Variation is function: Are single cell differences functionally important?

Simultaneous neuron- and astrocyte-specific fluorescent marking

(2015) Wiebke Schulze et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

(2015) Nicola K. Wilson et al.   Cell Stem Cell

Editorial overview: Genome architecture and expression

(2015) Barbara Panning et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Population genetics of non-genetic traits: Evolutionary roles of stochasticity in gene expression

(2015) Katsuhiko Mineta et al.   GENE

The reduction of gene expression variability from single cells to populations follows simple statistical laws

(2015) Vincent Piras et al.   GENOMICS

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

(2015) S. S. Dey et al.   Molecular Systems Biology

Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold

(2015) J. Roux et al.   Molecular Systems Biology

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

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

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

Programmed synthesis of three-dimensional tissues

(2015) Michael E Todhunter et al.   NATURE METHODS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

MicroRNA control of protein expression noise

(2015) J. M. Schmiedel et al.   SCIENCE

Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-β response to viral infection

(2015) Sonali Patil et al.   Science Signaling

Analysis of single-cell cytokine secretion reveals a role for paracrine signaling in coordinating macrophage responses to TLR4 stimulation

(2015) Qiong Xue et al.   Science Signaling

Cellular Deconstruction: Finding Meaning in Individual Cell Variation

(2015) James Eberwine et al.   TRENDS IN CELL BIOLOGY

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation

(2015) Hannah Dueck et al.   GENOME BIOLOGY

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

(2015) Kyu-Tae Kim et al.   GENOME BIOLOGY

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-β response to viral infection

(2015) Sonali Patil et al.   Science Signaling

Analysis of single-cell cytokine secretion reveals a role for paracrine signaling in coordinating macrophage responses to TLR4 stimulation

(2015) Qiong Xue et al.   Science Signaling

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Reconstruction of the Mouse Otocyst and Early Neuroblast Lineage at Single-Cell Resolution

(2014) Robert Durruthy-Durruthy et al.   CELL

Random Monoallelic Gene Expression Increases upon Embryonic Stem Cell Differentiation

(2014) Mélanie A. Eckersley-Maslin et al.   DEVELOPMENTAL CELL

Population and single-cell genomics reveal theAiredependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

(2014) Stephen N. Sansom et al.   GENOME RESEARCH

Inputs drive cell phenotype variability

(2014) J. Park et al.   GENOME RESEARCH

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

(2014) Eilon Sharon et al.   GENOME RESEARCH

A multi-phenotypic cancer model with cell plasticity

(2014) Da Zhou et al.   JOURNAL OF THEORETICAL BIOLOGY

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

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

Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells

(2014) J. Bieler et al.   Molecular Systems Biology

Deconstructing transcriptional heterogeneity in pluripotent stem cells

(2014) Roshan M. Kumar et al.   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

(2014) Ditte Lovatt et al.   NATURE METHODS

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Mobile DNA elements in the generation of diversity and complexity in the brain

(2014) Jennifer A. Erwin et al.   NATURE REVIEWS NEUROSCIENCE

Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles

(2014) Sameer S. Bajikar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing

(2014) M.-C. W. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network of mutually repressive metastasis regulators can promote cell heterogeneity and metastatic transitions

(2014) J. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Basal p21 controls population heterogeneity in cycling and quiescent cell cycle states

(2014) K. W. Overton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells

(2014) Q. Deng et al.   SCIENCE

Controlling low rates of cell differentiation through noise and ultrahigh feedback

(2014) R. Ahrends et al.   SCIENCE

Screening for noise in gene expression identifies drug synergies

(2014) R. D. Dar et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Transcriptome-wide Variability in Single Embryonic Development Cells

(2014) Vincent Piras et al.   Scientific Reports

Defining Midbrain Dopaminergic Neuron Diversity by Single-Cell Gene Expression Profiling

(2014) Jean-Francois Poulin et al.   Cell Reports

Transcription Factors Modulate c-Fos Transcriptional Bursts

(2014) Adrien Senecal et al.   Cell Reports

Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells

(2014) Andrew McDavid et al.   PLoS Computational Biology

Modeling Dynamics of Cell-to-Cell Variability in TRAIL-Induced Apoptosis Explains Fractional Killing and Predicts Reversible Resistance

(2014) François Bertaux et al.   PLoS Computational Biology

Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

(2014) Isaac M Chiu et al.   eLife

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

Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo

(2013) Mounia Lagha et al.   CELL

Mosaic physiology from developmental noise: within-organism physiological diversity as an alternative to phenotypic plasticity and phenotypic flexibility

(2013) H. A. Woods   JOURNAL OF EXPERIMENTAL BIOLOGY

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

(2013) Yusuke Ohnishi et al.   NATURE CELL BIOLOGY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

‘Particle genetics’: treating every cell as unique

(2013) Gaël Yvert   TRENDS IN GENETICS

Stochastic Cytokine Expression Induces Mixed T Helper Cell States

(2013) Miaoqing Fang et al.   PLOS BIOLOGY

Secondary mechanisms of diversification in the human antibody repertoire

(2013) Bryan S. Briney et al.   Frontiers in Immunology

Epigenetic aspects of lymphocyte antigen receptor gene rearrangement or ‘when stochasticity completes randomness’

(2012) Sébastien Jaeger et al.   IMMUNOLOGY

Multi-layered stochasticity and paracrine signal propagation shape the type-I interferon response

(2012) Ulfert Rand et al.   Molecular Systems Biology

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Programmed Cell-to-Cell Variability in Ras Activity Triggers Emergent Behaviors during Mammary Epithelial Morphogenesis

(2012) Jennifer S. Liu et al.   Cell Reports

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

(2011) Piyush B. Gupta et al.   CELL

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities

(2010) Dinesh Kumar Singh et al.   Molecular Systems Biology

L1 retrotransposition in neurons is modulated by MeCP2

(2010) Alysson R. Muotri et al.   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

RNA: state memory and mediator of cellular phenotype

(2010) Junhyong Kim et al.   TRENDS IN CELL BIOLOGY

Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits

(2009) Tolga Çağatay et al.   CELL

Experimental evolution of bet hedging

(2009) Hubertus J. E. Beaumont et al.   NATURE

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

(2009) Sabrina L. Spencer et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Transcriptome transfer produces a predictable cellular phenotype

(2009) J.-Y. Sul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS

Stochasticity and Cell Fate

(2008) R. Losick et al.   SCIENCE