Resolving early mesoderm diversification through single-cell expression profiling

Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation

(2016) Debbie K. Goode et al.   DEVELOPMENTAL CELL

Hoxb5 marks long-term haematopoietic stem cells and reveals a homogenous perivascular niche

(2016) James Y. Chen et al.   NATURE

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence

(2015) T. Org et al.   EMBO JOURNAL

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

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Myosin-II-mediated cell shape changes and cell intercalation contribute to primitive streak formation

(2015) Emil Rozbicki et al.   NATURE CELL BIOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Selective expression of sense and antisense transcripts of the sushi-ichi-related retrotransposon – derived family during mouse placentogenesis

(2015) Christine Henke et al.   Retrovirology

TBX1 Represses Vegfr2 Gene Expression and Enhances the Cardiac Fate of VEGFR2+ Cells

(2015) Gabriella Lania et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Clonal analysis identifies hemogenic endothelium as the source of the blood-endothelial common lineage in the mouse embryo

(2014) L. Padron-Barthe et al.   BLOOD

Prdm1 functions in the mesoderm of the second heart field, where it interacts genetically with Tbx1, during outflow tract morphogenesis in the mouse embryo

(2014) Stéphane D. Vincent et al.   HUMAN MOLECULAR GENETICS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities

(2014) Manuel Sánchez-Castillo et al.   NUCLEIC ACIDS RESEARCH

PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information

(2014) Hao Wu et al.   PLoS One

Dose-dependent Nodal/Smad signals pattern the early mouse embryo

(2014) Elizabeth J. Robertson   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Epigenetics reloaded: the single-cell revolution

(2014) Poonam Bheda et al.   TRENDS IN CELL BIOLOGY

Direct Reprogramming of Murine Fibroblasts to Hematopoietic Progenitor Cells

(2014) Kiran Batta et al.   Cell Reports

Circulation-Independent Differentiation Pathway from Extraembryonic Mesoderm toward Hematopoietic Stem Cells via Hemogenic Angioblasts

(2014) Yosuke Tanaka et al.   Cell Reports

A carrier-assisted ChIP-seq method for estrogen receptor-chromatin interactions from breast cancer core needle biopsy samples

(2013) Wilbert Zwart et al.   BMC GENOMICS

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

(2013) Philip Brennecke et al.   NATURE METHODS

Expression of Podocalyxin Separates the Hematopoietic and Vascular Potentials of Mouse Embryonic Stem Cell-Derived Mesoderm

(2013) Hailan Zhang et al.   STEM CELLS

Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses

(2013) A. C. Wilkinson et al.   Biology Open

TBX3 Directs Cell-Fate Decision toward Mesendoderm

(2013) Clair E. Weidgang et al.   Stem Cell Reports

Scl Represses Cardiomyogenesis in Prospective Hemogenic Endothelium and Endocardium

(2012) Ben Van Handel et al.   CELL

The transcriptional programme controlled by Runx1 during early embryonic blood development

(2012) Yosuke Tanaka et al.   DEVELOPMENTAL BIOLOGY

Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data

(2012) Anagha Joshi et al.   EXPERIMENTAL HEMATOLOGY

Gastrulation: Making and Shaping Germ Layers

(2011) Lila Solnica-Krezel et al.   Annual Review of Cell and Developmental Biology

Single-lineage transcriptome analysis reveals key regulatory pathways in primitive erythroid progenitors in the mouse embryo

(2011) J. Isern et al.   BLOOD

Identity and fate of Tbx4-expressing cells reveal developmental cell fate decisions in the allantois, limb, and external genitalia

(2011) L.A. Naiche et al.   DEVELOPMENTAL DYNAMICS

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

O-fucosylation of thrombospondin type 1 repeats restricts epithelial to mesenchymal transition (EMT) and maintains epiblast pluripotency during mouse gastrulation

(2010) Jianguang Du et al.   DEVELOPMENTAL BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Foxa2 regulates polarity and epithelialization in the endoderm germ layer of the mouse embryo

(2009) I. Burtscher et al.   DEVELOPMENT

The haemangioblast generates haematopoietic cells through a haemogenic endothelium stage

(2009) Christophe Lancrin et al.   NATURE

Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives

(2008) Owen J Tamplin et al.   BMC GENOMICS

ER71 Acts Downstream of BMP, Notch, and Wnt Signaling in Blood and Vessel Progenitor Specification

(2008) Dongjun Lee et al.   Cell Stem Cell

Mesp2 and Tbx6 cooperatively create periodic patterns coupled with the clock machinery during mouse somitogenesis

(2008) M. Oginuma et al.   DEVELOPMENT

Expression of the hyaluronan receptor LYVE-1 is not restricted to the lymphatic vasculature; LYVE-1 is also expressed on embryonic blood vessels

(2008) Emma J. Gordon et al.   DEVELOPMENTAL DYNAMICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY