Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis

Single-Cell Analysis Identifies Distinct Stages of Human Endothelial-to-Hematopoietic Transition

(2017) Carolina Guibentif et al.   Cell Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

Hematopoietic Reprogramming In Vitro Informs In Vivo Identification of Hemogenic Precursors to Definitive Hematopoietic Stem Cells

(2016) Carlos-Filipe Pereira et al.   DEVELOPMENTAL CELL

Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation

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

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

Activation of the TGFβ pathway impairs endothelial to haematopoietic transition

(2016) Özge Vargel et al.   Scientific Reports

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

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

(2015) T. Org et al.   EMBO JOURNAL

The RUNX1–PU.1 axis in the control of hematopoiesis

(2015) Maria Rosaria Imperato et al.   INTERNATIONAL JOURNAL OF HEMATOLOGY

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

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1

(2015) Roshana Thambyrajah et al.   NATURE CELL BIOLOGY

Partial distance correlation with methods for dissimilarities

(2014) Gábor J. Székely et al.   ANNALS OF STATISTICS

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

Whole-transcriptome analysis of endothelial to hematopoietic stem cell transition reveals a requirement for Gpr56 in HSC generation

(2014) Parham Solaimani Kartalaei et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Defining an essential transcription factor program for naive pluripotency

(2014) S.- J. Dunn et al.   SCIENCE

Tracing the Origin of the HSC Hierarchy Reveals an SCF-Dependent, IL-3-Independent CD43− Embryonic Precursor

(2014) Stanislav Rybtsov et al.   Stem Cell Reports

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

(2013) Nicola Bonzanni et al.   BIOINFORMATICS

Genome-wide analysis of transcriptional regulators in human HSPCs reveals a densely interconnected network of coding and noncoding genes

(2013) D. Beck et al.   BLOOD

Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis

(2013) A. Mylona et al.   BLOOD

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GFI1 and GFI1B control the loss of endothelial identity of hemogenic endothelium during hematopoietic commitment

(2012) C. Lancrin et al.   BLOOD

The transcriptional programme controlled by Runx1 during early embryonic blood development

(2012) Yosuke Tanaka et al.   DEVELOPMENTAL BIOLOGY

RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis

(2012) Monika Lichtinger et al.   EMBO JOURNAL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software

(2011) Lee Kamentsky et al.   BIOINFORMATICS

Master Transcription Factors Determine Cell-Type-Specific Responses to TGF-β Signaling

(2011) Alan C. Mullen et al.   CELL

The distinctive roles of erythroid specific activator GATA-1 and NF-E2 in transcription of the human fetal γ-globin genes

(2011) Yea Woon Kim et al.   NUCLEIC ACIDS RESEARCH

Inducible Cassette Exchange: A Rapid and Efficient System Enabling Conditional Gene Expression in Embryonic Stem and Primary Cells

(2011) Michelina Iacovino et al.   STEM CELLS

Endothelial Fli1 Deficiency Impairs Vascular Homeostasis

(2010) Yoshihide Asano et al.   AMERICAN JOURNAL OF PATHOLOGY

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

Dissecting hematopoietic differentiation using the embryonic stem cell differentiation model

(2010) Tara L. Huber   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

In vivo imaging of haematopoietic cells emerging from the mouse aortic endothelium

(2010) Jean-Charles Boisset et al.   NATURE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The differential activities of Runx1 promoters define milestones during embryonic hematopoiesis

(2009) P. Sroczynska et al.   BLOOD

Differentiation-Dependent Interactions between RUNX-1 and FLI-1 during Megakaryocyte Development

(2009) H. Huang et al.   MOLECULAR AND CELLULAR BIOLOGY

Continuous single-cell imaging of blood generation from haemogenic endothelium

(2009) Hanna M. Eilken et al.   NATURE

The haemangioblast generates haematopoietic cells through a haemogenic endothelium stage

(2009) Christophe Lancrin et al.   NATURE

Extensive Hematopoietic Stem Cell Generation in the AGM Region via Maturation of VE-Cadherin+CD45+ Pre-Definitive HSCs

(2008) Samir Taoudi et al.   Cell Stem Cell

Fate Tracing Reveals the Endothelial Origin of Hematopoietic Stem Cells

(2008) Ann C. Zovein et al.   Cell Stem Cell