Transcriptional mechanisms of cell fate decisions revealed by single cell expression profiling

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model

(2013) Nicola Bonzanni et al.   BIOINFORMATICS

Growth Factor Independence 1 Antagonizes a p53-Induced DNA Damage Response Pathway in Lymphoblastic Leukemia

(2013) Cyrus Khandanpour et al.   CANCER CELL

Statistical Mechanics of Pluripotency

(2013) Ben D. MacArthur et al.   CELL

Single-Cell Analysis Reveals that Expression of Nanog Is Biallelic and Equally Variable as that of Other Pluripotency Factors in Mouse ESCs

(2013) Dina A. Faddah et al.   Cell Stem Cell

Mapping Cellular Hierarchy by Single-Cell Analysis of the Cell Surface Repertoire

(2013) Guoji Guo et al.   Cell Stem Cell

Network link prediction by global silencing of indirect correlations

(2013) Baruch Barzel et al.   NATURE BIOTECHNOLOGY

Network deconvolution as a general method to distinguish direct dependencies in networks

(2013) Soheil Feizi et al.   NATURE BIOTECHNOLOGY

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Erratum: Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

(2013) Victoria Moignard et al.   NATURE CELL BIOLOGY

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcriptional Regulation of Lineage Commitment - A Stochastic Model of Cell Fate Decisions

(2013) Jose Teles et al.   PLoS Computational Biology

Population transcriptomics with single-cell resolution: A new field made possible by microfluidics

(2012) Charles Plessy et al.   BIOESSAYS

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst

(2012) F. Buettner et al.   BIOINFORMATICS

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

(2012) Yosef Buganim et al.   CELL

Hematopoietic Stem Cell Heterogeneity Takes Center Stage

(2012) Michael R. Copley et al.   Cell Stem Cell

Quantitative PCR Analysis of DNA, RNAs, and Proteins in the Same Single Cell

(2012) A. Stahlberg et al.   CLINICAL CHEMISTRY

Investigating transcriptional states at single-cell-resolution

(2012) Julia Tischler et al.   CURRENT OPINION IN BIOTECHNOLOGY

Microfluidic single cell analysis: from promise to practice

(2012) Véronique Lecault et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8+ T Cell Phenotypes

(2012) Evan W. Newell et al.   IMMUNITY

RT-qPCR work-flow for single-cell data analysis

(2012) Anders Ståhlberg et al.   METHODS

Inferring rules of lineage commitment in haematopoiesis

(2012) Cristina Pina et al.   NATURE CELL BIOLOGY

Nanog-dependent feedback loops regulate murine embryonic stem cell heterogeneity

(2012) Ben D. MacArthur et al.   NATURE CELL BIOLOGY

Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns

(2012) Veronica Sanchez-Freire et al.   Nature Protocols

A deep profiler's guide to cytometry

(2012) Sean C. Bendall et al.   TRENDS IN IMMUNOLOGY

Establishing the stem cell state: insights from regulatory network analysis of blood stem cell development

(2012) Judith Schütte et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

(2011) Peng Qiu et al.   NATURE BIOTECHNOLOGY

Heritable GATA2 mutations associated with familial myelodysplastic syndrome and acute myeloid leukemia

(2011) Christopher N Hahn et al.   NATURE GENETICS

Comprehensive qPCR profiling of gene expression in single neuronal cells

(2011) Ami Citri et al.   Nature Protocols

Genome-Wide Analysis of Transcriptional Reprogramming in Mouse Models of Acute Myeloid Leukaemia

(2011) Nicolas Bonadies et al.   PLoS One

An Information Theoretic, Microfluidic-Based Single Cell Analysis Permits Identification of Subpopulations among Putatively Homogeneous Stem Cells

(2011) Jason P. Glotzbach et al.   PLoS One

High-throughput microfluidic single-cell RT-qPCR

(2011) A. K. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) S. C. Bendall et al.   SCIENCE

Reconstructing regulatory network transitions

(2011) Jalean J. Petricka et al.   TRENDS IN CELL BIOLOGY

Hematopoietic Stem Cell Heterogeneity: Subtypes, Not Unpredictable Behavior

(2010) Timm Schroeder   Cell Stem Cell

Single-cell gene profiling of planarian stem cells using fluorescent activated cell sorting and its “index sorting” function for stem cell research

(2010) Tetsutaro Hayashi et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Gene regulatory networks governing haematopoietic stem cell development and identity

(2010) John E. Pimanda et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Single-cell gene expression profiling using reverse transcription quantitative real-time PCR

(2010) Anders Ståhlberg et al.   METHODS

Functional roles for noise in genetic circuits

(2010) Avigdor Eldar et al.   NATURE

Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations

(2010) Anders Ståhlberg et al.   NUCLEIC ACIDS RESEARCH

Modeling Reveals Bistability and Low-Pass Filtering in the Network Module Determining Blood Stem Cell Fate

(2010) Jatin Narula et al.   PLoS Computational Biology

Prospective isolation and molecular characterization of hematopoietic stem cells with durable self-renewal potential

(2009) D. G. Kent et al.   BLOOD

Stem Cell States, Fates, and the Rules of Attraction

(2009) Tariq Enver et al.   Cell Stem Cell

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

(2009) S. Huang   DEVELOPMENT

From genes to cells to tissues—modelling the haematopoietic system

(2009) Samuel D. Foster et al.   Molecular BioSystems

Direct cell reprogramming is a stochastic process amenable to acceleration

(2009) Jacob Hanna et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

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

(2008) Arjun Raj et al.   CELL

Heterogeneity of Embryonic and Adult Stem Cells

(2008) Thomas Graf et al.   Cell Stem Cell

Dynamic Equilibrium and Heterogeneity of Mouse Pluripotent Stem Cells with Distinct Functional and Epigenetic States

(2008) Katsuhiko Hayashi et al.   Cell Stem Cell

Extreme Makeover: Converting One Cell into Another

(2008) Qiao Zhou et al.   Cell Stem Cell

Identification and characterization of subpopulations in undifferentiated ES cell culture

(2008) Y. Toyooka et al.   DEVELOPMENT

In vivo reprogramming of adult pancreatic exocrine cells to β-cells

(2008) Qiao Zhou et al.   NATURE

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Integrated microfluidic bioprocessor for single-cell gene expression analysis

(2008) N. M. Toriello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Techniques for clustering gene expression data

(2007) G. Kerr et al.   COMPUTERS IN BIOLOGY AND MEDICINE