Cell-cycle inhibition preserves robust development but rebalances lineages in mouse gastruloids

M. Leonardi; Y. Paychère; F. Naef 

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. 

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

Y. Paychere; A. Salati; C. Gobet; F. Naef 

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. 

Clock-dependent chromatin topology modulates circadian transcription and behavior

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

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. 

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. 

Modulation of transcriptional burst frequency by histone acetylation

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

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. 

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

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 

Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver

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

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

J. Mermet; J. Yeung; 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 

Ribosome profiling and dynamic regulation of translation in mammals

C. Gobet; F. Naef 

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

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 

Structure of silent transcription intervals and noise characteristics of mammalian genes

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

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

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

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

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. 

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. 

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

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

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. 

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

Spatio-temporal synchronization of biological oscillators

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

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

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

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. 

Analysis of precision in chemical oscillators: implications for circadian clocks

T. d’Eysmond; A. De Simone; F. Naef 

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. 

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

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

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. 

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 

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

J. Rougemont; F. Naef 

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

J. Bieler; C. Pozzorini; F. Naef 

Analysis of the dynamics of limb transcriptomes during mouse development

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

Mammalian genes are transcribed with widely different bursting kinetics

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

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 

On the Precision of Circadian Oscillators

Assembly Mechanisms and Cellular Effects of Bacterial Pore-Forming Toxins

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

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. 

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

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

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 

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

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. 

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. 

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 

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. 

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. 

Genotypic features of lentivirus transgenic mice

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

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 

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 

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 

Similarities and differences of polyadenylation signals in human and fly

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

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. 

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

J. Rougemont; 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 

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

F. Naef; J. Huelsken 

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. 

Cellular oscillators: rhythmic gene expression and metabolism

U. Schibler; F. Naef 

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

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. 

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. 

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

F. Naef; M. O. Magnasco 

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. 

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

F. Naef; N. D. Socci; M. Magnasco 

DNA hybridization to mismatched templates: a chip study

F. Naef; D. A. Lim; 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. 

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

F. Naef; C. R. Hacker; 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.