Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states

Discovering sparse transcription factor codes for cell states and state transitions during development

(2017) Leon A Furchtgott et al.   eLife

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity

(2015) Chang-Lin Li et al.   CELL RESEARCH

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

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

Snai1 Promotes ESC Exit from the Pluripotency by Direct Repression of Self-Renewal Genes

(2015) Federico Galvagni et al.   STEM CELLS

Ectodermal progenitors derived from epiblast stem cells by inhibition of Nodal signaling

(2015) Lingyu Li et al.   Journal of Molecular Cell Biology

Statistical significance of variables driving systematic variation in high-dimensional data

(2014) Neo Christopher Chung et al.   BIOINFORMATICS

Characterizing cancer subtypes as attractors of Hopfield networks

(2014) Stefan R. Maetschke et al.   BIOINFORMATICS

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Neuron-specific chromatin remodeling: A missing link in epigenetic mechanisms underlying synaptic plasticity, memory, and intellectual disability disorders

(2013) Annie Vogel-Ciernia et al.   NEUROPHARMACOLOGY

Parameter Space Compression Underlies Emergent Theories and Predictive Models

(2013) B. B. Machta et al.   SCIENCE

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Predicting stem cell fate changes by differential cell cycle progression patterns

(2012) M. Roccio et al.   DEVELOPMENT

FLASH assembly of TALENs for high-throughput genome editing

(2012) Deepak Reyon et al.   NATURE BIOTECHNOLOGY

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

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

(2012) Tamar Hashimshony et al.   Cell Reports

Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers

(2011) Matt Thomson et al.   CELL

Control of the Embryonic Stem Cell State

(2011) Richard A. Young   CELL

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS

Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo

(2009) Sebastian J. Arnold et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Level of the Transcription Factor Pax6 Is Essential for Controlling the Balance between Neural Stem Cell Self-Renewal and Neurogenesis

(2009) Stephen N. Sansom et al.   PLoS Genetics

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

Roles of TGF-β family signaling in stem cell renewal and differentiation

(2008) Tetsuro Watabe et al.   CELL RESEARCH

Defining early lineage specification of human embryonic stem cells by the orchestrated balance of canonical Wnt/ -catenin, Activin/Nodal and BMP signaling

(2008) T. Sumi et al.   DEVELOPMENT

Directed induction of anterior and posterior primitive streak by Wnt from embryonic stem cells cultured in a chemically defined serum-free medium

(2008) Mio Nakanishi et al.   FASEB JOURNAL

Zic2 is expressed in pluripotent cells in the blastocyst and adult brain expression overlaps with makers of neurogenesis

(2008) Lucia Brown et al.   GENE EXPRESSION PATTERNS

Transcriptional Regulator BPTF/FAC1 Is Essential for Trophoblast Differentiation during Early Mouse Development

(2008) T. Goller et al.   MOLECULAR AND CELLULAR BIOLOGY

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

An intrinsic mechanism of corticogenesis from embryonic stem cells

(2008) Nicolas Gaspard et al.   NATURE