A DNA repair pathway can regulate transcriptional noise to promote cell fate transitions

Transcription in Living Cells: Molecular Mechanisms of Bursting

(2020) Joseph Rodriguez et al.   Annual Review of Biochemistry

Noise-driven cellular heterogeneity in circadian periodicity

(2020) Yan Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Sangjin Kim et al.   CELL

Mitigating Antagonism between Transcription and Proliferation Allows Near-Deterministic Cellular Reprogramming

(2019) Kimberley N. Babos et al.   Cell Stem Cell

Mechanism of stimulation of DNA binding of the transcription factors by human apurinic/apyrimidinic endonuclease 1, APE1

(2019) Milena Bazlekowa-Karaban et al.   DNA REPAIR

A Post-Transcriptional Feedback Mechanism for Noise Suppression and Fate Stabilization

(2018) Maike M.K. Hansen et al.   CELL

The role of the N-terminal domain of human apurinic/apyrimidinic endonuclease 1, APE1, in DNA glycosylase stimulation

(2018) Olga A. Kladova et al.   DNA REPAIR

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Modulation of transcriptional burst frequency by histone acetylation

(2018) Damien Nicolas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dual inhibition of MDMX and MDM2 as a therapeutic strategy in leukemia

(2018) Luis A. Carvajal et al.   Science Translational Medicine

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

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

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

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

(2018) Nils Eling et al.   Cell Systems

Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes

(2017) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

Measurement of incorporation kinetics of non-fluorescent native nucleotides by DNA polymerases using fluorescence microscopy

(2017) Matthew T. Walsh et al.   NUCLEIC ACIDS RESEARCH

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

(2017) Rhishikesh Bargaje et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

(2017) Stefan Semrau et al.   Nature Communications

Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data

(2016) Mihails Delmans et al.   BMC BIOINFORMATICS

Mechanical bounds to transcriptional noise

(2016) Stuart A. Sevier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single-molecule view of transcription reveals convoys of RNA polymerases and multi-scale bursting

(2016) Katjana Tantale et al.   Nature Communications

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Transcriptional Bursting Explains the Noise–Versus–Mean Relationship in mRNA and Protein Levels

(2016) Roy D. Dar et al.   PLoS One

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

A Hardwired HIV Latency Program

(2015) Brandon S. Razooky et al.   CELL

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

Structure of silent transcription intervals and noise characteristics of mammalian genes

(2015) B. Zoller et al.   Molecular Systems Biology

Nuclear Retention of mRNA in Mammalian Tissues

(2015) Keren Bahar Halpern et al.   Cell Reports

Neural Differentiation of Mouse Embryonic Stem Cells in Serum-free Monolayer Culture

(2015) Wikrom Wongpaiboonwattana et al.   Jove-Journal of Visualized Experiments

Transcription Factor Competition Allows Embryonic Stem Cells to Distinguish Authentic Signals from Noise

(2015) Cameron Sokolik et al.   Cell Systems

Transient Changes in Intercellular Protein Variability Identify Sources of Noise in Gene Expression

(2014) Abhyudai Singh   BIOPHYSICAL JOURNAL

Mechanism of Transcriptional Bursting in Bacteria

(2014) Shasha Chong et al.   CELL

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

(2014) Elsa Abranches et al.   DEVELOPMENT

Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA

(2014) Toni Pfaffeneder et al.   Nature Chemical Biology

TET-mediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent gene reactivation

(2014) Udo Müller et al.   NUCLEIC ACIDS RESEARCH

Screening for noise in gene expression identifies drug synergies

(2014) R. D. Dar et al.   SCIENCE

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

(2014) Hiroshi Ochiai et al.   Scientific Reports

Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics

(2013) Li Shen et al.   CELL

FISH-quant: automatic counting of transcripts in 3D FISH images

(2013) Florian Mueller et al.   NATURE METHODS

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

(2013) Catherine Naughton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription-generated torsional stress destabilizes nucleosomes

(2013) Sheila S Teves et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells

(2011) Piyush B. Gupta et al.   CELL

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

(2010) Shinsuke Ito et al.   NATURE

Thymidine analog methods for studies of adult neurogenesis are not equally sensitive

(2009) Benedetta Leuner et al.   JOURNAL OF COMPARATIVE NEUROLOGY

CD15, CD24 and CD29 Define a Surface Biomarker Code for Neural Lineage Differentiation of Stem Cells

(2009) Jan Pruszak et al.   STEM CELLS

Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells

(2009) Tibor Kalmar et al.   PLOS BIOLOGY

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells

(2008) Muralidhar L Hegde et al.   CELL RESEARCH

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

The functional response of upstream DNA to dynamic supercoiling in vivo

(2008) Fedor Kouzine et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nuclear protein-induced bending and flexing of the hypoxic response element of the rat vascular endothelial growth factor promoter

(2007) Jeffrey F. Breit et al.   FASEB JOURNAL