cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes

Fibroblast polarization over the myocardial infarction time continuum shifts roles from inflammation to angiogenesis

(2019) Alan J. Mouton et al.   BASIC RESEARCH IN CARDIOLOGY

A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia

(2019) Ninib Baryawno et al.   CELL

The bone marrow microenvironment at single-cell resolution

(2019) Anastasia N. Tikhonova et al.   NATURE

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Joint analysis of heterogeneous single-cell RNA-seq dataset collections

(2019) Nikolas Barkas et al.   NATURE METHODS

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

(2019) Jurrian K de Kanter et al.   NUCLEIC ACIDS RESEARCH

SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species

(2019) Yuqi Tan et al.   Cell Systems

Supervised classification enables rapid annotation of cell atlases

(2019) Hannah A. Pliner et al.   NATURE METHODS

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Cross-platform single cell analysis of kidney development shows stromal cells express Gdnf

(2018) Bliss Magella et al.   DEVELOPMENTAL BIOLOGY

Gfi1b: a key player in the genesis and maintenance of acute myeloid leukemia and myelodysplastic syndrome

(2018) Aniththa Thivakaran et al.   HAEMATOLOGICA

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Gfi1b: a key player in the genesis and maintenance of acute myeloid leukemia and myelodysplastic syndrome

(2018) Aniththa Thivakaran et al.   HAEMATOLOGICA

The Human Cell Atlas Bone Marrow Single-Cell Interactive Web Portal

(2018) Stuart Hay et al.   EXPERIMENTAL HEMATOLOGY

IKZF2 Drives Leukemia Stem Cell Self-Renewal and Inhibits Myeloid Differentiation

(2018) Sun-Mi Park et al.   Cell Stem Cell

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes

(2018) Timothy R. Hammond et al.   IMMUNITY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification

(2018) Yi-Chien Lu et al.   Cell Reports

Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes

(2017) Alberto Yáñez et al.   IMMUNITY

The extracellular matrix in myocardial injury, repair, and remodeling

(2017) Nikolaos G. Frangogiannis   JOURNAL OF CLINICAL INVESTIGATION

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

BET bromodomain inhibition suppresses innate inflammatory and profibrotic transcriptional networks in heart failure

(2017) Qiming Duan et al.   Science Translational Medicine

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods

(2017) Jared M. Churko et al.   Nature Biomedical Engineering

Runx1 Deficiency Protects Against Adverse Cardiac Remodeling After Myocardial Infarction

(2017) Charlotte S. McCarroll et al.   CIRCULATION

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

(2016) Andre Olsson et al.   NATURE

DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia

(2016) S. E. Meyer et al.   Cancer Discovery

The transcriptomic landscape and directed chemical interrogation of MLL-rearranged acute myeloid leukemias

(2015) Vincent-Philippe Lavallée et al.   NATURE GENETICS

Hypoxia-Inducible Factor 1 and Cardiovascular Disease

(2013) Gregg L. Semenza   Annual Review of Physiology

Membrane-Associated Matrix Proteolysis and Heart Failure

(2013) Francis G. Spinale et al.   CIRCULATION RESEARCH

GO-Elite: a flexible solution for pathway and ontology over-representation

(2012) Alexander C. Zambon et al.   BIOINFORMATICS

Intracoronary delivery of DNAzymes targeting human EGR-1 reduces infarct size following myocardial ischaemia reperfusion

(2011) Ravinay Bhindi et al.   JOURNAL OF PATHOLOGY

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data

(2010) Dorothea Emig et al.   NUCLEIC ACIDS RESEARCH

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

Accumulation of fibronectin in the heart after myocardial infarction: a putative stimulator of adhesion and proliferation of adipose-derived stem cells

(2008) A. van Dijk et al.   CELL AND TISSUE RESEARCH