Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

ANN-Benchmarks: A benchmarking tool for approximate nearest neighbor algorithms

(2019) Martin Aumüller et al.   INFORMATION SYSTEMS

Maturation of heart valve cell populations during postnatal remodeling

(2019) Alexia Hulin et al.   DEVELOPMENT

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

(2019) Yingxin Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Joshua D. Welch et al.   CELL

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

(2019) Erica A K DePasquale et al.   NUCLEIC ACIDS RESEARCH

Decoding human fetal liver haematopoiesis

(2019) Dorin-Mirel Popescu et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky 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

bigSCale: an analytical framework for big-scale single-cell data

(2018) Giovanni Iacono et al.   GENOME RESEARCH

Identifying cell populations with scRNASeq

(2018) Tallulah S. Andrews et al.   MOLECULAR ASPECTS OF MEDICINE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

CLEC10A Is a Specific Marker for Human CD1c+ Dendritic Cells and Enhances Their Toll-Like Receptor 7/8-Induced Cytokine Secretion

(2018) Lukas Heger et al.   Frontiers in Immunology

An innovative immunotherapeutic strategy for ovarian cancer: CLEC10A and glycomimetic peptides

(2018) Laura L. Eggink et al.   Journal for ImmunoTherapy of Cancer

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

(2018) Stuart Hay et al.   EXPERIMENTAL HEMATOLOGY

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis

(2018) Jared M. Churko et al.   Nature Communications

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

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

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

(2016) Andre Olsson et al.   NATURE

A novel peptide targeting Clec9a on dendritic cell for cancer immunotherapy

(2016) Zhongyi Yan et al.   Oncotarget

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

NMF-mGPU: non-negative matrix factorization on multi-GPU systems

(2015) Edgardo Mejía-Roa et al.   BMC BIOINFORMATICS

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

(2015) Minzhe Guo et al.   PLoS Computational Biology

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

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

(2012) Alexander C. Zambon et al.   BIOINFORMATICS

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data

(2010) Dorothea Emig et al.   NUCLEIC ACIDS RESEARCH

SVD based initialization: A head start for nonnegative matrix factorization

(2007) C. Boutsidis et al.   PATTERN RECOGNITION