Geometry of the Gene Expression Space of Individual Cells

Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

(2015) Daniel H. Kim et al.   Cell Stem Cell

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

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

(2014) Sean C. Bendall et al.   CELL

Repair and Regeneration of the Respiratory System: Complexity, Plasticity, and Mechanisms of Lung Stem Cell Function

(2014) Brigid L.M. Hogan et al.   Cell Stem Cell

Development and Function of Dendritic Cell Subsets

(2014) Alexander Mildner et al.   IMMUNITY

Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging

(2014) Laila Ritsma et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

Mathematical model of adult stem cell regeneration with cross-talk between genetic and epigenetic regulation

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

Plasticity of epithelial stem cells in tissue regeneration

(2014) C. Blanpain 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

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

(2014) Andrew McDavid et al.   PLoS Computational Biology

Robust Cre-Mediated Recombination in Small Intestinal Stem Cells Utilizing the Olfm4 Locus

(2014) Jurian Schuijers et al.   Stem Cell Reports

The Dendritic Cell Lineage: Ontogeny and Function of Dendritic Cells and Their Subsets in the Steady State and the Inflamed Setting

(2013) Miriam Merad et al.   Annual Review of Immunology

Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways

(2013) Juliane Thøgersen et al.   BMC BIOINFORMATICS

The Intestinal Crypt, A Prototype Stem Cell Compartment

(2013) Hans Clevers   CELL

Can cell mortality determine division of labor in tissue organization?

(2013) Carlos Rodríguez-Caso   JOURNAL OF THEORETICAL BIOLOGY

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

(2013) Ran Kafri et al.   NATURE

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

(2013) Alex K. Shalek et al.   NATURE

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

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

Critical assessment of automated flow cytometry data analysis techniques

(2013) Nima Aghaeepour et al.   NATURE METHODS

Dissecting genomic diversity, one cell at a time

(2013) Paul C Blainey et al.   NATURE METHODS

The promise of single-cell sequencing

(2013) James Eberwine et al.   NATURE METHODS

The Geometry of Locomotive Behavioral States in C. elegans

(2013) Thomas Gallagher et al.   PLoS One

Developmental bias in the evolution of phalanges

(2013) K. D. Kavanagh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The geometry of the Pareto front in biological phenotype space

(2013) Hila Sheftel et al.   Ecology and Evolution

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

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

Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems

(2013) Pablo Szekely et al.   PLoS Computational Biology

Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments

(2012) Andrew McDavid et al.   BIOINFORMATICS

The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers

(2012) Javier Muñoz et al.   EMBO JOURNAL

Identification of a cKit+ Colonic Crypt Base Secretory Cell That Supports Lgr5+ Stem Cells in Mice

(2012) Michael E. Rothenberg et al.   GASTROENTEROLOGY

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

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

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

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

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

Evolutionary Trade-Offs, Pareto Optimality, and the Geometry of Phenotype Space

(2012) O. Shoval et al.   SCIENCE

Modeling transcriptional networks in Drosophila development at multiple scales

(2011) Zeba Wunderlich et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Universal patterns of stem cell fate in cycling adult tissues

(2011) A. M. Klein et al.   DEVELOPMENT

Stem cell self-renewal in intestinal crypt

(2011) Benjamin D. Simons et al.   EXPERIMENTAL CELL RESEARCH

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

(2011) S. Islam et al.   GENOME RESEARCH

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

Archetypal analysis for machine learning and data mining

(2011) Morten Mørup et al.   NEUROCOMPUTING

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

(2011) S. C. Bendall et al.   SCIENCE

Dendritic Cell Apoptosis: Regulation of Tolerance versus Immunity

(2010) R. Kushwah et al.   JOURNAL OF IMMUNOLOGY

Tmem176B and Tmem176A are associated with the immature state of dendritic cells

(2010) Thomas Condamine et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Transcription Factor Achaete Scute-Like 2 Controls Intestinal Stem Cell Fate

(2009) Laurens G. van der Flier et al.   CELL

SAM pointed domain ETS factor (SPDEF) regulates terminal differentiation and maturation of intestinal goblet cells

(2009) Taeko K. Noah et al.   EXPERIMENTAL CELL RESEARCH

The Ets-Domain Transcription Factor Spdef Promotes Maturation of Goblet and Paneth Cells in the Intestinal Epithelium

(2009) Alex Gregorieff et al.   GASTROENTEROLOGY

CD14 regulates the dendritic cell life cycle after LPS exposure through NFAT activation

(2009) Ivan Zanoni et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

A Continuum of Cell States Spans Pluripotency and Lineage Commitment in Human Embryonic Stem Cells

(2009) Shelley R. Hough et al.   PLoS One

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Stem Cells, Self-Renewal, and Differentiation in the Intestinal Epithelium

(2008) Laurens G. van der Flier et al.   Annual Review of Physiology

MS4A12 Is a Colon-Selective Store-Operated Calcium Channel Promoting Malignant Cell Processes

(2008) M. Koslowski et al.   CANCER RESEARCH

Serrated Adenoma of the Colorectum Undergoes a Proliferation versus Differentiation Process: New Conceptual Interpretation of Morphogenesis

(2008) Yu-Fei Jiao et al.   ONCOLOGY

Transmembrane proteins of tight junctions

(2007) Hideki Chiba et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES