Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus

Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms

(2019) Joanna Zyla et al.   BIOINFORMATICS

Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans

(2019) Thomas Hagan et al.   CELL

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

(2018) Etienne Patin et al.   NATURE IMMUNOLOGY

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

(2018) Carsten Krieg et al.   NATURE MEDICINE

Type I interferon in rheumatic diseases

(2018) Theresa L. Wampler Muskardin et al.   Nature Reviews Rheumatology

Clustering trees: a visualisation for evaluating clusterings at multiple resolutions

(2018) Luke Zappia et al.   GigaScience

Elements of cancer immunity and the cancer–immune set point

(2017) Daniel S. Chen et al.   NATURE

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

The worldwide incidence and prevalence of systemic lupus erythematosus: a systematic review of epidemiological studies

(2017) Frances Rees et al.   RHEUMATOLOGY

WS7_1 Organ Damage and Hospitalization in Elderly Patients with Anti-Neutrophil Cytoplasmic Antibody (ANCA)-Associated Vasculitis

(2017) Maria Weiner et al.   RHEUMATOLOGY

Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients

(2016) Romain Banchereau et al.   CELL

Systematic Analysis of Cell-to-Cell Expression Variation of T Lymphocytes in a Human Cohort Identifies Aging and Genetic Associations

(2016) Yong Lu et al.   IMMUNITY

Distinctions among Circulating Antibody-Secreting Cell Populations, Including B-1 Cells, in Human Adult Peripheral Blood

(2016) Tâm D. Quách et al.   JOURNAL OF IMMUNOLOGY

New insights into the immunopathogenesis of systemic lupus erythematosus

(2016) George C. Tsokos et al.   Nature Reviews Rheumatology

Pre-vaccination inflammation and B-cell signalling predict age-related hyporesponse to hepatitis B vaccination

(2016) Slim Fourati et al.   Nature Communications

Variation in the Human Immune System Is Largely Driven by Non-Heritable Influences

(2015) Petter Brodin et al.   CELL

Homeostasis, Inflammation, and Disease Susceptibility

(2015) Maya E. Kotas et al.   CELL

Biomarkers for rheumatoid and psoriatic arthritis

(2015) M.K. Verheul et al.   CLINICAL IMMUNOLOGY

Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures

(2015) Helder I. Nakaya et al.   IMMUNITY

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

High Preexisting Serological Antibody Levels Correlate with Diversification of the Influenza Vaccine Response

(2015) Sarah F. Andrews et al.   JOURNAL OF VIROLOGY

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

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

Utilizing population variation, vaccination, and systems biology to study human immunology

(2015) John S. Tsang   TRENDS IN IMMUNOLOGY

Global Analyses of Human Immune Variation Reveal Baseline Predictors of Postvaccination Responses

(2014) John S. Tsang et al.   CELL

ImmPort: disseminating data to the public for the future of immunology

(2014) Sanchita Bhattacharya et al.   IMMUNOLOGIC RESEARCH

Inhibition of Protein Geranylgeranylation Specifically Interferes with CD40-Dependent B Cell Activation, Resulting in a Reduced Capacity To Induce T Cell Immunity

(2014) Alexander Shimabukuro-Vornhagen et al.   JOURNAL OF IMMUNOLOGY

A smart local moving algorithm for large-scale modularity-based community detection

(2013) Ludo Waltman et al.   EUROPEAN PHYSICAL JOURNAL B

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

Molecular signatures of antibody responses derived from a systems biology study of five human vaccines

(2013) Shuzhao Li et al.   NATURE IMMUNOLOGY

An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection

(2012) Xingbin Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Molecular mechanism and function of CD40/CD40L engagement in the immune system

(2009) Raul Elgueta et al.   IMMUNOLOGICAL REVIEWS

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus

(2008) Damien Chaussabel et al.   IMMUNITY

Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans

(2008) Troy D Querec et al.   NATURE IMMUNOLOGY

Baseline Levels of Influenza-Specific CD4 Memory T-Cells Affect T-Cell Responses to Influenza Vaccines

(2008) Xiao-Song He et al.   PLoS One