Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process

Metabolic regulation of hematopoietic stem cell commitment and erythroid differentiation

(2016) Leal Oburoglu et al.   CURRENT OPINION IN HEMATOLOGY

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

(2016) Barbara Treutlein et al.   NATURE

Breast Cancer MDA-MB-231 Cells Use Secreted Heat Shock Protein-90alpha (Hsp90α) to Survive a Hostile Hypoxic Environment

(2016) Hangming Dong et al.   Scientific Reports

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

Individual T Helper Cells Have a Quantitative Cytokine Memory

(2015) Caroline Helmstetter et al.   IMMUNITY

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

(2015) Olivia Padovan-Merhar et al.   MOLECULAR CELL

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands

(2015) Yao Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A six gene expression signature defines aggressive subtypes and predicts outcome in childhood and adult acute lymphoblastic leukemia

(2015) Jin Wang et al.   Oncotarget

Identifying early-warning signals of critical transitions with strong noise by dynamical network markers

(2015) Rui Liu et al.   Scientific Reports

Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis

(2015) Cristina Pina et al.   Cell Reports

Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation

(2015) Nicolás Peláez et al.   eLife

Identifying critical differentiation state of MCF-7 cells for breast cancer by dynamical network biomarkers

(2015) Pei Chen et al.   Frontiers in Genetics

Cell-State-Specific Metabolic Dependency in Hematopoiesis and Leukemogenesis

(2014) Ying-Hua Wang et al.   CELL

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage

(2014) M.-E. Torres-Padilla et al.   DEVELOPMENT

An animated landscape representation of CD4+T-cell differentiation, variability, and plasticity: Insights into the behavior of populations versus cells

(2014) Jonathan A. Rebhahn et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

High expression of heat shock protein 90 alpha and its significance in human acute leukemia cells

(2014) Wen-Liang Tian et al.   GENE

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

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

Deconstructing transcriptional heterogeneity in pluripotent stem cells

(2014) Roshan M. Kumar et al.   NATURE

Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses

(2014) Janilyn Arsenio et al.   NATURE IMMUNOLOGY

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Hiroshi Ochiai et al.   Scientific Reports

Transcription Factors Modulate c-Fos Transcriptional Bursts

(2014) Adrien Senecal et al.   Cell Reports

Deconstructing stem cell population heterogeneity: Single-cell analysis and modeling approaches

(2013) Jincheng Wu et al.   BIOTECHNOLOGY ADVANCES

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts

(2013) José Viñuelas et al.   BMC BIOLOGY

Regulation of Glycolysis by Pdk Functions as a Metabolic Checkpoint for Cell Cycle Quiescence in Hematopoietic Stem Cells

(2013) Keiyo Takubo et al.   Cell Stem Cell

Spatial stochastic modelling of the Hes1 gene regulatory network: intrinsic noise can explain heterogeneity in embryonic stem cell differentiation

(2013) M. Sturrock et al.   Journal of the Royal Society Interface

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Concise Review: Erythroid Versus Myeloid Lineage Commitment: Regulating the Master Regulators

(2013) Linda Wolff et al.   STEM CELLS

‘Particle genetics’: treating every cell as unique

(2013) Gaël Yvert   TRENDS IN GENETICS

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

(2013) Jong Kim et al.   GENOME BIOLOGY

Temporal dynamics and transcriptional control using single-cell gene expression analysis

(2013) Tsukasa Kouno et al.   GENOME BIOLOGY

Cell-Cycle Control of Developmentally Regulated Transcription Factors Accounts for Heterogeneity in Human Pluripotent Cells

(2013) Amar M. Singh et al.   Stem Cell Reports

Probing the role of stochasticity in a model of the embryonic stem cell – heterogeneous gene expression and reprogramming efficiency

(2012) Vijay Chickarmane et al.   BMC Systems Biology

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

Inferring rules of lineage commitment in haematopoiesis

(2012) Cristina Pina et al.   NATURE CELL BIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Towards experimental manipulation of stochasticity in gene expression

(2012) José Viñuelas et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

What makes the cell differentiate?

(2012) Andras Paldi   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Cholesterol synthesis-related enzyme oxidosqualene cyclase is required to maintain self-renewal in primary erythroid progenitors

(2011) C. Mejia-Pous et al.   CELL PROLIFERATION

A potentially common peptide target in secreted heat shock protein-90α for hypoxia-inducible factor-1α–positive tumors

(2011) Divya Sahu et al.   MOLECULAR BIOLOGY OF THE CELL

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Fundamental limits on the suppression of molecular fluctuations

(2010) Ioannis Lestas et al.   NATURE

Non-genetic heterogeneity from stochastic partitioning at cell division

(2010) Dann Huh et al.   NATURE GENETICS

Inhibition of lactate dehydrogenase A induces oxidative stress and inhibits tumor progression

(2010) A. Le et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits

(2009) Tolga Çağatay et al.   CELL

Non-genetic heterogeneity of cells in development: more than just noise

(2009) S. Huang   DEVELOPMENT

A single molecule view of gene expression

(2009) Daniel R. Larson et al.   TRENDS IN CELL BIOLOGY

Stem cell antigen 2: a new gene involved in the self-renewal of erythroid progenitors

(2008) C. Bresson-Mazet et al.   CELL PROLIFERATION

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Analytical distributions for stochastic gene expression

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

Variability and Robustness in T Cell Activation from Regulated Heterogeneity in Protein Levels

(2008) O. Feinerman et al.   SCIENCE

Adding self-renewal in committed erythroid progenitors improves the biological relevance of a mathematical model of erythropoiesis

(2007) Fabien Crauste et al.   JOURNAL OF THEORETICAL BIOLOGY