOI : 10.1016/j.bpj.2016.02.035.Mechanisms of centrosome separation in C. elegans
Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-6916.Phase specific transcriptional regulation of circadian clock and metabolism in mouse liver
Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-7188.Quantitative single-cell analysis of S. cerevisiae using a microfluidic live-cell imaging platform
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6519.Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2015. DOI : 10.1073/pnas.1515308112.Structure of silent transcription intervals and noise characteristics of mammalian genes
Molecular Systems Biology. 2015. DOI : 10.15252/msb.20156257.Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells
Molecular Systems Biology. 2014. DOI : 10.15252/msb.20145218.Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters
Genome Biology. 2014. DOI : 10.1186/gb-2014-15-6-r85.Spatio-temporal synchronization of biological oscillators
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6319.Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription
Genes & Development. 2014. DOI : 10.1101/gad.244434.114.Non-Circadian Expression Masking Clock-Driven Weak Transcription Rhythms in U2OS Cells
Plos One. 2014. DOI : 10.1371/journal.pone.0102238.Context-specific regulation of BMAL1 target genes during the circadian rhythm in mouse
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6308.Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2014. DOI : 10.1073/pnas.1314066111.Modeling of transcription mechanisms in mammals from kinetic measurements in single cells
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6414.A chemostat array enables the spatio-temporal analysis of the yeast proteome
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2013. DOI : 10.1073/pnas.1308265110.A microfluidic live-cell imaging platform to study large collections of microbial genotypes
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5593.Stimulus-induced modulation of transcriptional bursting in a single mammalian gene
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2013. DOI : 10.1073/pnas.1312310110.Quantitative analysis and mathematical modeling of polarity establishment in C. elegans embryos
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5863.Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics
Nature methods. 2013. DOI : 10.1038/nmeth.2441.Kinetic Analysis of Transcriptional and Post-Transcriptional Processes During Circadian Cycles
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5911.Analysis of precision in chemical oscillators: implications for circadian clocks
Physical biology. 2013. DOI : 10.1088/1478-3975/10/5/056005.The Circadian Clock Coordinates Ribosome Biogenesis
Plos Biology. 2013. DOI : 10.1371/journal.pbio.1001455.Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles
Plos Biology. 2012. DOI : 10.1371/journal.pbio.1001442.Cold-Inducible RNA-Binding Protein Modulates Circadian Gene Expression Posttranscriptionally
Science. 2012. DOI : 10.1126/science.1217726.Circadian Dbp Transcription Relies on Highly Dynamic BMAL1-CLOCK Interaction with E Boxes and Requires the Proteasome
Molecular Cell. 2012. DOI : 10.1016/j.molcel.2012.08.012.Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver
PLoS biology. 2011. DOI : 10.1371/journal.pbio.1000595.Mammalian genes are transcribed with widely different bursting kinetics
Science. 2011. DOI : 10.1126/science.1198817.Computational analysis of protein-DNA interactions from ChIP-seq data
Methods in molecular biology (Clifton, N.J.). 2011. DOI : 10.1007/978-1-61779-292-2_16.Origins and consequences of transcriptional discontinuity
Current opinion in cell biology. 2011. DOI : 10.1016/j.ceb.2011.09.004.Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains
Biophysical Journal. 2011. DOI : 10.1016/j.bpj.2011.05.060.Analysis of the dynamics of limb transcriptomes during mouse development
BMC developmental biology. 2011. DOI : 10.1186/1471-213X-11-47.The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae
Molecular cell. 2010. DOI : 10.1016/j.molcel.2010.04.016.Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico
Bio Systems. 2010. DOI : 10.1016/j.biosystems.2010.07.014.A self-regulatory system of interlinked signaling feedback loops controls mouse limb patterning
Science. 2009. DOI : 10.1126/science.1168755.Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays
Genome biology. 2009. DOI : 10.1186/gb-2009-10-2-r17.Circadian gene expression is resilient to large fluctuations in overall transcription rates
The EMBO journal. 2009. DOI : 10.1038/emboj.2008.262.Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors
BMC genomics. 2009. DOI : 10.1186/1471-2164-10-381.Probabilistic base calling of Solexa sequencing data
BMC bioinformatics. 2008. DOI : 10.1186/1471-2105-9-431.Modeling an evolutionary conserved circadian cis-element
PLoS Computational Biology. 2008. DOI : 10.1371/journal.pcbi.0040038.Stochastic phase oscillator models for circadian clocks
Cellular Oscillatory Mechanisms; Springer, 2008. p. 141 - 149.Stochastic phase oscillators and circadian bioluminescence recordings
2007. 72nd Cold Spring Harbor Symposium on Quantitative Biology, Cold Spring Harbor, NY, May 30, 2007. p. 405 - 411.Representing perturbed dynamics in biological network models
Physical Review E. 2007. DOI : 10.1103/PhysRevE.76.011917.Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks
Molecular systems biology. 2007. DOI : 10.1038/msb4100130.Identifying synergistic regulation involving c-Myc and sp1 in human tissues
Nucleic Acids Research. 2007. DOI : 10.1093/nar/gkl1157.Integration of light and temperature in the regulation of circadian gene expression in Drosophila
PLoS genetics. 2007. DOI : 10.1371/journal.pgen.0030054.Stochastic phase oscillators and circadian bioluminescence recordings
Cold Spring Harbor symposia on quantitative biology. 2007. DOI : 10.1101/sqb.2007.72.044.Similarities and differences of polyadenylation signals in human and fly
BMC Genomics. 2006. DOI : 10.1186/1471-2164-7-176.Collective synchronization in populations of globally coupled phase oscillators with drifting frequencies
Physical Review E. 2006. DOI : 10.1103/PhysRevE.73.011104.In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis
Molecular and cellular neurosciences. 2006. DOI : 10.1016/j.mcn.2005.10.005.The nodal precursor acting via activin receptors induces mesoderm by maintaining a source of its convertases and BMP4
Developmental Cell. 2006. DOI : 10.1016/j.devcel.2006.07.005.Control of daily transcript oscillations in Drosophila by light and the circadian clock
PLoS genetics. 2006. DOI : 10.1371/journal.pgen.0020039.Molecular and statistical tools for circadian transcript profiling
Circadian Rhythms; Elsevier, 2005. p. 341 - 365.Cellular oscillators: rhythmic gene expression and metabolism
Current opinion in cell biology. 2005. DOI : 10.1016/j.ceb.2005.01.007.Circadian clocks go in vitro: purely post-translational oscillators in cyanobacteria
Molecular systems biology. 2005. DOI : 10.1038/msb4100027.Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks
Nucleic Acids Research. 2005. DOI : 10.1093/nar/gni104.Freedom and rules: the acquisition and reprogramming of a bird's learned song
Science. 2005. DOI : 10.1126/science.1108214.Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells
Cell. 2004. DOI : 10.1016/j.cell.2004.11.015.Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays
Nucleic Acids Research. 2003. DOI : 10.1093/nar/gkg283.Molecular signature of human embryonic stem cells and its comparison with the mouse
Developmental biology. 2003. DOI : 10.1016/S0012-1606(03)00256-2.A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations
Bioinformatics. 2003. DOI : 10.1093/bioinformatics/19.2.178.Production of ribosome components in effector CD4+ T cells is accelerated by TCR stimulation and coordinated by ERK-MAPK
Immunity. 2003. DOI : 10.1016/S1074-7613(03)00268-1.Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays
Physical Review E. 2003. DOI : 10.1103/PhysRevE.68.011906.Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays
Genome biology. 2002. DOI : 10.1186/gb-2002-3-4-research0018.DNA hybridization to mismatched templates: a chip study
Physical Review E. 2002. DOI : 10.1103/PhysRevE.65.040902.Circadian regulation of gene expression systems in the Drosophila head
Neuron. 2001. DOI : 10.1016/S0896-6273(01)00515-3.Dynamical properties of quasi one-dimensional correlated electrons
Lausanne, EPFL, 2000. DOI : 10.5075/epfl-thesis-2127.Teaching & PhD
PhD Students
Eliane Duperrex, Patricia Reinert, Florian Curvaia, Elena Tonin, Maxine Leonardi, Arsh Yusuf Shaikh, Yves Jean Paychère, Andrea Salati
Past EPFL PhD Students
Guillaume Rey, Thomas d'Eysmond, Mirko Bischofberger, Laura Symul, Jonathan Bieler, Benjamin Zoller, Julia Catharina Cajan, Johannes Becker, Jonathan Aryeh Sobel, Rosamaria Cannavo, Damien Lionel Nicolas, Jérôme Mermet, Cédric Gobet, Jake Yeung, Colas Noé Droin, Clémence Yumie Syloun Hurni, Lorenzo Talamanca, Irene Lamberti
Past EPFL PhD Students as codirector
Haleh Yasrebi, Simon Blanchoud, Nicolas Dénervaud, Alessandro De Simone, Onur Tidin
Courses
Dynamical systems in biology
BIO-341
Life is non-linear. This course introduces dynamical systems as a technique for modelling simple biological processes. The emphasis is on the qualitative and numerical analysis of non-linear dynamical models. Examples are taken from biology and population models.
Life Sciences engineering: genome to function
BIO-411
Students will acquire fundamental knowledge regarding how genomes can be engineered, how their function can be deciphered, and how their dynamic outputs can be analyzed and modeled, exemplified with a focus on cell cycle progression and proliferation control.