Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance

Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8 + T Cells in Chronic versus Acute Infection

(2017) David Wolski et al.   IMMUNITY

Genetic Variation at IFNL4 Influences Extrahepatic Interferon-Stimulated Gene Expression in Chronic HCV Patients

(2017) Brad R Rosenberg et al.   JOURNAL OF INFECTIOUS DISEASES

Systems analysis of protective immune responses to RTS,S malaria vaccination in humans

(2017) Dmitri Kazmin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alanine aminotransferase, HCV RNA levels and pro-inflammatory and pro-fibrogenic cytokines/chemokines during acute hepatitis C virus infection

(2016) Behzad Hajarizadeh et al.   Virology Journal

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

(2016) Slim Fourati et al.   Nature Communications

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

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

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

Vaccinology in the era of high-throughput biology

(2015) H. I. Nakaya et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The hepatitis C virus epidemics in key populations (including people who inject drugs, prisoners and MSM)

(2015) Natasha K. Martin et al.   Current Opinion in HIV and AIDS

The past, present and future of neutralizing antibodies for hepatitis C virus

(2014) Jonathan K. Ball et al.   ANTIVIRAL RESEARCH

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

(2014) John S. Tsang et al.   CELL

Dengue Virus Infection Induces Expansion of a CD14+CD16+ Monocyte Population that Stimulates Plasmablast Differentiation

(2014) Marcin Kwissa et al.   Cell Host & Microbe

Immune Responses to HCV and Other Hepatitis Viruses

(2014) Su-Hyung Park et al.   IMMUNITY

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Plasma interferon-gamma-inducible protein-10 (IP-10) levels during acute hepatitis C virus infection

(2013) Jason Grebely et al.   HEPATOLOGY

Systems Scale Interactive Exploration Reveals Quantitative and Qualitative Differences in Response to Influenza and Pneumococcal Vaccines

(2013) Gerlinde Obermoser et al.   IMMUNITY

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

(2013) Shuzhao Li et al.   NATURE IMMUNOLOGY

Epidemiology and natural history of HCV infection

(2013) Behzad Hajarizadeh et al.   Nature Reviews Gastroenterology & Hepatology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Interferon-γ–Stimulated Genes, but Not USP18, Are Expressed in Livers of Patients With Acute Hepatitis C

(2012) Michael T. Dill et al.   GASTROENTEROLOGY

Cohort Profile: The International Collaboration of Incident HIV and Hepatitis C in Injecting Cohorts (InC3) Study

(2012) J. Grebely et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

Delayed Induction, Not Impaired Recruitment, of Specific CD8+ T Cells Causes the Late Onset of Acute Hepatitis C

(2011) Eui–Cheol Shin et al.   GASTROENTEROLOGY

Serum Level of IP-10 Increases Predictive Value of IL28B Polymorphisms for Spontaneous Clearance of Acute HCV Infection

(2011) Sandra Beinhardt et al.   GASTROENTEROLOGY

Induction of CXCR3- and CCR5-associated chemokines during acute hepatitis C virus infection

(2011) Marija Zeremski et al.   JOURNAL OF HEPATOLOGY

Systems biology of vaccination for seasonal influenza in humans

(2011) Helder I Nakaya et al.   NATURE IMMUNOLOGY

ROAST: rotation gene set tests for complex microarray experiments

(2010) Di Wu et al.   BIOINFORMATICS

Assessing the human immune system through blood transcriptomics

(2010) Damien Chaussabel et al.   BMC BIOLOGY

Pathogenesis of Hepatitis E Virus and Hepatitis C Virus in Chimpanzees: Similarities and Differences

(2010) C. Yu et al.   JOURNAL OF VIROLOGY

Hepatitis C: viral and host factors associated with non-response to pegylated interferon plus ribavirin

(2010) Tarik Asselah et al.   LIVER INTERNATIONAL

Dissecting Interferon-Induced Transcriptional Programs in Human Peripheral Blood Cells

(2010) Simon J. Waddell et al.   PLoS One

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Rare Birds in North America: Acute Hepatitis C Cohorts

(2008) Andrea L. Cox et al.   GASTROENTEROLOGY

Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses

(2008) Denis Gaucher et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

(2008) Troy D Querec et al.   NATURE IMMUNOLOGY