Exploring single-cell data with deep multitasking neural networks

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

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

(2018) Elham Azizi et al.   CELL

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

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

An accurate and robust imputation method scImpute for single-cell RNA-seq data

(2018) Wei Vivian Li et al.   Nature Communications

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Human Zika infection induces a reduction of IFN-γ producing CD4 T-cells and a parallel expansion of effector Vδ2 T-cells

(2017) Eleonora Cimini et al.   Scientific Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks

(2017) Jie Tan et al.   Cell Systems

The natural killer cell response to West Nile virus in young and old individuals with or without a prior history of infection

(2017) Yi Yao et al.   PLoS One

Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model

(2016) Lujia Chen et al.   BMC BIOINFORMATICS

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions

(2016) Jie Tan et al.   mSystems

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry

(2015) Eli R. Zunder et al.   Cell Stem Cell

Type I IFNs and IL-18 Regulate the Antiviral Response of Primary Human γδ T Cells against Dendritic Cells Infected with Dengue Virus

(2015) Chen-Yu Tsai et al.   JOURNAL OF IMMUNOLOGY

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

(2015) A. Zeisel et al.   SCIENCE

γδ T Lymphocytes in the Diagnosis of Human T Cell Receptor Immunodeficiencies

(2015) Beatriz Garcillán et al.   Frontiers in Immunology

γδT Cells: First Line of Defense and Beyond

(2014) Yueh-hsiu Chien et al.   Annual Review of Immunology

CyTOF supports efficient detection of immune cell subsets from small samples

(2014) Yi Yao et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Shannon and von Neumann entropy of random networks with heterogeneous expected degree

(2011) Kartik Anand et al.   PHYSICAL REVIEW E

Age-Associated Decrease in TLR Function in Primary Human Dendritic Cells Predicts Influenza Vaccine Response

(2010) Alexander Panda et al.   JOURNAL OF IMMUNOLOGY