Shaping development by stochasticity and dynamics in gene regulation

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Transcription Dynamics in Living Cells

(2016) Tineke L. Lenstra et al.   Annual Review of Biophysics

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells

(2016) Chong Wang et al.   CELL

Passive Noise Filtering by Cellular Compartmentalization

(2016) Thomas Stoeger et al.   CELL

Information Integration and Energy Expenditure in Gene Regulation

(2016) Javier Estrada et al.   CELL

Dynamics of Translation of Single mRNA Molecules In Vivo

(2016) Xiaowei Yan et al.   CELL

Long-Lived Binding of Sox2 to DNA Predicts Cell Fate in the Four-Cell Mouse Embryo

(2016) Melanie D. White et al.   CELL

Collective Space-Sensing Coordinates Pattern Scaling in Engineered Bacteria

(2016) Yangxiaolu Cao et al.   CELL

Real-Time Three-Dimensional Cell Segmentation in Large-Scale Microscopy Data of Developing Embryos

(2016) Johannes Stegmaier et al.   DEVELOPMENTAL CELL

Emerging Imaging and Genomic Tools for Developmental Systems Biology

(2016) Zhe Liu et al.   DEVELOPMENTAL CELL

Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells

(2016) Xavier Pichon et al.   JOURNAL OF CELL BIOLOGY

Intercellular Coupling of the Cell Cycle and Circadian Clock in Adult Stem Cell Culture

(2016) Toru Matsu-ura et al.   MOLECULAR CELL

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Challenges in long-term imaging and quantification of single-cell dynamics

(2016) Stavroula Skylaki et al.   NATURE BIOTECHNOLOGY

Bright photoactivatable fluorophores for single-molecule imaging

(2016) Jonathan B Grimm et al.   NATURE METHODS

Transcriptional architecture of the mammalian circadian clock

(2016) Joseph S. Takahashi   NATURE REVIEWS GENETICS

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Translation dynamics of single mRNAs in live cells and neurons

(2016) B. Wu et al.   SCIENCE

Real-time quantification of single RNA translation dynamics in living cells

(2016) T. Morisaki et al.   SCIENCE

Dynamics of epigenetic regulation at the single-cell level

(2016) L. Bintu et al.   SCIENCE

RNA Polymerase II cluster dynamics predict mRNA output in living cells

(2016) Won-Ki Cho et al.   eLife

The Branching Point in Erythro-Myeloid Differentiation

(2015) Leïla Perié et al.   CELL

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

Noise Facilitates Transcriptional Control under Dynamic Inputs

(2015) Ryan A. Kellogg et al.   CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Bursty Gene Expression in the Intact Mammalian Liver

(2015) Keren Bahar Halpern et al.   MOLECULAR CELL

Imaging Live-Cell Dynamics and Structure at the Single-Molecule Level

(2015) Zhe Liu et al.   MOLECULAR CELL

Network plasticity of pluripotency transcription factors in embryonic stem cells

(2015) Adam Filipczyk et al.   NATURE CELL BIOLOGY

High-performance probes for light and electron microscopy

(2015) Sarada Viswanathan et al.   NATURE METHODS

A general method to improve fluorophores for live-cell and single-molecule microscopy

(2015) Jonathan B Grimm et al.   NATURE METHODS

Visualizing Whole-Brain Activity and Development at the Single-Cell Level Using Light-Sheet Microscopy

(2015) Philipp J. Keller et al.   NEURON

Dynamics of CRISPR-Cas9 genome interrogation in living cells

(2015) Spencer C. Knight et al.   SCIENCE

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

High-Sensitivity Measurements of Multiple Kinase Activities in Live Single Cells

(2014) Sergi Regot et al.   CELL

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Encoding of Temporal Signals by the TGF-β Pathway and Implications for Embryonic Patterning

(2014) Benoit Sorre et al.   DEVELOPMENTAL CELL

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

(2014) Zakary S. Singer et al.   MOLECULAR CELL

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution

(2014) Bi-Chang Chen et al.   SCIENCE

Division of labour between Myc and G1 cyclins in cell cycle commitment and pace control

(2014) Peng Dong et al.   Nature Communications

Single-molecule analysis of transcription factor binding at transcription sites in live cells

(2014) Tatsuya Morisaki et al.   Nature Communications

Stochastic promoter activation affects Nanog expression variability in mouse embryonic stem cells

(2014) Hiroshi Ochiai et al.   Scientific Reports

3D imaging of Sox2 enhancer clusters in embryonic stem cells

(2014) Zhe Liu et al.   eLife

Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states

(2014) Lauren LeBon et al.   eLife

The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity

(2013) Siim Pauklin et al.   CELL

Phosphorylation-Regulated Binding of RNA Polymerase II to Fibrous Polymers of Low-Complexity Domains

(2013) Ilmin Kwon et al.   CELL

Live Imaging of Bicoid-Dependent Transcription in Drosophila Embryos

(2013) Tanguy Lucas et al.   CURRENT BIOLOGY

Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning

(2013) Hernan G. Garcia et al.   CURRENT BIOLOGY

Stochastic ERK Activation Induced by Noise and Cell-to-Cell Propagation Regulates Cell Density-Dependent Proliferation

(2013) Kazuhiro Aoki et al.   MOLECULAR CELL

Synthetic mammalian transgene negative autoregulation

(2013) V. Shimoga et al.   Molecular Systems Biology

Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

(2013) J Christof M Gebhardt et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Imaging Morphogenesis: Technological Advances and Biological Insights

(2013) P. J. Keller   SCIENCE

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

(2013) I. I. Cisse et al.   SCIENCE

Positive Feedback Between PU.1 and the Cell Cycle Controls Myeloid Differentiation

(2013) H. Y. Kueh et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Probing transcription factor diffusion dynamics in the living mammalian embryo with photoactivatable fluorescence correlation spectroscopy

(2013) Gurpreet Kaur et al.   Nature Communications

Rapid Transcription Fosters Coordinate snail Expression in the Drosophila Embryo

(2013) Alistair Nicol Boettiger et al.   Cell Reports

Quantitative Analysis of Embryogenesis: A Perspective for Light Sheet Microscopy

(2012) Burkhard Höckendorf et al.   DEVELOPMENTAL CELL

Transcription goes digital

(2012) Timothée Lionnet et al.   EMBO REPORTS

Expression Noise and Acetylation Profiles Distinguish HDAC Functions

(2012) Leehee Weinberger et al.   MOLECULAR CELL

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

Fast multicolor 3D imaging using aberration-corrected multifocus microscopy

(2012) Sara Abrahamsson et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Computational Approaches to Developmental Patterning

(2012) L. G. Morelli et al.   SCIENCE

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Interplay between gene expression noise and regulatory network architecture

(2012) Guilhem Chalancon et al.   TRENDS IN GENETICS

Transient Noise Amplification and Gene Expression Synchronization in a Bistable Mammalian Cell-Fate Switch

(2012) Santhosh Palani et al.   Cell Reports

Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Modeling the Cell Cycle: Why Do Certain Circuits Oscillate?

(2011) James E. Ferrell et al.   CELL

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Pattern, Growth, and Control

(2011) Arthur D. Lander   CELL

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

(2011) D. R. Larson et al.   SCIENCE

The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized mRNA

(2011) Shawn C. Little et al.   PLOS BIOLOGY

The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering

(2011) Matteo Osella et al.   PLoS Computational Biology

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Cis-interactions between Notch and Delta generate mutually exclusive signalling states

(2010) David Sprinzak et al.   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Reaction-Diffusion Model as a Framework for Understanding Biological Pattern Formation

(2010) S. Kondo et al.   SCIENCE

Cell cycle control of mammalian neural stem cells: putting a speed limit on G1

(2010) Paolo Salomoni et al.   TRENDS IN CELL BIOLOGY

Vertebrate Endoderm Development and Organ Formation

(2009) Aaron M. Zorn et al.   Annual Review of Cell and Developmental Biology

Cdk4/CyclinD1 Overexpression in Neural Stem Cells Shortens G1, Delays Neurogenesis, and Promotes the Generation and Expansion of Basal Progenitors

(2009) Christian Lange et al.   Cell Stem Cell

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues

(2009) Na Ji et al.   NATURE METHODS

Canalization of Gene Expression in the Drosophila Blastoderm by Gap Gene Cross Regulation

(2009) Manu et al.   PLOS BIOLOGY

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors

(2009) Manu et al.   PLoS Computational Biology

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS

Noise Propagation and Signaling Sensitivity in Biological Networks: A Role for Positive Feedback

(2008) Gil Hornung et al.   PLoS Computational Biology

Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression

(2008) J. M. Pedraza et al.   SCIENCE