Felix Naef
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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Web site: Web site: https://naef-lab.epfl.ch
+41 21 693 16 21
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Web site: Web site: https://sv.epfl.ch/education
Web site: Web site: https://dms.epfl.ch/DOCS/E/CDS
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
Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations
2024. DOI : 10.1101/2024.04.08.588507.Light-Driven Thermo-Optical Effects in Nanoresonator Arrays
Advanced Optical Materials. 2023-09-07. DOI : 10.1002/adom.202300698.Uncovering personalized glucose responses and circadian rhythms from multiple wearable biosensors with Bayesian dynamical modeling
Cell Reports Methods. 2023-08-28. DOI : 10.1016/j.crmeth.2023.100545.Sex-dimorphic and age-dependent organization of 24-hour gene expression rhythms in humans
Science. 2023-02-03. DOI : 10.1126/science.add0846.Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology
Annual Review Of Pathology-Mechanisms Of Disease. 2023-01-01. DOI : 10.1146/annurev-pathmechdis-031521-024831.Statistical physics of periodic biological processes
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-9772.V-ATPase/TORC1-mediated ATFS-1 translation directs mitochondrial UPR activation in C. elegans
Journal of Cell Biology. 2022-10-31. DOI : 10.1083/jcb.202205045.Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver
Plos Genetics. 2022-08-01. DOI : 10.1371/journal.pgen.1009903.Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data
Methods. 2022-07-01. DOI : 10.1016/j.ymeth.2021.10.004.Comment on "Circadian rhythms in the absence of the clock gene Bmal1"
Science. 2021-04-16. 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. 2021-03-23. DOI : 10.3390/nu13031042.The circadian oscillator analysed at the single-transcript level
Molecular Systems Biology. 2021-03-01. DOI : 10.15252/msb.202010135.Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle
PLOS Genetics. 2021-02-01. 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. 2021-01-19. DOI : 10.1073/pnas.2015803118.Space-time logic of liver gene expression at sub-lobular scale
Nature Metabolism. 2021-01-11. 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. 2020-12-09. DOI : 10.1098/rsob.200292.Arm-hand motion-force coordination for physical interactions with non-flat surfaces using dynamical systems: Toward compliant robotic massage
2020-05-31. International Conference on Robotics and Automation, Paris, France, Virtual Conference, May 31-June 4, 2020. p. 4724-4730. DOI : 10.1109/ICRA40945.2020.9196593.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. 2020-04-28. 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. 2019-12-17. DOI : 10.1073/pnas.1910590116.Low-dimensional dynamics of two coupled biological oscillators
Nature Physics. 2019-10-01. DOI : 10.1038/s41567-019-0598-1.Organization of temporal gene expression: from circadian clocks to promoter cycles and back
2019-07-01. p. 49-49.Engineered signaling centers for the spatially controlled patterning of human pluripotent stem cells
Nature Methods. 2019-07-01. DOI : 10.1038/s41592-019-0455-2.Quantitative relationships between SMAD dynamics and target gene activation kinetics in single live cells
Scientific Reports. 2019-03-29. DOI : 10.1038/s41598-019-41870-2.Differential regulation of RNA polymerase III genes during liver regeneration
Nucleic Acids Research. 2019-02-28. DOI : 10.1093/nar/gky1282.The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism
Cell Metabolism. 2019-02-05. DOI : 10.1016/j.cmet.2018.09.023.Memory and relatedness of transcriptional activity in mammalian cell lineages
Nature Communications. 2019. DOI : 10.1038/s41467-019-09189-8.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. 2018-12-01. DOI : 10.1016/j.tig.2018.09.005.Cross-regulatory circuits linking inflammation, high-fat diet, and the circadian clock
Genes & Development. 2018-11-01. 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. 2018-09-20. DOI : 10.1016/j.molcel.2018.07.023.Long- and short-term molecular consequences of sleep loss in mice
2018-09-01. 24th Congress of the European-Sleep-Research-Society (ESRS), Basel, SWITZERLAND, Sep 25-28, 2018.Circadian clock- and feeding-dependent regulation of translation initiation and elongation in the liver
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8900.Quantitative single cell dynamics of signaling and transcriptional response in mammalian cells
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8629.Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs
GENOME RESEARCH. 2018. DOI : 10.1101/gr.222430.117.Modulation of transcriptional burst frequency by histone acetylation
Proceedings of the National Academy of Sciences of the United States of America. 2018. DOI : 10.1073/pnas.1722330115.Impact of Powered Knee-Ankle Prosthesis on Low Back Muscle Mechanics in Transfemoral Amputees: A Case Series
Frontiers in Neuroscience. 2018. DOI : 10.3389/fnins.2018.00134.Clock-dependent chromatin topology modulates circadian transcription and behavior
GENES AND DEVELOPMENT. 2018. DOI : 10.1101/gad.312397.118.Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver
Proceedings of the National Academy of Sciences of the United States of America. 2018. DOI : 10.1073/pnas.1715225115.Guidelines for Genome-Scale Analysis of Biological Rhythms
Journal Of Biological Rhythms. 2017. DOI : 10.1177/0748730417728663.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.Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome
Cell Reports. 2017. DOI : 10.1016/j.celrep.2017.07.065.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.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.Temperature regulates splicing efficiency of the cold-inducible RNA-binding protein gene Cirbp
Genes & Development. 2016-09-01. DOI : 10.1101/gad.287094.116.Learning from Tokyo: translation, seuils et interstices à Berlin
2016Phase specific transcriptional regulation of circadian clock and metabolism in mouse liver
Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-7188.Circadian rhythm and cell cycle
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.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. 2015. DOI : 10.1073/pnas.1515308112.Concept of a soft exosuit for the support of leg function in rehabilitation
2015. 2015 IEEE International Conference on Rehabilitation Robotics (ICORR), Singapore, Singapore, 11-14 August 2015. p. 125-130. DOI : 10.1109/ICORR.2015.7281187.Culture, Argent, Public et Société
Cycle La Culture Créatrice de Valeurs, Palais Eynard, Genève, Suisse, Novembre 23, 2015.Structure of silent transcription intervals and noise characteristics of mammalian genes
Molecular Systems Biology. 2015. DOI : 10.15252/msb.20156257.CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings
Methods (San Diego, Calif.). 2015. DOI : 10.1016/j.ymeth.2015.04.023.Quantitative Analysis and Modeling Probe Polarity Establishment in C. elegans Embryos
Biophysical journal. 2015. DOI : 10.1016/j.bpj.2014.12.022.Quantitative single-cell analysis of S. cerevisiae using a microfluidic live-cell imaging platform
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6519.Modeling of transcription mechanisms in mammals from kinetic measurements in single cells
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6414.Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters
Genome Biology. 2014. DOI : 10.1186/gb-2014-15-6-r85.Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells
Molecular Systems Biology. 2014. DOI : 10.15252/msb.20145218.Spatio-temporal synchronization of biological oscillators
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6319.Non-Circadian Expression Masking Clock-Driven Weak Transcription Rhythms in U2OS Cells
Plos One. 2014. DOI : 10.1371/journal.pone.0102238.Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription
Genes & Development. 2014. DOI : 10.1101/gad.244434.114.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. 2014. DOI : 10.1073/pnas.1314066111.Stimulus-induced modulation of transcriptional bursting in a single mammalian gene
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2013. DOI : 10.1073/pnas.1312310110.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.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. 2013. DOI : 10.1073/pnas.1308265110.Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics
Nature methods. 2013. DOI : 10.1038/nmeth.2441.Quantitative analysis and mathematical modeling of polarity establishment in C. elegans embryos
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5863.The CORALIE survey for southern extrasolar planets XVII. New and updated long period and massive planets
Astronomy & Astrophysics. 2013. DOI : 10.1051/0004-6361/201219639.The Circadian Clock Coordinates Ribosome Biogenesis
Plos Biology. 2013. DOI : 10.1371/journal.pbio.1001455.A microfluidic live-cell imaging platform to study large collections of microbial genotypes
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5593.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.Promotion of Science among Youngsters: Today's Crucial Mission for Tomorrow's Society
Chimia. 2012.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.Mammalian genes are transcribed with widely different bursting kinetics
Science (New York, N.Y.). 2011. DOI : 10.1126/science.1198817.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.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.Analysis of the dynamics of limb transcriptomes during mouse development
BMC developmental biology. 2011. DOI : 10.1186/1471-213X-11-47.On the Precision of Circadian Oscillators
Lausanne, EPFL, 2011. DOI : 10.5075/epfl-thesis-5157.On the Relationship Between Protein-DNA Interactions and Circadian Gene Expression in Mouse Liver
Lausanne, EPFL, 2011. DOI : 10.5075/epfl-thesis-5101.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.Assembly Mechanisms and Cellular Effects of Bacterial Pore-Forming Toxins
Lausanne, EPFL, 2011. DOI : 10.5075/epfl-thesis-4896.The CORALIE survey for southern extrasolar planets XVI. Discovery of a planetary system around HD 147018 and of two long period and massive planets orbiting HD 171238 and HD 204313
Astronomy & Astrophysics. 2010. DOI : 10.1051/0004-6361/200912136.Information processing in cells and tissues (IPCAT'2009): from small scale dynamics to understanding systems behavior
Bio Systems. 2010. DOI : 10.1016/j.biosystems.2010.07.015.ASSET: A robust algorithm for the automated segmentation and standardization of early Caenorhabditis elegans embryos
Developmental dynamics. 2010. DOI : 10.1002/dvdy.22486.Development of an interactive genome browser to visualize and analyse large scale genomic data
2010Dissecting the regulation of the key transcription factors T-bet and GATA3 in T-helper cells
2010Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico
Bio Systems. 2010. DOI : 10.1016/j.biosystems.2010.07.014.The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae
Molecular cell. 2010. DOI : 10.1016/j.molcel.2010.04.016.Teaching & PhD
Teaching
Life Sciences Engineering
PhD Students
Curvaia Florian, Duperrex Eliane Jeanne, Leonardi Maxine, Reinert Patricia Barbara, Salati Andrea, Shaikh Arsh Yusuf, Tonin Elena,Past EPFL PhD Students
Becker Johannes , Bieler Jonathan , Bischofberger Mirko , Blanchoud Simon , Cajan Julia Catharina , Cannavo Rosamaria , De Simone Alessandro , Droin Colas Noé , Dénervaud Nicolas , Gobet Cédric , Hurni Clémence Yumie Syloun , Lamberti Irene , Mermet Jérôme , Nicolas Damien Lionel , Rey Guillaume , Sobel Jonathan Aryeh , Symul Laura , Talamanca Lorenzo , Tidin Onur , Yasrebi Haleh , Yeung Jake , Zoller Benjamin , d'Eysmond Thomas ,Courses
Dynamical systems in biology
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
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.