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

M. V. Nallapareddy; F. Craighero; L. Worpenberg; F. Naef; C. Gobet et al. 

Cadherins modulate the self-organizing potential of pseudo-embryos

A. Mayran; D. Kolly; L. Lopez-Delisle; Y. Romaniuk; M. Leonardi et al. 

Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation

L. Worpenberg; C. Gobet; F. Naef 

Daily liver rhythms: Coupling morphological and molecular oscillations

U. Schibler; F. Sinturel; F. Naef; A. Gerber; D. Gatfield 

Molecular Systems Biology at 20: reflecting on the past, envisioning the future

P. Bheda; J. Hou; R. Aebersold; U. Alon; J. S. Bader et al. 

Chrono-atlas of cell-type specific daily gene expression rhythms in the regenerating colon

V. C. Alcocer; C. Gobet; J. MacDonald; Z. Taleb; F. Naef et al. 

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

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

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

A. R. Lederer; M. Leonardi; L. Talamanca; D. M. Bobrovskiy; A. Herrera et al. 

The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation

M. Henis; T. Ruecker; R. Scharrenberg; M. Richter; L. Baltussen et al. 

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

N. E. Phillips; J. Mareschal; A. D. Biancolin; F. Sinturel; S. Umwali et al. 

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

M. V. Nallapareddy; F. Craighero; F. Naef; C. Gobet; P. Vandergheynst 

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

N. E. Phillips; T-H. Collet; F. Naef 

ASIC1a affects hypothalamic signaling and regulates the daily rhythm of body temperature in mice

Z. Peng; P. G. Ziros; T. Martini; X-H. Liao; R. Stoop et al. 

Mice with humanized livers reveal the role of hepatocyte clocks in rhythmic behavior

A-S. Delbes; M. Quinones; C. Gobet; J. Castel; R. G. P. Denis et al. 

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

L. Talamanca; C. Gobet; F. Naef 

Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology

T. Martini; F. Naef; J. S. Tchorz 

Statistical physics of periodic biological processes

The Role of Molecular Clock Genes in Astrocytes of the Nucleus Accumbens in Reward- and Mood- Related Behavior in Mice

T. Martini 

The effects of time-restricted eating and weight loss on bone metabolism and health: a 6-month randomized controlled trial

M. Papageorgiou; E. Biver; J. Mareschal; N. E. Phillips; A. Hemmer et al. 

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

C. S. Hurni; B. Weger; C. S. Gobet; F. Naef 

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

C. Gobet; F. Naef 

Pum2 and TDP-43 refine area-specific cytoarchitecture post-mitotically and modulate translation of Sox5, Bcl11b, and Rorb mRNAs in developing mouse neocortex

K. Harb; M. Richter; N. Neelagandan; E. Magrinelli; H. Harfoush et al. 

The integrated stress response contributes to tRNA synthetase-associated peripheral neuropathy

E. L. Spaulding; T. J. Hines; P. Bais; A. L. D. Tadenev; R. Schneider et al. 

Comment on “Circadian rhythms in the absence of the clock gene Bmal1”

K. C. Abruzzi; C. Gobet; F. Naef; M. Rosbash 

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

N. E. Phillips; J. Mareschal; N. Schwab; E. N. C. Manoogian; S. Borloz et al. 

The circadian oscillator analysed at the single-transcript level

N. E. Phillips; A. Hugues; J. Yeung; E. Durandau; D. Nicolas et al. 

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

J. Mermet; J. Yeung; F. Naef 

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

B. D. Weger; C. Gobet; F. P. A. David; F. Atger; E. Martin et al. 

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

C. Droin; J. El Kholtei; K. B. Halpern; C. Hurni; M. Rozenberg et al. 

Circadian dynamics of RNA localisation in the mammalian liver

Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory

P. Bheda; D. Aguilar-Gomez; N. B. Becker; J. Becker; E. Stavrou et al. 

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

C. Gobet; B. D. Weger; J. Marquis; E. Martin; N. Neelagandan et al. 

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

N. Neelagandan; I. Lamberti; H. J. F. Carvalho; C. Gobet; F. Naef 

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

C. N. Hor; J. Yeung; M. Jan; Y. Emmenegger; J. Hubbard et al. 

Low-dimensional dynamics of two coupled biological oscillators

C. Droin; E. R. Paquet; F. Naef 

Circadian rhythms and proteomics: It’s all about posttranslational modifications!

D. Mauvoisin 

Circadian Regulation of Cochlear Sensitivity to Noise by Circulating Glucocorticoids

C. R. Cederroth; J-s. Park; V. Basinou; B. D. Weger; E. Tserga et al. 

Assessment of menstrual health status and evolution through mobile apps for fertility awareness

L. Symul; K. Wac; P. Hillard; M. Salathe 

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

A. Manfrin; Y. Tabata; E. R. Paquet; A. R. Vuaridel; F. R. Rivest et al. 

Microbiota and the clock: sexual dimorphism matters!

B. D. Weger; F. Gachon 

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

O. Tidin; E. T. Friman; F. Naef; D. M. Suter 

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

B. D. Weger; C. Gobet; J. Yeung; E. Martin; S. Jimenez et al. 

Memory and relatedness of transcriptional activity in mammalian cell lineages

N. E. Phillips; A. Mandic; S. Omidi; F. Naef; D. M. Suter 

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

F. Naef 

At the Intersection of Microbiota and Circadian Clock: Are Sexual Dimorphism and Growth Hormones the Missing Link to Pathology? Circadian Clock and Microbiota: Potential Egffect on Growth Hormone and Sexual Development

B. D. Weger; O. Rawashdeh; F. Gachon 

Tissue-specific circadian transcriptional regulation

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

F. Gachon; J. Yeung; F. Naef 

Glucocorticoid deficiency causes transcriptional and post-transcriptional reprogramming of glutamine metabolism

M. Weger; B. D. Weger; B. Goerling; G. Poschet; M. Yildiz et al. 

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

A. B. Alber; E. R. Paquet; M. Biserni; F. Naef; D. M. Suter 

Casein kinase 2 mediated phosphorylation of Spt6 modulates histone dynamics and regulates spurious transcription

E. Gouot; W. Bhat; A. Rufiange; E. Fournier; E. Paquet et al. 

Circadian clock-dependent and -independent posttranscriptional regulation underlies temporal mRNA accumulation in mouse liver

J. Wang; L. Symul; J. Yeung; C. Gobet; J. Sobel et al. 

Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs

J. Yeung; J. Mermet; C. Jouffe; J. Marquis; A. Charpagne et al. 

Transcriptomic analyses reveal rhythmic and CLOCK-driven pathways in human skeletal muscle

L. Perrin; U. Loizides-Mangold; S. Chanon; C. Gobet; N. Hulo et al. 

Clock-dependent chromatin topology modulates circadian transcription and behavior

J. Mermet; J. Yeung; C. Hurni; D. Mauvoisin; K. Gustafson et al. 

Modulation of transcriptional burst frequency by histone acetylation

D. Nicolas; B. Zoller; D. Suter; F. Naef 

Impact of Powered Knee-Ankle Prosthesis on Low Back Muscle Mechanics in Transfemoral Amputees: A Case Series

C. Jayaraman; S. Hoppe-Ludwig; S. Deems-Dluhy; M. McGuire; C. Mummidisetty et al. 

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

C. N. Hor; J. Yeung; M. Jan; Y. Emmenegger; J. Hubbard et al. 

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

J. Yeung; F. Naef 

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

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

J. Mermet; J. Yeung; F. Naef 

Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver

J. Wang; D. Mauvoisin; E. Martin; F. Atger; A. N. Galindo et al. 

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

J. A. Sobel; I. Krier; T. Andersin; S. Raghav; D. Canella et al. 

Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome

D. Mauvoisin; F. Atger; L. Dayon; A. N. Galindo; J. Wang et al. 

A new promoter element associated with daily time keeping in Drosophila

B. Sharp; E. Paquet; F. Naef; A. Bafna; H. Wijnen 

Ribosome profiling and dynamic regulation of translation in mammals

C. Gobet; F. Naef 

What shapes eukaryotic transcriptional bursting?

D. Nicolas; N. E. Phillips; F. Naef 

Regulation of Mammalian Physiology by interconnected Circadian and Feeding Rhythms

F. Atger; D. Mauvoisin; B. Weger; C. Gobet; F. Gachon 

Rhythmic modulation of transcriptional burst frequency in circadian gene promoters

Rhythmic and clock-dependent chromatin loops regulate circadian gene expression

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

I. Gotic; S. Omidi; F. Fleury-Olela; N. Molina; F. Naef et al. 

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

M. Bischofberger; I. Iacovache; D. Boss; F. Naef; F. G. van der Goot et al. 

Circadian rhythm and cell cycle : two synchronized processes

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

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

F. Atger; C. Gobet; J. Marquis; E. Martin; J. Wang et al. 

Quantitative Analysis and Modeling Probe Polarity Establishment in C. elegans Embryos

S. Blanchoud; C. Busso; F. Naef; P. Gönczy 

Structure of silent transcription intervals and noise characteristics of mammalian genes

B. Zoller; D. L. Nicolas; N. Molina; F. Naef 

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

S. Blanchoud; D. Nicolas; B. Zoller; O. Tidin; F. Naef 

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

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

D. Mauvoisin; J. Wang; C. Jouffe; E. Martin; F. Atger et al. 

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

M. Quinodoz; C. Gobet; F. Naef; K. B. Gustafson 

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

B. Knight; S. Kubik; B. Ghosh; M. J. Bruzzone; M. Geertz et al. 

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

J. Hoffmann; L. Symul; A. Shostak; T. Fischer; F. Naef et al. 

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

J. Bieler; R. Cannavo; K. Gustafson; C. A. Gobet; G. David et al. 

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

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

Spatio-temporal synchronization of biological oscillators

The Circadian Clock Coordinates Ribosome Biogenesis

C. Jouffe; G. Cretenet; L. Symul; E. Martin; F. Atger et al. 

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

N. Dénervaud; J. Becker; R. Delgado-Gonzalo; P. Damay; A. S. Rajkumar et al. 

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

J. Simicevic; A. W. Schmid; P. A. Gilardoni; B. Zoller; S. K. Raghav et al. 

Analysis of precision in chemical oscillators: implications for circadian clocks

T. d’Eysmond; A. De Simone; F. Naef 

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

N. Molina; D. M. Suter; R. Cannavo; B. Zoller; I. Gotic et al. 

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

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

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

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

M. Stratmann; D. M. Suter; N. Molina; F. Naef; U. Schibler 

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

G. Le Martelot; D. Canella; L. Symul; E. Migliavacca; F. Gilardi et al. 

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

J. Morf; G. Rey; K. Schneider; M. Stratmann; J. Fujita et al. 

Mammalian genes are transcribed with widely different bursting kinetics

D. M. Suter; N. Molina; D. Gatfield; K. Schneider; U. Schibler et al. 

Analysis of the dynamics of limb transcriptomes during mouse development

I. Gyurján; B. Sonderegger; F. Naef; D. Duboule 

Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains

J. Bieler; C. Pozzorini; F. Naef 

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

G. Rey; F. Cesbron; J. Rougemont; H. Reinke; M. Brunner et al. 

Origins and consequences of transcriptional discontinuity

D. M. Suter; N. Molina; F. Naef; U. Schibler 

Computational analysis of protein-DNA interactions from ChIP-seq data

J. Rougemont; F. Naef 

On the Relationship Between Protein-DNA Interactions and Circadian Gene Expression in Mouse Liver

On the Precision of Circadian Oscillators

Assembly Mechanisms and Cellular Effects of Bacterial Pore-Forming Toxins

Information processing in cells and tissues (IPCAT’2009): from small scale dynamics to understanding systems behavior

A. Egri-Nagy; B. Galliot; F. Naef; C. L. Nehaniv 

ASSET: A robust algorithm for the automated segmentation and standardization of early Caenorhabditis elegans embryos

S. Blanchoud; Y. Budirahardja; F. Naef; P. Gönczy 

The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae

M. Preti; C. Ribeyre; C. Pascali; M. C. Bosio; B. Cortelazzi et al. 

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

G. Stoll; M. Bischofberger; J. Rougemont; F. Naef 

Prediction of Survival and Risk Assessment Using Joint Analysis of Microarray Gene Expression Data

Circadian gene expression is resilient to large fluctuations in overall transcription rates

C. Dibner; D. Sage; M. Unser; C. Bauer; T. d’Eysmond et al. 

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

S. P. Hazen; F. Naef; T. Quisel; J. M. Gendron; H. Chen et al. 

Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors

F. Parisi; B. Sonderegger; P. Wirapati; M. Delorenzi; F. Naef 

A self-regulatory system of interlinked signaling feedback loops controls mouse limb patterning

J-D. Bénazet; M. Bischofberger; E. Tiecke; A. Gonçalves; J. F. Martin et al. 

Genotypic features of lentivirus transgenic mice

M-O. Sauvain; A. P. Dorr; B. Stevenson; A. Quazzola; F. Naef et al. 

Modeling an evolutionary conserved circadian cis-element

E. R. Paquet; G. Rey; F. Naef 

Probabilistic base calling of Solexa sequencing data

J. Rougemont; A. Amzallag; C. Iseli; L. Farinelli; I. Xenarios et al. 

Effects of base-pair sequence, nicks and gaps on DNA minicircle shapes : analysis and experiment

Stochastic phase oscillator models for circadian clocks

J. Rougemont; F. Naef 

Representing perturbed dynamics in biological network models

G. Stoll; J. Rougemont; F. Naef 

Dynamical signatures of cellular fluctuations and oscillator stability in peripheral circadian clocks

J. Rougemont; F. Naef 

Integration of light and temperature in the regulation of circadian gene expression in Drosophila

C. E. Boothroyd; H. Wijnen; F. Naef; L. Saez; M. W. Young 

Identifying synergistic regulation involving c-Myc and sp1 in human tissues

F. Parisi; P. Wirapati; F. Naef 

Stochastic phase oscillators and circadian bioluminescence recordings

J. Rougemont; F. Naef 

Stochastic phase oscillators and circadian bioluminescence recordings

J. Rougemont; F. Naef 

The nodal precursor acting via activin receptors induces mesoderm by maintaining a source of its convertases and BMP4

N. Ben-Haim; C. Lu; M. Guzman-Ayala; L. Pescatore; D. Mesnard et al. 

Few crucial links assure checkpoint efficiency in the yeast cell-cycle network

G. Stoll; J. Rougemont; F. Naef 

Collective synchronization in populations of globally coupled phase oscillators with drifting frequencies

J. Rougemont; F. Naef 

Similarities and differences of polyadenylation signals in human and fly

D. Retelska; C. Iseli; P. Bucher; C. V. Jongeneel; F. Naef 

Control of daily transcript oscillations in Drosophila by light and the circadian clock

H. Wijnen; F. Naef; C. Boothroyd; A. Claridge-Chang; M. W. Young 

In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis

D. A. Lim; M. Suárez-Fariñas; F. Naef; C. R. Hacker; B. Menn et al. 

Freedom and rules: the acquisition and reprogramming of a bird’s learned song

T. J. Gardner; F. Naef; F. Nottebohm 

Chemotaxis behavior mediated by single larval olfactory neurons in Drosophila

E. Fishilevich; A. I. Domingos; K. Asahina; F. Naef; L. B. Vosshall et al. 

Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks

F. Naef; J. Huelsken 

Circadian clocks go in vitro: purely post-translational oscillators in cyanobacteria

F. Naef 

Cellular oscillators: rhythmic gene expression and metabolism

U. Schibler; F. Naef 

Molecular and statistical tools for circadian transcript profiling

H. Wijnen; F. Naef; M. W. Young 

Circadian gene expression in individual fibroblasts: cell-autonomous and self-sustained oscillators pass time to daughter cells

E. Nagoshi; C. Saini; C. Bauer; T. Laroche; F. Naef et al. 

Molecular signature of human embryonic stem cells and its comparison with the mouse

N. Sato; I. M. Sanjuan; M. Heke; M. Uchida; F. Naef et al. 

Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays

D. Hekstra; A. R. Taussig; M. Magnasco; F. Naef 

Production of ribosome components in effector CD4+ T cells is accelerated by TCR stimulation and coordinated by ERK-MAPK

M. Asmal; J. Colgan; F. Naef; B. Yu; Y. Lee et al. 

A study of accuracy and precision in oligonucleotide arrays: extracting more signal at large concentrations

F. Naef; N. D. Socci; M. Magnasco 

Solving the riddle of the bright mismatches: labeling and effective binding in oligonucleotide arrays

F. Naef; M. O. Magnasco 

Empirical characterization of the expression ratio noise structure in high-density oligonucleotide arrays

F. Naef; C. R. Hacker; N. Patil; M. Magnasco 

Genomic and expression analysis of the 12p11-p12 amplicon using EST arrays identifies two novel amplified and overexpressed genes

V. Bourdon; F. Naef; P. H. Rao; V. Reuter; S. C. Mok et al. 

DNA hybridization to mismatched templates: a chip study

F. Naef; D. A. Lim; N. Patil; M. Magnasco 

Circadian regulation of gene expression systems in the Drosophila head

A. Claridge-Chang; H. Wijnen; F. Naef; C. Boothroyd; N. Rajewsky et al.