Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes

What time is it? Deep learning approaches for circadian rhythms

(2016) Forest Agostinelli et al.   BIOINFORMATICS

A Statistical Approach Reveals Designs for the Most Robust Stochastic Gene Oscillators

(2016) Mae L. Woods et al.   ACS Synthetic Biology

Stochasticity in the miR-9/Hes1 oscillatory network can account for clonal heterogeneity in the timing of differentiation

(2016) Nick E Phillips et al.   eLife

A stochastic transcriptional switch model for single cell imaging data

(2015) Kirsty L. Hey et al.   BIOSTATISTICS

Bayesian inference of reaction kinetics from single-cell recordings across a heterogeneous cell population

(2015) L. Bronstein et al.   METHODS

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

(2015) Ning Leng et al.   NATURE METHODS

Nuclear Retention of mRNA in Mammalian Tissues

(2015) Keren Bahar Halpern et al.   Cell Reports

Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation

(2015) Gabriele Micali et al.   PLoS Computational Biology

MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells

(2015) Richard Moore et al.   PLoS Computational Biology

Limits on information transduction through amplitude and frequency regulation of transcription factor activity

(2015) Anders S Hansen et al.   eLife

Polyphasic feedback enables tunable cellular timers

(2014) Joe H. Levine et al.   CURRENT BIOLOGY

Evaluation of Five Methods for Genome-Wide Circadian Gene Identification

(2014) Gang Wu et al.   JOURNAL OF BIOLOGICAL RHYTHMS

Detecting Rhythms in Time Series with RAIN

(2014) Paul F. Thaben et al.   JOURNAL OF BIOLOGICAL RHYTHMS

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

(2014) J. Bieler et al.   Molecular Systems Biology

Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings

(2014) Christoph Zechner et al.   NATURE METHODS

Strengths and Limitations of Period Estimation Methods for Circadian Data

(2014) Tomasz Zielinski et al.   PLoS One

Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle

(2014) Céline Feillet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic signal encoding—From cells to organisms

(2014) Katharina F. Sonnen et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

microRNA input into a neural ultradian oscillator controls emergence and timing of alternative cell states

(2014) Marc Goodfellow et al.   Nature Communications

Inference on periodicity of circadian time series

(2013) M. J. Costa et al.   BIOSTATISTICS

Using Optogenetics to Interrogate the Dynamic Control of Signal Transmission by the Ras/Erk Module

(2013) Jared E. Toettcher et al.   CELL

Signatures of nonlinearity in single cell noise-induced oscillations

(2013) Philipp Thomas et al.   JOURNAL OF THEORETICAL BIOLOGY

Analysis of precision in chemical oscillators: implications for circadian clocks

(2013) Thomas d'Eysmond et al.   PHYSICAL BIOLOGY

Infinite-dimensional Bayesian filtering for detection of quasiperiodic phenomena in spatiotemporal data

(2013) Arno Solin et al.   PHYSICAL REVIEW E

Stochastic Processes with Distributed Delays: Chemical Langevin Equation and Linear-Noise Approximation

(2013) Tobias Brett et al.   PHYSICAL REVIEW LETTERS

Oscillatory Control of Factors Determining Multipotency and Fate in Mouse Neural Progenitors

(2013) I. Imayoshi et al.   SCIENCE

Patterning embryos with oscillations: structure, function and dynamics of the vertebrate segmentation clock

(2012) A. C. Oates et al.   DEVELOPMENT

Systems biology of cellular rhythms

(2012) A. Goldbeter et al.   FEBS LETTERS

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Digit patterning during limb development as a result of the BMP-receptor interaction

(2012) Amarendra Badugu et al.   Scientific Reports

MicroRNA-9 Modulates Hes1 Ultradian Oscillations by Forming a Double-Negative Feedback Loop

(2012) Boyan Bonev et al.   Cell Reports

Modeling the Cell Cycle: Why Do Certain Circuits Oscillate?

(2011) James E. Ferrell et al.   CELL

Origins and consequences of transcriptional discontinuity

(2011) David M Suter et al.   CURRENT OPINION IN CELL BIOLOGY

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

JTK_CYCLE: An Efficient Nonparametric Algorithm for Detecting Rhythmic Components in Genome-Scale Data Sets

(2010) Michael E. Hughes et al.   JOURNAL OF BIOLOGICAL RHYTHMS

An effective rate equation approach to reaction kinetics in small volumes: Theory and application to biochemical reactions in nonequilibrium steady-state conditions

(2010) R. Grima   JOURNAL OF CHEMICAL PHYSICS

Stochastic Turing patterns in the Brusselator model

(2010) Tommaso Biancalani et al.   PHYSICAL REVIEW E

Fourier analysis and systems identification of the p53 feedback loop

(2010) N. Geva-Zatorsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Calcium Oscillations

(2010) G. Dupont et al.   Cold Spring Harbor Perspectives in Biology

Intrinsic fluctuations in stochastic delay systems: Theoretical description and application to a simple model of gene regulation

(2009) Tobias Galla   PHYSICAL REVIEW E

Quantification of Circadian Rhythms in Single Cells

(2009) Pål O. Westermark et al.   PLoS Computational Biology

Temporal Organization of the Cell Cycle

(2008) John J. Tyson et al.   CURRENT BIOLOGY

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Oscillations in Notch Signaling Regulate Maintenance of Neural Progenitors

(2008) Hiromi Shimojo et al.   NEURON