Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis

[1]  Michael L. Simpson,et al.  A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization , 2018, Cell.

[2]  Allon M. Klein,et al.  The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution , 2018, Science.

[3]  Allon M. Klein,et al.  Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo , 2018, Science.

[4]  A. Regev,et al.  Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis , 2018, Science.

[5]  Christoph A. Merten,et al.  Modulation of Phase Shift between Wnt and Notch Signaling Oscillations Controls Mesoderm Segmentation , 2018, Cell.

[6]  J. Ellenberg,et al.  Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four-dimensional imaging , 2017, Nature Protocols.

[7]  Nicolas E. Buchler,et al.  BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells , 2017, Genome Biology.

[8]  Felix Naef,et al.  What shapes eukaryotic transcriptional bursting? , 2017, Molecular bioSystems.

[9]  James Briscoe,et al.  Olig2 and Hes regulatory dynamics during motor neuron differentiation revealed by single cell transcriptomics , 2017, bioRxiv.

[10]  Magnus Rattray,et al.  Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes , 2016, PLoS computational biology.

[11]  M. Rattray,et al.  Stochasticity in the miR-9/Hes1 oscillatory network can account for clonal heterogeneity in the timing of differentiation , 2016, eLife.

[12]  A. Loudon,et al.  Visualizing and Quantifying Intracellular Behavior and Abundance of the Core Circadian Clock Protein PERIOD2 , 2016, Current Biology.

[13]  J. Tukey,et al.  An Algorithm for the Machine Calculation of , 2016 .

[14]  Ryoichiro Kageyama,et al.  Oscillatory control of Delta-like1 in cell interactions regulates dynamic gene expression and tissue morphogenesis , 2016, Genes & development.

[15]  Fabian J. Theis,et al.  Network plasticity of pluripotency transcription factors in embryonic stem cells , 2015, Nature Cell Biology.

[16]  R. Kageyama,et al.  Real-time imaging of bHLH transcription factors reveals their dynamic control in the multipotency and fate choice of neural stem cells , 2015, Front. Cell. Neurosci..

[17]  K. Kawakami,et al.  Deubiquitinating enzymes regulate Hes1 stability and neuronal differentiation , 2015, The FEBS journal.

[18]  D. Spiller,et al.  Quantitative dynamic imaging of immune cell signalling using lentiviral gene transfer. , 2015, Integrative biology : quantitative biosciences from nano to macro.

[19]  A. Martinez Arias,et al.  Cell dynamics and gene expression control in tissue homeostasis and development , 2015, Molecular systems biology.

[20]  James Briscoe,et al.  Coordination of progenitor specification and growth in mouse and chick spinal cord , 2014, Science.

[21]  Jean Peccoud,et al.  Adaptive Imaging Cytometry to Estimate Parameters of Gene Networks Models in Systems and Synthetic Biology , 2014, PloS one.

[22]  Petr Svoboda,et al.  Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency , 2014, Development.

[23]  Tobias Galla,et al.  microRNA input into a neural ultradian oscillator controls emergence and timing of alternative cell states , 2014, Nature Communications.

[24]  T. Galla,et al.  Gaussian approximations for stochastic systems with delay: chemical Langevin equation and application to a Brusselator system. , 2013, The Journal of chemical physics.

[25]  Ryoichiro Kageyama,et al.  Oscillatory Control of Factors Determining Multipotency and Fate in Mouse Neural Progenitors , 2013, Science.

[26]  Felix Naef,et al.  Stimulus-induced modulation of transcriptional bursting in a single mammalian gene , 2013, Proceedings of the National Academy of Sciences.

[27]  James Briscoe,et al.  Morphogen interpretation: the transcriptional logic of neural tube patterning. , 2013, Current opinion in genetics & development.

[28]  K. Page,et al.  A gene regulatory motif that generates oscillatory or multiway switch outputs , 2013, Journal of The Royal Society Interface.

[29]  Ryoichiro Kageyama,et al.  MicroRNA9 regulates neural stem cell differentiation by controlling Hes1 expression dynamics in the developing brain , 2012, Genes to cells : devoted to molecular & cellular mechanisms.

[30]  C. Furusawa,et al.  A Dynamical-Systems View of Stem Cell Biology , 2012, Science.

[31]  Nancy Papalopulu,et al.  MicroRNA-9 Modulates Hes1 Ultradian Oscillations by Forming a Double-Negative Feedback Loop , 2012, Cell reports.

[32]  Elliot L Elson,et al.  Fluorescence correlation spectroscopy: past, present, future. , 2011, Biophysical journal.

[33]  Felix Naef,et al.  Origins and consequences of transcriptional discontinuity. , 2011, Current opinion in cell biology.

[34]  Nicholas T. Ingolia,et al.  Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.

[35]  J. Swedlow,et al.  A novel reporter of notch signalling indicates regulated and random notch activation during vertebrate neurogenesis , 2011, BMC Biology.

[36]  Johan Paulsson,et al.  Random partitioning of molecules at cell division , 2011, Proceedings of the National Academy of Sciences.

[37]  Hiroshi Kiyonari,et al.  Establishment of conditional reporter mouse lines at ROSA26 locus for live cell imaging , 2011, Genesis.

[38]  M. Selbach,et al.  Global quantification of mammalian gene expression control , 2011, Nature.

[39]  Xiaoqin Wu,et al.  Bifurcation analysis for a model of gene expression with delays , 2011 .

[40]  M. Beaumont Approximate Bayesian Computation in Evolution and Ecology , 2010 .

[41]  Nicholas T Ingolia,et al.  Genome-wide translational profiling by ribosome footprinting. , 2010, Methods in enzymology.

[42]  Sui Huang Non-genetic heterogeneity of cells in development: more than just noise , 2009, Development.

[43]  R. Padgett,et al.  Rates of in situ transcription and splicing in large human genes , 2009, Nature Structural &Molecular Biology.

[44]  Tobias Galla,et al.  Intrinsic fluctuations in stochastic delay systems: theoretical description and application to a simple model of gene regulation. , 2009, Physical review. E, Statistical, nonlinear, and soft matter physics.

[45]  Carl E. Rasmussen,et al.  Gaussian processes for machine learning , 2005, Adaptive computation and machine learning.

[46]  J. Tyson,et al.  Design principles of biochemical oscillators , 2008, Nature Reviews Molecular Cell Biology.

[47]  James Briscoe,et al.  Pattern formation in the vertebrate neural tube: a sonic hedgehog morphogen-regulated transcriptional network , 2008, Development.

[48]  Hannah H. Chang,et al.  Transcriptome-wide noise controls lineage choice in mammalian progenitor cells , 2008, Nature.

[49]  Ryoichiro Kageyama,et al.  Oscillations in Notch Signaling Regulate Maintenance of Neural Progenitors , 2008, Neuron.

[50]  Richard H. Rand,et al.  Hopf bifurcation in a DDE model of gene expression , 2008 .

[51]  Enrico Gratton,et al.  Mapping the Number of Molecules and Brightness in the Laser Scanning Microscope , 2007, Biophysical journal.

[52]  下條 博美 Oscillations in Notch signaling regulate maintenance of neural progenitors , 2008 .

[53]  J. Swedlow,et al.  Mitotic spindle orientation distinguishes stem cell and terminal modes of neuron production in the early spinal cord , 2007, Development.

[54]  Ryoichiro Kageyama,et al.  The Hes gene family: repressors and oscillators that orchestrate embryogenesis , 2007, Development.

[55]  O. Basak,et al.  Identification of self‐replicating multipotent progenitors in the embryonic nervous system by high Notch activity and Hes5 expression , 2007, The European journal of neuroscience.

[56]  N. G. Van Kampen,et al.  Chapter III – STOCHASTIC PROCESSES , 2007 .

[57]  M. Pascual,et al.  Stochastic amplification in epidemics , 2007, Journal of The Royal Society Interface.

[58]  Tianhai Tian,et al.  Oscillatory Regulation of Hes1: Discrete Stochastic Delay Modelling and Simulation , 2006, PLoS Comput. Biol..

[59]  R. Singer,et al.  Transcriptional Pulsing of a Developmental Gene , 2006, Current Biology.

[60]  Tianhai Tian,et al.  Oscillatory Regulation of Hes 1 : Discrete Stochastic Delay Modelling and Simulation , 2006 .

[61]  M. Götz,et al.  Developmental cell biology: The cell biology of neurogenesis , 2005, Nature Reviews Molecular Cell Biology.

[62]  J. Raser,et al.  Noise in Gene Expression: Origins, Consequences, and Control , 2005, Science.

[63]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

[64]  Ryoichiro Kageyama,et al.  Hes genes regulate size, shape and histogenesis of the nervous system by control of the timing of neural stem cell differentiation , 2004, Development.

[65]  N. Monk Oscillatory Expression of Hes1, p53, and NF-κB Driven by Transcriptional Time Delays , 2003, Current Biology.

[66]  Julian Lewis Autoinhibition with Transcriptional Delay A Simple Mechanism for the Zebrafish Somitogenesis Oscillator , 2003, Current Biology.

[67]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[68]  Colin Camerer : Past , Present , Future , 2003 .

[69]  D. Balding,et al.  Approximate Bayesian computation in population genetics. , 2002, Genetics.

[70]  H. Hirata,et al.  Oscillatory Expression of the bHLH Factor Hes1 Regulated by a Negative Feedback Loop , 2002, Science.

[71]  P. Swain,et al.  Stochastic Gene Expression in a Single Cell , 2002, Science.

[72]  T. Ohtsuka,et al.  Roles of the Basic Helix-Loop-Helix Genes Hes1 and Hes5 in Expansion of Neural Stem Cells of the Developing Brain* , 2001, The Journal of Biological Chemistry.

[73]  D. Gillespie The chemical Langevin equation , 2000 .

[74]  T. Ohtsuka,et al.  Hes1 and Hes5 as Notch effectors in mammalian neuronal differentiation , 1999, The EMBO journal.

[75]  O. Pourquié,et al.  Avian hairy Gene Expression Identifies a Molecular Clock Linked to Vertebrate Segmentation and Somitogenesis , 1997, Cell.

[76]  K. Moriyoshi,et al.  Persistent expression of helix‐loop‐helix factor HES‐1 prevents mammalian neural differentiation in the central nervous system. , 1994, The EMBO journal.

[77]  R. Shigemoto,et al.  Two mammalian helix-loop-helix factors structurally related to Drosophila hairy and Enhancer of split. , 1992, Genes & development.

[78]  R. Kageyama,et al.  Molecular characterization of a rat negative regulator with a basic helix-loop-helix structure predominantly expressed in the developing nervous system. , 1992, The Journal of biological chemistry.

[79]  A. Emons,et al.  Boekbespreking: Molecular biology of the cell, B. Alberts, D. Bray, J. Lewis, M. Raff, K. Robers, D.J. Watson. Garland Publ., New York. 1989. , 1990 .

[80]  Alan V. Oppenheim,et al.  Discrete-Time Signal Pro-cessing , 1989 .

[81]  J. Borén,et al.  Pulse-chase studies of the synthesis and intracellular transport of apolipoprotein B-100 in Hep G2 cells. , 1986, The Journal of biological chemistry.

[82]  J. Davies,et al.  Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.

[83]  D. Sherrington Stochastic Processes in Physics and Chemistry , 1983 .

[84]  J. Tukey,et al.  An algorithm for the machine calculation of complex Fourier series , 1965 .

[85]  A. Savitzky,et al.  Smoothing and Differentiation of Data by Simplified Least Squares Procedures. , 1964 .