Multiplexed enrichment and genomic profiling of peripheral blood cells reveal subset-specific immune signatures

Mapping the human DC lineage through the integration of high-dimensional techniques

(2017) Peter See et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

High-throughput automated microfluidic sample preparation for accurate microbial genomics

(2017) Soohong Kim et al.   Nature Communications

Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients

(2016) Romain Banchereau et al.   CELL

Robust classification of bacterial and viral infections via integrated host gene expression diagnostics

(2016) Timothy E. Sweeney et al.   Science Translational Medicine

Host gene expression classifiers diagnose acute respiratory illness etiology

(2016) Ephraim L. Tsalik et al.   Science Translational Medicine

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

What was old is new again: using the host response to diagnose infectious disease

(2015) Emily R Ko et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

T-cell exhaustion, co-stimulation and clinical outcome in autoimmunity and infection

(2015) Eoin F. McKinney et al.   NATURE

Immune cell profiling to guide therapeutic decisions in rheumatic diseases

(2015) Joerg Ermann et al.   Nature Reviews Rheumatology

A comprehensive time-course–based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set

(2015) Timothy E. Sweeney et al.   Science Translational Medicine

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

SLE Peripheral Blood B Cell, T Cell and Myeloid Cell Transcriptomes Display Unique Profiles and Each Subset Contributes to the Interferon Signature

(2013) Amy M. Becker et al.   PLoS One

Genomic responses in mouse models poorly mimic human inflammatory diseases

(2013) Junhee Seok et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Meta-analysis of microarray data using a pathway-based approach identifies a 37-gene expression signature for systemic lupus erythematosus in human peripheral blood mononuclear cells

(2011) Dhivya Arasappan et al.   BMC Medicine

Direct Effects of Type I Interferons on Cells of the Immune System

(2011) S. Hervas-Stubbs et al.   CLINICAL CANCER RESEARCH

Animal Models in Autoimmune Diseases: Lessons Learned from Mouse Models for Sjögren’s Syndrome

(2011) Byung Ha Lee et al.   CLINICAL REVIEWS IN ALLERGY & IMMUNOLOGY

IFN-α produced by human plasmacytoid dendritic cells enhances T cell-dependent naïve B cell differentiation

(2011) Cornelia Gujer et al.   JOURNAL OF LEUKOCYTE BIOLOGY

A Genomic Approach to Human Autoimmune Diseases

(2010) Virginia Pascual et al.   Annual Review of Immunology

The interferon-α signature of systemic lupus erythematosus

(2010) G. Obermoser et al.   LUPUS

A CD8+ T cell transcription signature predicts prognosis in autoimmune disease

(2010) Eoin F McKinney et al.   NATURE MEDICINE

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Novel expression signatures identified by transcriptional analysis of separated leucocyte subsets in systemic lupus erythematosus and vasculitis

(2009) P. A. Lyons et al.   ANNALS OF THE RHEUMATIC DISEASES

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

Gene Expression Signatures Diagnose Influenza and Other Symptomatic Respiratory Viral Infections in Humans

(2009) Aimee K. Zaas et al.   Cell Host & Microbe

Lupus and cancer

(2009) M Gayed et al.   LUPUS

Deconvolution of Blood Microarray Data Identifies Cellular Activation Patterns in Systemic Lupus Erythematosus

(2009) Alexander R. Abbas et al.   PLoS One