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

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

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

N. E. Phillips; T-H. Collet; F. Naef 

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

V-ATPase/TORC1-mediated ATFS-1 translation directs mitochondrial UPR activation in C. elegans

T. Y. Li; A. W. Gao; X. Li; H. Li; Y. J. Liu 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 

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

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 

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. 

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

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

Differential regulation of RNA polymerase III genes during liver regeneration

M. Yeganeh; V. Praz; C. Carmeli; D. Villeneuve; L. Rib et al. 

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 

Tissue-specific circadian transcriptional regulation

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

F. Gachon; J. Yeung; F. Naef 

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 

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. 

Modulation of transcriptional burst frequency by histone acetylation

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

Clock-dependent chromatin topology modulates circadian transcription and behavior

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

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

Quantitative single cell dynamics of signaling and transcriptional response in mammalian cells

Guidelines for Genome-Scale Analysis of Biological Rhythms

M. E. Hughes; K. C. Abruzzi; R. Allada; R. Anafi; A. B. Arpat 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 

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

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

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. 

What shapes eukaryotic transcriptional bursting?

D. Nicolas; N. E. Phillips; F. Naef 

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. 

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

Circadian rhythm and cell cycle

Mechanisms of centrosome separation in C. elegans

Learning from Tokyo: translation, seuils et interstices à Berlin

C. Naef 

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. 

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 Analysis and Modeling Probe Polarity Establishment in C. elegans Embryos

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

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

Culture, Argent, Public et Société

L. Pattaroni; F. Benhamou; I. Naef Galuba; C. Schiaretti; S. Kanaan 

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

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

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. 

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

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

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. 

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

Mathematical models and computational methods for the analysis of genome-scale protein synthesis

Spatio-temporal synchronization of biological oscillators

Computational studies in epigenomics using histone modification data

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

Antibiotic-Induced Killing and Persistence of Mycobacteria

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

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

Analysis of precision in chemical oscillators: implications for circadian clocks

T. d’Eysmond; A. De Simone; F. Naef 

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. 

The CORALIE survey for southern extrasolar planets XVII. New and updated long period and massive planets

M. Marmier; D. Segransan; S. Udry; M. Mayor; F. Pepe et al. 

The Circadian Clock Coordinates Ribosome Biogenesis

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

Systematic Analysis of Yeast Gene Expression by Synthetic Promoter Libraries

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

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

Sliced Inverse Regression for Lifetimes and a Remark on High-Dimensional Graphical Models

Molecular Modeling of Membrane Embedded Proteins

Involvement of the THO complex subunit Thp2 in telomere stability

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

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. 

Promotion of Science among Youngsters: Today’s Crucial Mission for Tomorrow’s Society

F. Moser; R. Naef 

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 

Dissecting Gene Regulatory Networks Using Targeted Quantitative Proteomics

Mammalian genes are transcribed with widely different bursting kinetics

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

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

J. Bieler; C. Pozzorini; F. Naef 

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

J. Rougemont; F. Naef 

Origins and consequences of transcriptional discontinuity

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

Analysis of the dynamics of limb transcriptomes during mouse development

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

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. 

On the Precision of Circadian Oscillators

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

Assembly Mechanisms and Cellular Effects of Bacterial Pore-Forming Toxins

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

D. Segransan; S. Udry; M. Mayor; D. Naef; F. Pepe et al. 

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 autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation

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

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 

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 

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. 

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 

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. 

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. 

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 

Microbiota and the clock: sexual dimorphism matters!

B. D. Weger; F. Gachon 

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 

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 

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

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

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. 

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. 

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. 

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. 

Clock-dependent chromatin topology modulates circadian transcription and behavior

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

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

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 

Transcriptional regulatory logic of the diurnal cycle in the mouse liver

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

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. 

What shapes eukaryotic transcriptional bursting?

D. Nicolas; N. E. Phillips; F. Naef 

Ribosome profiling and dynamic regulation of translation in mammals

C. Gobet; 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. 

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

Circadian rhythm and cell cycle

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. 

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 Analysis and Modeling Probe Polarity Establishment in C. elegans Embryos

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

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

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

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

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. 

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

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

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. 

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

Spatio-temporal synchronization of biological oscillators

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

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

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

Analysis of precision in chemical oscillators: implications for circadian clocks

T. d’Eysmond; A. De Simone; F. Naef 

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. 

The Circadian Clock Coordinates Ribosome Biogenesis

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

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 

Mammalian genes are transcribed with widely different bursting kinetics

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

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

J. Bieler; C. Pozzorini; F. Naef 

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

J. Rougemont; F. Naef 

Origins and consequences of transcriptional discontinuity

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

Analysis of the dynamics of limb transcriptomes during mouse development

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

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. 

On the Precision of Circadian Oscillators

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

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 

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

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