Models of global gene expression define major domains of cell type and tissue identity

Plasticity in the Adult: How Should the Waddington Diagram Be Applied to Regenerating Tissues?

(2016) Jayaraj Rajagopal et al.   DEVELOPMENTAL CELL

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

(2016) Guangdun Peng et al.   DEVELOPMENTAL CELL

Transcriptomics resources of human tissues and organs

(2016) M. Uhlen et al.   Molecular Systems Biology

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

A predictive computational framework for direct reprogramming between human cell types

(2016) Owen J L Rackham et al.   NATURE GENETICS

Polycomb Regulates Mesoderm Cell Fate-Specification in Embryonic Stem Cells through Activation and Repression Mechanisms

(2015) Lluis Morey et al.   Cell Stem Cell

Direct Lineage Reprogramming: Strategies, Mechanisms, and Applications

(2015) Jun Xu et al.   Cell Stem Cell

Waddington’s Valleys and Captain Cook’s Islands

(2015) Michael H. Sieweke   Cell Stem Cell

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

An alternative pluripotent state confers interspecies chimaeric competency

(2015) Jun Wu et al.   NATURE

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

Genomic analysis of LPS-stimulated myeloid cells identifies a common pro-inflammatory response but divergent IL-10 anti-inflammatory responses

(2015) Andrew Paul Hutchins et al.   Scientific Reports

A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

(2015) Ana C. D’Alessio et al.   Stem Cell Reports

Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming, and long non-coding RNAs

(2015) Andrew Paul Hutchins et al.   Science Bulletin

Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet

(2014) Samantha A. Morris et al.   CELL

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

Where cell fate conversions meet Chinese philosophy

(2014) Hui Zheng et al.   CELL RESEARCH

The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters

(2014) Xichen Bao et al.   CELL RESEARCH

Formation of Proximal and Anterior Limb Skeleton Requires Early Function of Irx3 and Irx5 and Is Negatively Regulated by Shh Signaling

(2014) Danyi Li et al.   DEVELOPMENTAL CELL

Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation

(2014) Jia Xue et al.   IMMUNITY

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

SOX17 links gut endoderm morphogenesis and germ layer segregation

(2014) Manuel Viotti et al.   NATURE CELL BIOLOGY

Notch signaling represses p63 expression in the developing surface ectoderm

(2013) A. M. B. Tadeu et al.   DEVELOPMENT

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm

(2013) Irene Aksoy et al.   EMBO JOURNAL

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Generation of oligodendroglial cells by direct lineage conversion

(2013) Nan Yang et al.   NATURE BIOTECHNOLOGY

Transcription factor–mediated reprogramming of fibroblasts to expandable, myelinogenic oligodendrocyte progenitor cells

(2013) Fadi J Najm et al.   NATURE BIOTECHNOLOGY

Gene-pair expression signatures reveal lineage control

(2013) Merja Heinäniemi et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation

(2013) R. N. Plasschaert et al.   NUCLEIC ACIDS RESEARCH

LifeMap Discovery™: The Embryonic Development, Stem Cells, and Regenerative Medicine Research Portal

(2013) Ron Edgar et al.   PLoS One

Cellular network entropy as the energy potential in Waddington's differentiation landscape

(2013) Christopher R. S. Banerji et al.   Scientific Reports

Epigenomic Annotation of Enhancers Predicts Transcriptional Regulators of Human Neural Crest

(2012) Alvaro Rada-Iglesias et al.   Cell Stem Cell

Development and evolution of the neural crest: An overview

(2012) Marianne E. Bronner et al.   DEVELOPMENTAL BIOLOGY

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Co-Motif Discovery Identifies an Esrrb-Sox2-DNA Ternary Complex as a Mediator of Transcriptional Differences Between Mouse Embryonic and Epiblast Stem Cells

(2012) Andrew Paul Hutchins et al.   STEM CELLS

Expression cartography of human tissues using self organizing maps

(2011) Henry Wirth et al.   BMC BIOINFORMATICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Mapping Gene Expression in Two Xenopus Species: Evolutionary Constraints and Developmental Flexibility

(2011) Itai Yanai et al.   DEVELOPMENTAL CELL

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

(2011) Håvard Aanes et al.   GENOME RESEARCH

Direct generation of functional dopaminergic neurons from mouse and human fibroblasts

(2011) Massimiliano Caiazzo et al.   NATURE

Pluripotency and Cellular Reprogramming: Facts, Hypotheses, Unresolved Issues

(2010) Jacob H. Hanna et al.   CELL

Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors

(2010) Masaki Ieda et al.   CELL

Combinatorial Transcriptional Control In Blood Stem/Progenitor Cells: Genome-wide Analysis of Ten Major Transcriptional Regulators

(2010) Nicola K. Wilson et al.   Cell Stem Cell

Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal

(2010) K. K. Niakan et al.   GENES & DEVELOPMENT

A global map of human gene expression

(2010) Margus Lukk et al.   NATURE BIOTECHNOLOGY

Transitions between epithelial and mesenchymal states and the morphogenesis of the early mouse embryo

(2010) Anna Ferrer-Vaquer et al.   Cell Adhesion & Migration

Redefining the Progression of Lineage Segregations during Mammalian Embryogenesis by Clonal Analysis

(2009) Elena Tzouanacou et al.   DEVELOPMENTAL CELL

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL