Stochastic simulation and statistical inference platform for visualization and estimation of transcriptional kinetics

Contribution of RNA Degradation to Intrinsic and Extrinsic Noise in Gene Expression

(2019) Antoine Baudrimont et al.   Cell Reports

Extracellular microRNAs exhibit sequence-dependent stability and cellular release kinetics

(2019) Anna M. L. Coenen-Stass et al.   RNA Biology

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Long-Distance Cooperative and Antagonistic RNA Polymerase Dynamics via DNA Supercoiling

(2019) Sangjin Kim et al.   CELL

Measuring transcription at a single gene copy reveals hidden drivers of bacterial individuality

(2019) Mengyu Wang et al.   Nature Microbiology

Multimodal transcriptional control of pattern formation in embryonic development

(2019) Nicholas C. Lammers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of mRNA Degradation and Site-Specific Transcriptional Pausing on Protein Expression Noise

(2018) Sangjin Kim et al.   BIOPHYSICAL JOURNAL

Distribution shapes govern the discovery of predictive models for gene regulation

(2018) Brian Munsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability

(2018) Maike M.K. Hansen et al.   Cell Systems

Intracellular RNA-tracking methods

(2018) Logan George et al.   Open Biology

Approximation and inference methods for stochastic biochemical kinetics—a tutorial review

(2017) David Schnoerr et al.   Journal of Physics A-Mathematical and Theoretical

Biophysically Motivated Regulatory Network Inference: Progress and Prospects

(2016) Tarmo Äijö et al.   HUMAN HEREDITY

Absolute quantitative measurement of transcriptional kinetic parametersin vivo

(2016) Sukanya Iyer et al.   NUCLEIC ACIDS RESEARCH

Stochastic Kinetics of Nascent RNA

(2016) Heng Xu et al.   PHYSICAL REVIEW LETTERS

Quantitative approaches for investigating the spatial context of gene expression

(2016) Je H. Lee   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Single-cell analysis of transcription kinetics across the cell cycle

(2016) Samuel O Skinner et al.   eLife

A continuum model of transcriptional bursting

(2016) Adam M Corrigan et al.   eLife

Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamics

(2015) Brian Munsky et al.   METHODS

Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli

(2015) H. Chen et al.   Molecular Systems Biology

Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays

(2015) Antti Honkela et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequence-Dependent Elongation Dynamics on Macrolide-Bound Ribosomes

(2014) Magnus Johansson et al.   Cell Reports

Genetic Determinants and Cellular Constraints in Noisy Gene Expression

(2013) A. Sanchez et al.   SCIENCE

Systematic Identification of Signal-Activated Stochastic Gene Regulation

(2013) G. Neuert et al.   SCIENCE

Accelerated maximum likelihood parameter estimation for stochastic biochemical systems

(2012) Bernie J Daigle et al.   BMC BIOINFORMATICS

Transcriptional burst frequency and burst size are equally modulated across the human genome

(2012) R. D. Dar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Gene Expression Noise to Understand Gene Regulation

(2012) B. Munsky et al.   SCIENCE

Analytical Results for a Multistate Gene Model

(2012) Tianshou Zhou et al.   SIAM JOURNAL ON APPLIED MATHEMATICS

Exact and approximate distributions of protein and mRNA levels in the low-copy regime of gene expression

(2011) Pavol Bokes et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Bayesian parameter inference for stochastic biochemical network models using particle Markov chain Monte Carlo

(2011) A. Golightly et al.   Interface Focus

Global parameter estimation methods for stochastic biochemical systems

(2010) Suresh Poovathingal et al.   BMC BIOINFORMATICS

Single-RNA counting reveals alternative modes of gene expression in yeast

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Interacting RNA polymerase motors on a DNA track: Effects of traffic congestion and intrinsic noise on RNA synthesis

(2008) Tripti Tripathi et al.   PHYSICAL REVIEW E

Analytical distributions for stochastic gene expression

(2008) V. Shahrezaei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA