Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines

Memory CD4+ T cells are generated in the human fetal intestine

(2019) Na Li et al.   NATURE IMMUNOLOGY

Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions

(2019) Maria Gutierrez-Arcelus et al.   Nature Communications

The Intestine Harbors Functionally Distinct Homeostatic Tissue-Resident and Inflammatory Th17 Cells

(2019) Sara Omenetti et al.   IMMUNITY

Chromatin activity at GWAS loci identifies T cell states driving complex immune diseases

(2019) Blagoje Soskic et al.   NATURE GENETICS

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells

(2018) Ubaid Ullah et al.   Cell Reports

Early TCR Signaling Induces Rapid Aerobic Glycolysis Enabling Distinct Acute T Cell Effector Functions

(2018) Ashley V. Menk et al.   Cell Reports

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Quantitative assessment of cell population diversity in single-cell landscapes

(2018) Qi Liu et al.   PLOS BIOLOGY

New Insights into the Role of IL-1β in Experimental Autoimmune Encephalomyelitis and Multiple Sclerosis

(2017) Chih-Chung Lin et al.   JOURNAL OF IMMUNOLOGY

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA

(2017) Yuan Tian et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

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

Heterogeneity of Human CD4+T Cells Against Microbes

(2016) Federica Sallusto   Annual Review of Immunology

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome

(2016) Shaojun Tang et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Cytokines and chemokines: At the crossroads of cell signalling and inflammatory disease

(2014) Mark D. Turner et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

OX40 Costimulatory Signals Potentiate the Memory Commitment of Effector CD8+ T Cells

(2014) S. F. Mousavi et al.   JOURNAL OF IMMUNOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

Biased Treg/Th17 balance away from regulatory toward inflammatory phenotype in relapsed multiple sclerosis and its correlation with severity of symptoms

(2013) Azam Jamshidian et al.   JOURNAL OF NEUROIMMUNOLOGY

Pathogenic conversion of Foxp3+ T cells into TH17 cells in autoimmune arthritis

(2013) Noriko Komatsu et al.   NATURE MEDICINE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data

(2012) Juergen Cox et al.   BMC BIOINFORMATICS

An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation

(2012) Tarmo Äijö et al.   BMC GENOMICS

Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification

(2012) Robert M. Samstein et al.   CELL

STATs Shape the Active Enhancer Landscape of T Cell Populations

(2012) Golnaz Vahedi et al.   CELL

Interferon-Inducible Protein Mx1 Inhibits Influenza Virus by Interfering with Functional Viral Ribonucleoprotein Complex Assembly

(2012) J. Verhelst et al.   JOURNAL OF VIROLOGY

Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements

(2012) Aditi Kanhere et al.   Nature Communications

Integrating Autoimmune Risk Loci with Gene-Expression Data Identifies Specific Pathogenic Immune Cell Subsets

(2011) Xinli Hu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Human Th1 and Th17 Cells Exhibit Epigenetic Stability at Signature Cytokine and Transcription Factor Loci

(2011) C. J. Cohen et al.   JOURNAL OF IMMUNOLOGY

Differentiation of Effector CD4 T Cell Populations

(2010) Jinfang Zhu et al.   Annual Review of Immunology

Low-strength T-cell activation promotes Th17 responses

(2010) H. A. Purvis et al.   BLOOD

Human CD4+ Memory T Cells Can Become CD4+IL-9+ T Cells

(2010) Prabhakar Putheti et al.   PLoS One

Th17 plasticity in human autoimmune arthritis is driven by the inflammatory environment

(2010) K. Nistala et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

T Helper 17 Lineage Differentiation Is Programmed by Orphan Nuclear Receptors RORα and RORγ

(2008) Xuexian O. Yang et al.   IMMUNITY

Transforming growth factor-β 'reprograms' the differentiation of T helper 2 cells and promotes an interleukin 9–producing subset

(2008) Marc Veldhoen et al.   NATURE IMMUNOLOGY

Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures

(2007) R. E. Randall et al.   JOURNAL OF GENERAL VIROLOGY