Challenges in measuring and understanding biological noise

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

(2019) Ilias Angelidis et al.   Nature Communications

Onset of differentiation is post-transcriptionally controlled in adult neural stem cells

(2019) Avni Baser et al.   NATURE

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

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

Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging

(2018) Peggie Cheung et al.   CELL

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen et al.   NATURE BIOTECHNOLOGY

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Symmetry Breaking in the Mammalian Embryo

(2018) Hui Ting Zhang et al.   Annual Review of Cell and Developmental Biology

Promoter-mediated diversification of transcriptional bursting dynamics following gene duplication

(2018) Edward Tunnacliffe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

Fitness effects of altering gene expression noise in Saccharomyces cerevisiae

(2018) Fabien Duveau et al.   eLife

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

Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity

(2018) Joseph Rodriguez et al.   CELL

Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation

(2018) Caroline R. Bartman et al.   MOLECULAR CELL

Gene expression variability across cells and species shapes innate immunity

(2018) Tzachi Hagai et al.   NATURE

Genomic encoding of transcriptional burst kinetics

(2018) Anton J. M. Larsson et al.   NATURE

Uniform gene expression in embryos is achieved by temporal averaging of transcription noise

(2017) L. Carine Stapel et al.   GENES & DEVELOPMENT

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Sequencing thousands of single-cell genomes with combinatorial indexing

(2017) Sarah A Vitak et al.   NATURE METHODS

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices

(2017) Sanjay M. Prakadan et al.   NATURE REVIEWS GENETICS

Aging increases cell-to-cell transcriptional variability upon immune stimulation

(2017) Celia Pilar Martinez-Jimenez et al.   SCIENCE

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression

(2017) Gozde Kar et al.   Nature Communications

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

Systematic Analysis of the Determinants of Gene Expression Noise in Embryonic Stem Cells

(2017) Andre J. Faure et al.   Cell Systems

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

(2017) Payam Shahi et al.   Scientific Reports

Cell-to-Cell Variation in p53 Dynamics Leads to Fractional Killing

(2016) Andrew L. Paek et al.   CELL

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

(2016) Mubeen Goolam et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

Systematic Analysis of Cell-to-Cell Expression Variation of T Lymphocytes in a Human Cohort Identifies Aging and Genetic Associations

(2016) Yong Lu et al.   IMMUNITY

Asymmetric division of contractile domains couples cell positioning and fate specification

(2016) Jean-Léon Maître et al.   NATURE

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios

(2016) Philipp S. Hoppe et al.   NATURE

Highly multiplexed simultaneous detection of RNAs and proteins in single cells

(2016) Andreas P Frei et al.   NATURE METHODS

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

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

(2016) Sheel Shah et al.   NEURON

Multi-Omics of Single Cells: Strategies and Applications

(2016) Christoph Bock et al.   TRENDS IN BIOTECHNOLOGY

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

(2016) Angélique Richard et al.   PLOS BIOLOGY

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway

(2016) Kazunari Iwamoto et al.   PLoS Computational Biology

Adequate immune response ensured by binary IL-2 and graded CD25 expression in a murine transfer model

(2016) Franziska Fuhrmann et al.   eLife

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

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

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

The volumes and transcript counts of single cells reveal concentration homeostasis and capture biological noise

(2015) Hermannus Kempe et al.   MOLECULAR BIOLOGY OF THE CELL

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

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

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

Selection on noise constrains variation in a eukaryotic promoter

(2015) Brian P. H. Metzger 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

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay 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

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Surviving apoptosis: life–death signaling in single cells

(2015) Deborah A. Flusberg et al.   TRENDS IN CELL BIOLOGY

Nuclear Retention of mRNA in Mammalian Tissues

(2015) Keren Bahar Halpern et al.   Cell Reports

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

(2015) Catalina A. Vallejos et al.   PLoS Computational Biology

Digital signaling decouples activation probability and population heterogeneity

(2015) Ryan A Kellogg et al.   eLife

Locally Disordered Methylation Forms the Basis of Intratumor Methylome Variation in Chronic Lymphocytic Leukemia

(2014) Dan A. Landau et al.   CANCER CELL

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

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

(2014) Eilon Sharon et al.   GENOME RESEARCH

Assessing Kinetics from Fixed Cells Reveals Activation of the Mitotic Entry Network at the S/G2 Transition

(2014) Karen Akopyan et al.   MOLECULAR CELL

Stochasticity of metabolism and growth at the single-cell level

(2014) Daniel J. Kiviet et al.   NATURE

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity

(2014) E. C. Small et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promoter architecture dictates cell-to-cell variability in gene expression

(2014) Daniel L. Jones et al.   SCIENCE

Heterogeneity in immune responses: from populations to single cells

(2014) Rahul Satija et al.   TRENDS IN IMMUNOLOGY

Regulation of Noise in Gene Expression

(2013) Alvaro Sanchez et al.   Annual Review of Biophysics

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

(2013) Ni Ji et al.   CELL

Dynamics extracted from fixed cells reveal feedback linking cell growth to cell cycle

(2013) Ran Kafri et al.   NATURE

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

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Single-molecule mRNA detection and counting in mammalian tissue

(2013) Anna Lyubimova et al.   Nature Protocols

Genetic Determinants and Cellular Constraints in Noisy Gene Expression

(2013) A. Sanchez et al.   SCIENCE

Stochastic Cytokine Expression Induces Mixed T Helper Cell States

(2013) Miaoqing Fang et al.   PLOS BIOLOGY

Mapping Differentiation under Mixed Culture Conditions Reveals a Tunable Continuum of T Cell Fates

(2013) Yaron E. Antebi et al.   PLOS BIOLOGY

Cell-Cycle Dependence of Transcription Dominates Noise in Gene Expression

(2013) C. J. Zopf et al.   PLoS Computational Biology

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

(2013) Jong Kim et al.   GENOME BIOLOGY

Noise-mean relationship in mutated promoters

(2012) G. Hornung et al.   GENOME RESEARCH

Cellular Noise Regulons Underlie Fluctuations in Saccharomyces cerevisiae

(2012) Jacob Stewart-Ornstein et al.   MOLECULAR CELL

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

Signals and Combinatorial Functions of Histone Modifications

(2011) Tamaki Suganuma et al.   Annual Review of Biochemistry

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Decision Making at a Subcellular Level Determines the Outcome of Bacteriophage Infection

(2010) Lanying Zeng et al.   CELL

A Coordinated Global Control over Cellular Transcription

(2010) Jacob Zhurinsky et al.   CURRENT BIOLOGY

Variability in gene expression underlies incomplete penetrance

(2010) Arjun Raj et al.   NATURE

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

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

(2009) S. Huang   DEVELOPMENT

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

(2009) Sabrina L. Spencer et al.   NATURE

Deciding fate in adverse times: Sporulation and competence inBacillus subtilis

(2009) Daniel Schultz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synchronous and Stochastic Patterns of Gene Activation in theDrosophilaEmbryo

(2009) Alistair N. Boettiger et al.   SCIENCE

Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective

(2009) Sui Huang et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A single molecule view of gene expression

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

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

(2008) Arjun Raj et al.   CELL

Two strategies for gene regulation by promoter nucleosomes

(2008) I. Tirosh et al.   GENOME RESEARCH

Selection to minimise noise in living systems and its implications for the evolution of gene expression

(2008) Ben Lehner   Molecular Systems Biology

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

Epigenetic regulation and the variability of gene expression

(2008) Jung Kyoon Choi et al.   NATURE GENETICS

Erratum: Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

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

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

Determination of cell fate selection during phage lambda infection

(2008) F. St-Pierre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA