Published in Wiley Interdiscip Rev Syst Biol Med on October 19, 2011
Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. Nat Immunol (2013) 2.87
Unravelling the mechanisms of durable control of HIV-1. Nat Rev Immunol (2013) 1.74
Priorities for research on meningococcal disease and the impact of serogroup A vaccination in the African meningitis belt. Vaccine (2012) 1.30
Systems vaccinology: probing humanity's diverse immune systems with vaccines. Proc Natl Acad Sci U S A (2014) 1.16
Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response. Eur J Immunol (2013) 1.15
Vaccinomics, adversomics, and the immune response network theory: individualized vaccinology in the 21st century. Semin Immunol (2013) 1.11
Study of the integrated immune response induced by an inactivated EV71 vaccine. PLoS One (2013) 1.07
Advances in structure-based vaccine design. Curr Opin Virol (2013) 1.04
Updates on the web-based VIOLIN vaccine database and analysis system. Nucleic Acids Res (2013) 1.01
Vaccines, reverse vaccinology, and bacterial pathogenesis. Cold Spring Harb Perspect Med (2013) 1.01
A systems biology approach to the effect of aging, immunosenescence and vaccine response. Curr Opin Immunol (2014) 0.93
Immunity to viruses: learning from successful human vaccines. Immunol Rev (2013) 0.92
Global gene transcriptome analysis in vaccinated cattle revealed a dominant role of IL-22 for protection against bovine tuberculosis. PLoS Pathog (2012) 0.92
Systems vaccinology: Enabling rational vaccine design with systems biological approaches. Vaccine (2015) 0.90
Roles for Treg expansion and HMGB1 signaling through the TLR1-2-6 axis in determining the magnitude of the antigen-specific immune response to MVA85A. PLoS One (2013) 0.89
A transcriptomic reporter assay employing neutrophils to measure immunogenic activity of septic patients' plasma. J Transl Med (2014) 0.86
Ontology-supported research on vaccine efficacy, safety and integrative biological networks. Expert Rev Vaccines (2014) 0.84
A systems framework for vaccine design. Curr Opin Immunol (2013) 0.83
The human side of influenza. J Leukoc Biol (2012) 0.83
Vaccinology in the era of high-throughput biology. Philos Trans R Soc Lond B Biol Sci (2015) 0.83
Innate immune sensing and response to influenza. Curr Top Microbiol Immunol (2015) 0.82
Human systems immunology: hypothesis-based modeling and unbiased data-driven approaches. Semin Immunol (2013) 0.80
Gene signatures related to HAI response following influenza A/H1N1 vaccine in older individuals. Heliyon (2016) 0.78
Impact of immunosuppression on recall immune responses to influenza vaccination in stable renal transplant recipients. Transplantation (2014) 0.78
A review of clinical models for the evaluation of human TB vaccines. Hum Vaccin Immunother (2016) 0.75
Human transcriptome response to immunization with live-attenuated Venezuelan equine encephalitis virus vaccine (TC-83): Analysis of whole blood. Hum Vaccin Immunother (2016) 0.75
Antiviral innate immunity through the lens of systems biology. Virus Res (2015) 0.75
Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial. PLoS One (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A (2001) 132.88
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
Signal integration in the endoplasmic reticulum unfolded protein response. Nat Rev Mol Cell Biol (2007) 33.06
Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A (2002) 30.32
KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (2009) 28.60
Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A (2000) 19.39
Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet (2006) 16.12
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
Reverse engineering of regulatory networks in human B cells. Nat Genet (2005) 13.16
Gene selection and classification of microarray data using random forest. BMC Bioinformatics (2006) 12.45
An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature (2010) 10.37
Computational systems biology. Nature (2002) 10.33
Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol (2008) 8.51
A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet (2001) 7.79
Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol (2008) 7.18
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol (2010) 7.08
Regulation of cap-dependent translation by eIF4E inhibitory proteins. Nature (2005) 6.69
Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci U S A (2006) 6.26
Molecular networks as sensors and drivers of common human diseases. Nature (2009) 6.14
Systems biology of vaccination for seasonal influenza in humans. Nat Immunol (2011) 6.09
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (2009) 6.07
A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity (2008) 5.89
Vaccines: correlates of vaccine-induced immunity. Clin Infect Dis (2008) 5.69
Human effector and memory CD8+ T cell responses to smallpox and yellow fever vaccines. Immunity (2008) 5.22
Gene expression patterns in blood leukocytes discriminate patients with acute infections. Blood (2006) 5.05
Mammalian stress granules and processing bodies. Methods Enzymol (2007) 4.76
Cell type-specific gene expression differences in complex tissues. Nat Methods (2010) 4.75
Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics (2006) 4.57
Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity. J Exp Med (2006) 4.23
Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J Exp Med (2008) 4.21
Insights into host responses against pathogens from transcriptional profiling. Nat Rev Microbiol (2005) 4.11
Translating innate immunity into immunological memory: implications for vaccine development. Cell (2006) 3.98
Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics (2007) 3.68
Estimating the size of the human interactome. Proc Natl Acad Sci U S A (2008) 3.66
Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat Immunol (2009) 3.60
Immunological mechanisms of vaccination. Nat Immunol (2011) 3.35
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS One (2009) 2.98
A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol (2010) 2.92
Multiplexed protein profiling on microarrays by rolling-circle amplification. Nat Biotechnol (2002) 2.86
Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nat Biotechnol (2009) 2.79
Transcriptional regulatory circuits: predicting numbers from alphabets. Science (2009) 2.61
Modulation of adaptive immunity with Toll-like receptors. Semin Immunol (2009) 2.56
Classification of microarrays to nearest centroids. Bioinformatics (2005) 2.56
Systems vaccinology. Immunity (2010) 2.36
Proteome-wide analysis of the serological response to vaccinia and smallpox. Proteomics (2007) 2.10
Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology. Nat Rev Immunol (2009) 1.94
Development of viremia and humoral and cellular parameters of immune activation after vaccination with yellow fever virus strain 17D: a model of human flavivirus infection. J Med Virol (1998) 1.90
Assessing the human immune system through blood transcriptomics. BMC Biol (2010) 1.86
Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. Curr Opin Chem Biol (2004) 1.86
Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine. J Infect Dis (2010) 1.81
Integrating multiple 'omics' analysis for microbial biology: application and methodologies. Microbiology (2009) 1.79
Integrating genomic signatures for immunologic discovery. Immunity (2010) 1.72
Gene-set analysis and reduction. Brief Bioinform (2008) 1.71
Vaccines: the fourth century. Clin Vaccine Immunol (2009) 1.61
BLyS and B cell homeostasis. Semin Immunol (2006) 1.58
Gene expression microarrays: glimpses of the immunological genome. Nat Immunol (2006) 1.48
Towards genome-scale signalling network reconstructions. Nat Rev Genet (2010) 1.39
Understanding biological functions through molecular networks. Cell Res (2008) 1.29
Differential type I IFN-inducing abilities of wild-type versus vaccine strains of measles virus. J Immunol (2007) 1.29
Identification of vaccine candidate antigens of Staphylococcus aureus by serological proteome analysis. Proteomics (2002) 1.27
Targeting and tinkering with interaction networks. Nat Chem Biol (2008) 1.27
Large-scale optimization-based classification models in medicine and biology. Ann Biomed Eng (2007) 1.25
Genome-scale metabolic networks. Wiley Interdiscip Rev Syst Biol Med (2010) 1.11
Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination. Genes Immun (2008) 1.08
Computational modeling of mammalian signaling networks. Wiley Interdiscip Rev Syst Biol Med (2010) 1.04
Distinct gene expression profiles in peripheral blood mononuclear cells from patients infected with vaccinia virus, yellow fever 17D virus, or upper respiratory infections. Vaccine (2007) 0.96
Immunoproteomic analysis of the development of natural immunity in subjects colonized by Neisseria meningitidis reveals potential vaccine candidates. Infect Immun (2009) 0.94
Gene expression patterns induced by HPV-16 L1 virus-like particles in leukocytes from vaccine recipients. J Immunol (2009) 0.93
Next-generation sequencing: a transformative tool for vaccinology. Expert Rev Vaccines (2009) 0.88
Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17-producing T cell responses. Nat Immunol (2007) 7.64
Systems biology of vaccination for seasonal influenza in humans. Nat Immunol (2011) 6.09
Activation of beta-catenin in dendritic cells regulates immunity versus tolerance in the intestine. Science (2010) 6.04
Programming the magnitude and persistence of antibody responses with innate immunity. Nature (2011) 5.18
Yellow fever vaccine YF-17D activates multiple dendritic cell subsets via TLR2, 7, 8, and 9 to stimulate polyvalent immunity. J Exp Med (2006) 4.23
Toll-like receptor-mediated induction of type I interferon in plasmacytoid dendritic cells requires the rapamycin-sensitive PI(3)K-mTOR-p70S6K pathway. Nat Immunol (2008) 3.43
Yeast zymosan, a stimulus for TLR2 and dectin-1, induces regulatory antigen-presenting cells and immunological tolerance. J Clin Invest (2006) 3.31
A Blueprint for HIV Vaccine Discovery. Cell Host Microbe (2012) 3.27
A Toll-like receptor 2 ligand stimulates Th2 responses in vivo, via induction of extracellular signal-regulated kinase mitogen-activated protein kinase and c-Fos in dendritic cells. J Immunol (2004) 3.25
Analysis of in vivo dynamics of influenza virus infection in mice using a GFP reporter virus. Proc Natl Acad Sci U S A (2010) 3.17
Impairment of dendritic cells and adaptive immunity by anthrax lethal toxin. Nature (2003) 2.83
Cutting edge: impairment of dendritic cells and adaptive immunity by Ebola and Lassa viruses. J Immunol (2003) 2.75
Modulation of adaptive immunity with Toll-like receptors. Semin Immunol (2009) 2.56
Systems vaccinology. Immunity (2010) 2.36
Toll-like receptor 2-dependent induction of vitamin A-metabolizing enzymes in dendritic cells promotes T regulatory responses and inhibits autoimmunity. Nat Med (2009) 2.30
The T helper type 2 response to cysteine proteases requires dendritic cell-basophil cooperation via ROS-mediated signaling. Nat Immunol (2010) 2.20
Dendritic cell control of tolerogenic responses. Immunol Rev (2011) 2.13
Toll-like receptor expression and responsiveness of distinct murine splenic and mucosal B-cell subsets. PLoS One (2007) 1.82
Rapid and massive virus-specific plasmablast responses during acute dengue virus infection in humans. J Virol (2012) 1.74
Phenotype, function, and gene expression profiles of programmed death-1(hi) CD8 T cells in healthy human adults. J Immunol (2011) 1.66
Retinoic acid-dependent regulation of immune responses by dendritic cells and macrophages. Semin Immunol (2008) 1.51
ERK1-/- mice exhibit Th1 cell polarization and increased susceptibility to experimental autoimmune encephalomyelitis. J Immunol (2006) 1.49
Hematopoietic cell types: prototype for a revised cell ontology. J Biomed Inform (2010) 1.48
Predicting network activity from high throughput metabolomics. PLoS Comput Biol (2013) 1.44
A versatile role of mammalian target of rapamycin in human dendritic cell function and differentiation. J Immunol (2010) 1.42
Vesicular stomatitis virus oncolysis is potentiated by impairing mTORC1-dependent type I IFN production. Proc Natl Acad Sci U S A (2010) 1.39
Chronic but not acute virus infection induces sustained expansion of myeloid suppressor cell numbers that inhibit viral-specific T cell immunity. Immunity (2013) 1.33
The science of adjuvants. Expert Rev Vaccines (2007) 1.31
Adjuvanting a DNA vaccine with a TLR9 ligand plus Flt3 ligand results in enhanced cellular immunity against the simian immunodeficiency virus. J Exp Med (2007) 1.30
Improving defences at the portal of HIV entry: mucosal and innate immunity. PLoS Med (2008) 1.27
Ebola virus-like particles produced in insect cells exhibit dendritic cell stimulating activity and induce neutralizing antibodies. Virology (2006) 1.23
Human dendritic cells respond to Porphyromonas gingivalis LPS by promoting a Th2 effector response in vitro. Eur J Immunol (2003) 1.21
Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response. Eur J Immunol (2013) 1.15
Distinct TLR adjuvants differentially stimulate systemic and local innate immune responses in nonhuman primates. Blood (2012) 1.15
Dendritic cells at the host-pathogen interface. Nat Immunol (2006) 1.14
Inhibition of T helper 2-type responses, IgE production and eosinophilia by synthetic lipopeptides. Eur J Immunol (2003) 1.14
Fatal multiorgan failure due to yellow fever vaccine-associated viscerotropic disease. Vaccine (2007) 1.13
Multiple innate immune pathways contribute to the immunogenicity of recombinant adenovirus vaccine vectors. J Virol (2010) 1.11
Gene profiling of Chikungunya virus arthritis in a mouse model reveals significant overlap with rheumatoid arthritis. Arthritis Rheum (2012) 1.10
The stimulation of CD8+ T cells by dendritic cells pulsed with polyketal microparticles containing ion-paired protein antigen and poly(inosinic acid)-poly(cytidylic acid). Biomaterials (2008) 1.03
Hepatic stellate cells preferentially induce Foxp3+ regulatory T cells by production of retinoic acid. J Immunol (2013) 1.02
Systems vaccinology: its promise and challenge for HIV vaccine development. Curr Opin HIV AIDS (2012) 1.01
Repression of bacterial lipoprotein production by Francisella novicida facilitates evasion of innate immune recognition. Cell Microbiol (2012) 1.00
Detailed mitochondrial phenotyping by high resolution metabolomics. PLoS One (2012) 0.99
Effects of age, sex, and genotype on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster. Aging Cell (2014) 0.99
Probing the 'labyrinth' linking the innate and adaptive immune systems. Nat Immunol (2007) 0.99
Hexa-acylation and KDO(2)-glycosylation determine the specific immunostimulatory activity of Neisseria meningitidis lipid A for human monocyte derived dendritic cells. Vaccine (2005) 0.98
Systems biological approaches to measure and understand vaccine immunity in humans. Semin Immunol (2013) 0.98
Hybrid feature detection and information accumulation using high-resolution LC-MS metabolomics data. J Proteome Res (2013) 0.97
Immunogenomics and systems biology of vaccines. Immunol Rev (2011) 0.97
Cross-presentation: avoiding trafficking chaos? Nat Immunol (2008) 0.93
The gut feeling of Treg cells: IL-10 is the silver lining during colitis. Nat Immunol (2009) 0.90
Identifying gnostic predictors of the vaccine response. Curr Opin Immunol (2012) 0.89
Systems biology of vaccination in the elderly. Curr Top Microbiol Immunol (2013) 0.88
CD28-B7 interaction modulates short- and long-lived plasma cell function. J Immunol (2012) 0.88
Division of labor and cooperation between dendritic cells. Nat Immunol (2006) 0.88
A shot in the arm for mast cells. Nat Med (2008) 0.85
Understanding the role of innate immunity in the mechanism of action of the live attenuated Yellow Fever Vaccine 17D. Adv Exp Med Biol (2007) 0.85
Learning vaccinology from viral infections. J Exp Med (2011) 0.83
Systems vaccinomics: the road ahead for vaccinology. OMICS (2011) 0.83
Mycobacterium tuberculosis impairs dendritic cell functions through the serine hydrolase Hip1. J Immunol (2014) 0.81
A microarray screen for direct targets of Zic1 identifies an aquaporin gene, aqp-3b, expressed in the neural folds. Dev Dyn (2009) 0.81
Restraining order for dendritic cells: all quiet on the fetal front. J Clin Invest (2009) 0.80
Peptide crosslinked micelles: a new strategy for the design and synthesis of peptide vaccines. Int J Nanomedicine (2006) 0.80
Systems biology in understanding HIV pathogenesis and guiding vaccine development. Curr Opin HIV AIDS (2012) 0.80
Host-pathogen interactions in the 21st century. Curr Opin Immunol (2005) 0.78
4th Aegean Conference on the Crossroads between Innate and Adaptive Immunity. Nat Immunol (2011) 0.78
An open-ended plea for the development of a global database of HIV vaccine responses. Curr Opin HIV AIDS (2012) 0.75
Editorial overview. Curr Opin Virol (2011) 0.75
Linking genome and immunity. Curr Opin Immunol (2013) 0.75