Systematic single-cell pathway analysis to characterize early T cell activation

Defective STAT5 Activation and Aberrant Expression of BCL6 in Naive CD4 T Cells Enhances Follicular Th Cell–like Differentiation in Patients with Granulomatosis with Polyangiitis

(2022) Sangmi Kim et al.   JOURNAL OF IMMUNOLOGY

A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines

(2021) Richa Nayak et al.   GENOMICS

Arachidonic acid-regulated calcium signaling in T cells from patients with rheumatoid arthritis promotes synovial inflammation

(2021) Zhongde Ye et al.   Nature Communications

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

scTPA: A web tool for single-cell transcriptome analysis of pathway activation signatures

(2020) Yan Zhang et al.   BIOINFORMATICS

Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies

(2020) Ying Ma et al.   Nature Communications

Defensins: A Double-Edged Sword in Host Immunity

(2020) Dan Xu et al.   Frontiers in Immunology

Distribution-Free Multisample Tests Based on Optimal Matchings with Applications to Single Cell Genomics

(2020) Somabha Mukherjee et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

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

Prostaglandin regulation of T cell biology

(2019) Damian Maseda et al.   PHARMACOLOGICAL RESEARCH

Functional interpretation of single cell similarity maps

(2019) David DeTomaso et al.   Nature Communications

Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease

(2019) Peter A. Szabo et al.   Nature Communications

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Human T Cell Development, Localization, and Function throughout Life

(2018) Brahma V. Kumar et al.   IMMUNITY

Multifaceted immune functions of human defensins and underlying mechanisms

(2018) Saahil Fruitwala et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A New Graph-Based Two-Sample Test for Multivariate and Object Data

(2017) Hao Chen et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

T helper 1 immunity requires complement-driven NLRP3 inflammasome activity in CD4+ T cells

(2016) G. Arbore et al.   SCIENCE

T cell metabolism drives immunity

(2015) Michael D. Buck et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The Immune-Metabolic Basis of Effector Memory CD4+T Cell Function under Hypoxic Conditions

(2015) Sarah Dimeloe et al.   JOURNAL OF IMMUNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

ROS Function in Redox Signaling and Oxidative Stress

(2014) Michael Schieber et al.   CURRENT BIOLOGY

Human memory T cells from the bone marrow are resting and maintain long-lasting systemic memory

(2014) A. Okhrimenko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Y. Liao et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Rapid effector function of memory CD8+ T cells requires an immediate-early glycolytic switch

(2013) Patrick M Gubser et al.   NATURE IMMUNOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

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

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

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols