The role of systems biology approaches in determining molecular signatures for the development of more effective vaccines

Application and utility of mass cytometry in vaccine development

(2018) Patrick M. Reeves et al.   FASEB JOURNAL

GoldiRunx and Remembering Cytotoxic Memory

(2018) Yohei Mikami et al.   IMMUNITY

Rapid response to an emerging infectious disease – Lessons learned from development of a synthetic DNA vaccine targeting Zika virus

(2018) Sagar B. Kudchodkar et al.   MICROBES AND INFECTION

The potential of metabolic profiling for vaccine development

(2018) January Weiner et al.   SEMINARS IN IMMUNOLOGY

Immunogenicity, reactogenicity and safety of 2 doses of an adjuvanted herpes zoster subunit vaccine administered 2, 6 or 12 months apart in older adults: Results of a phase III, randomized, open-label, multicenter study

(2018) Himal Lal et al.   VACCINE

The influence of the intestinal microbiome on vaccine responses

(2018) Petra Zimmermann et al.   VACCINE

The influence of prebiotic or probiotic supplementation on antibody titers after influenza vaccination: a systematic review and meta-analysis of randomized controlled trials

(2018) Tzu-Lin Yeh et al.   Drug Design Development and Therapy

Transcriptomic signatures of cellular and humoral immune responses in older adults after seasonal influenza vaccination identified by data-driven clustering

(2018) Emily A. Voigt et al.   Scientific Reports

Effect of Antibiotic-Mediated Microbiome Modulation on Rotavirus Vaccine Immunogenicity: A Human, Randomized-Control Proof-of-Concept Trial

(2018) Vanessa C. Harris et al.   Cell Host & Microbe

Identification and replication of RNA-Seq gene network modules associated with depression severity

(2018) Trang T. Le et al.   Translational Psychiatry

EpistasisRank and EpistasisKatz: interaction network centrality methods that integrate prior knowledge networks

(2018) Saeid Parvandeh et al.   BIOINFORMATICS

The chromatin accessibility signature of human immune aging stems from CD8+T cells

(2017) Duygu Ucar et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Cutting Edge: Chromatin Accessibility Programs CD8 T Cell Memory

(2017) Christopher D. Scharer et al.   JOURNAL OF IMMUNOLOGY

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Origin and differentiation of human memory CD8 T cells after vaccination

(2017) Rama S. Akondy et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Zika virus protection by a single low-dose nucleoside-modified mRNA vaccination

(2017) Norbert Pardi et al.   NATURE

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Systems serology: profiling vaccine induced humoral immunity against HIV

(2017) Amy W. Chung et al.   Retrovirology

Metabolites as biomarkers of adverse reactions following vaccination: A pilot study using nuclear magnetic resonance metabolomics

(2017) Bruce M. McClenathan et al.   VACCINE

Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines?

(2017) Mark M. Davis et al.   Cold Spring Harbor Perspectives in Biology

Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines?

(2017) Rino Rappuoli et al.   Cold Spring Harbor Perspectives in Biology

Systems Vaccinology Identifies an Early Innate Immune Signature as a Correlate of Antibody Responses to the Ebola Vaccine rVSV-ZEBOV

(2017) Anne Rechtien et al.   Cell Reports

xMAP Technology: Applications in Detection of Pathogens

(2017) Nikol Reslova et al.   Frontiers in Microbiology

Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial

(2017) Leigh M. Howard et al.   PLoS One

Interlaboratory Reproducibility of a Targeted Metabolomics Platform for Analysis of Human Serum and Plasma

(2016) Alexandros P. Siskos et al.   ANALYTICAL CHEMISTRY

Gene signatures associated with adaptive humoral immunity following seasonal influenza A/H1N1 vaccination

(2016) I G Ovsyannikova et al.   GENES AND IMMUNITY

An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data

(2016) C A Lareau et al.   GENES AND IMMUNITY

Topical imiquimod before intradermal trivalent influenza vaccine for protection against heterologous non-vaccine and antigenically drifted viruses: a single-centre, double-blind, randomised, controlled phase 2b/3 trial

(2016) Ivan Fan-Ngai Hung et al.   LANCET INFECTIOUS DISEASES

The Integration of Epistasis Network and Functional Interactions in a GWAS Implicates RXR Pathway Genes in the Immune Response to Smallpox Vaccine

(2016) Brett A. McKinney et al.   PLoS One

Systems biology of immunity to MF59-adjuvanted versus nonadjuvanted trivalent seasonal influenza vaccines in early childhood

(2016) Helder I. Nakaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recursive Indirect-Paths Modularity (RIP-M) for Detecting Community Structure in RNA-Seq Co-expression Networks

(2016) Bahareh Rahmani et al.   Frontiers in Genetics

Circulating follicular T helper cells and cytokine profile in humans following vaccination with the rVSV-ZEBOV Ebola vaccine

(2016) Fouzia Farooq et al.   Scientific Reports

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

(2015) Petter Brodin et al.   CELL

Quantification of the epitope diversity of HIV-1-specific binding antibodies by peptide microarrays for global HIV-1 vaccine development

(2015) Kathryn E. Stephenson et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Synthetic Toll-Like Receptor 4 (TLR4) and TLR7 Ligands as Influenza Virus Vaccine Adjuvants Induce Rapid, Sustained, and Broadly Protective Responses

(2015) Peter H. Goff et al.   JOURNAL OF VIROLOGY

Malnutrition and vaccination in developing countries

(2015) A. J. Prendergast   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

New approaches to understanding the immune response to vaccination and infection

(2015) David Furman et al.   VACCINE

Molecular signatures of vaccine adjuvants

(2015) Thorunn Olafsdottir et al.   VACCINE

Differential co-expression network centrality and machine learning feature selection for identifying susceptibility hubs in networks with scale-free structure

(2015) Caleb A Lareau et al.   BioData Mining

Luminex and Other Multiplex High Throughput Technologies for the Identification of, and Host Response to, Environmental Triggers of Type 1 Diabetes

(2015) Sharad Purohit et al.   Biomed Research International

dcVar: a method for identifying common variants that modulate differential correlation structures in gene expression data

(2015) Caleb A. Lareau et al.   Frontiers in Genetics

Deconstructing the Peptide-MHC Specificity of T Cell Recognition

(2014) Michael E. Birnbaum et al.   CELL

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

(2014) John S. Tsang et al.   CELL

Human Responses to Influenza Vaccination Show Seroconversion Signatures and Convergent Antibody Rearrangements

(2014) Katherine J.L. Jackson et al.   Cell Host & Microbe

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

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

High-throughput sequencing of natively paired antibody chains provides evidence for original antigenic sin shaping the antibody response to influenza vaccination

(2014) Yann-Chong Tan et al.   CLINICAL IMMUNOLOGY

Immunogenicity of Intradermal Trivalent Influenza Vaccine With Topical Imiquimod: A Double Blind Randomized Controlled Trial

(2014) Ivan F. N. Hung et al.   CLINICAL INFECTIOUS DISEASES

Nucleic acid vaccines: prospects for non-viral delivery of mRNA vaccines

(2014) Raquel P Deering et al.   Expert Opinion on Drug Delivery

Transcriptomic profiling facilitates classification of response to influenza challenge

(2014) Emma E. Davenport et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Profiling the humoral immune responses to Plasmodium vivax infection and identification of candidate immunogenic rhoptry-associated membrane antigen (RAMA)

(2014) Feng Lu et al.   Journal of Proteomics

Vaccinia Virus Requires Glutamine but Not Glucose for Efficient Replication

(2014) K. A. Fontaine et al.   JOURNAL OF VIROLOGY

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Sequencing the functional antibody repertoire—diagnostic and therapeutic discovery

(2014) William H. Robinson   Nature Reviews Rheumatology

Systems vaccinology: Probing humanity's diverse immune systems with vaccines

(2014) B. Pulendran   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A human vaccine strategy based on chimpanzee adenoviral and MVA vectors that primes, boosts, and sustains functional HCV-specific T cell memory

(2014) L. Swadling et al.   Science Translational Medicine

The Split Virus Influenza Vaccine rapidly activates immune cells through Fcγ receptors

(2014) William E. O’Gorman et al.   VACCINE

Identification of linear B epitopes of pertactin of Bordetella pertussis induced by immunization with whole and acellular vaccine

(2014) Flavio R. da Silva et al.   VACCINE

Plasmid DNA initiates replication of yellow fever vaccine in vitro and elicits virus-specific immune response in mice

(2014) Irina Tretyakova et al.   VIROLOGY

Cross-validation pitfalls when selecting and assessing regression and classification models

(2014) Damjan Krstajic et al.   Journal of Cheminformatics

An Immunomics Approach to Schistosome Antigen Discovery: Antibody Signatures of Naturally Resistant and Chronically Infected Individuals from Endemic Areas

(2014) Soraya Gaze et al.   PLoS Pathogens

Barcode-Enabled Sequencing of Plasmablast Antibody Repertoires in Rheumatoid Arthritis

(2014) Yann-Chong Tan et al.   Arthritis & Rheumatology

Recent Advances in Microarray Technologies for Proteomics

(2013) Hongyan Sun et al.   CHEMISTRY & BIOLOGY

Immunoproteomic Analysis of Antibody in Lymphocyte Supernatant in Patients with Typhoid Fever in Bangladesh

(2013) Richelle C. Charles et al.   Clinical and Vaccine Immunology

Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response

(2013) Yan Tan et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Virus-Specific CD4+ Memory-Phenotype T Cells Are Abundant in Unexposed Adults

(2013) Laura F. Su et al.   IMMUNITY

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

(2013) Gerlinde Obermoser et al.   IMMUNITY

T-cell memory differentiation: insights from transcriptional signatures and epigenetics

(2013) Ben Youngblood et al.   IMMUNOLOGY

Metabolomics in pneumonia and sepsis: an analysis of the GenIMS cohort study

(2013) Christopher W. Seymour et al.   INTENSIVE CARE MEDICINE

Effects of Aging, Cytomegalovirus Infection, and EBV Infection on Human B Cell Repertoires

(2013) C. Wang et al.   JOURNAL OF IMMUNOLOGY

Yellow Fever Vaccination Elicits Broad Functional CD4+T Cell Responses That Recognize Structural and Nonstructural Proteins

(2013) Eddie A. James et al.   JOURNAL OF VIROLOGY

Cytokine assays: An assessment of the preparation and treatment of blood and tissue samples

(2013) Genoveva C.E. Keustermans et al.   METHODS

Apoptosis and other immune biomarkers predict influenza vaccine responsiveness

(2013) D. Furman et al.   Molecular Systems Biology

Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization

(2013) Evan W Newell et al.   NATURE BIOTECHNOLOGY

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

(2013) Shuzhao Li et al.   NATURE IMMUNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Characterization of Influenza Vaccine Immunogenicity Using Influenza Antigen Microarrays

(2013) Jordan V. Price et al.   PLoS One

When Is Hub Gene Selection Better than Standard Meta-Analysis?

(2013) Peter Langfelder et al.   PLoS One

Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination

(2013) N. Jiang et al.   Science Translational Medicine

Vaccinomics, adversomics, and the immune response network theory: Individualized vaccinology in the 21st century

(2013) Gregory A. Poland et al.   SEMINARS IN IMMUNOLOGY

High-Resolution Temporal Response Patterns to Influenza Vaccine Reveal a Distinct Human Plasma Cell Gene Signature

(2013) Alicia D. Henn et al.   Scientific Reports

Using epigenetics to define vaccine-induced memory T cells

(2013) Ben Youngblood et al.   Current Opinion in Virology

Identification of Strain-Specific B-cell Epitopes in Trypanosoma cruzi Using Genome-Scale Epitope Prediction and High-Throughput Immunoscreening with Peptide Arrays

(2013) Tiago Antônio de Oliveira Mendes et al.   PLoS Neglected Tropical Diseases

Serum Metabolome and Lipidome Changes in Adult Patients with Primary Dengue Infection

(2013) Liang Cui et al.   PLoS Neglected Tropical Diseases

Nomenclature for Immune Correlates of Protection After Vaccination

(2012) S. A. Plotkin et al.   CLINICAL INFECTIOUS DISEASES

Broad heparin-binding haemagglutinin-specific cytokine and chemokine response in infants following Mycobacterium bovis BCG vaccination

(2012) Steven G. Smith et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8+ T Cell Phenotypes

(2012) Evan W. Newell et al.   IMMUNITY

T Cell Receptor Stimulation-Induced Epigenetic Changes and Foxp3 Expression Are Independent and Complementary Events Required for Treg Cell Development

(2012) Naganari Ohkura et al.   IMMUNITY

Vaccine applications of flow cytometry

(2012) Stephen C. De Rosa   METHODS

Age-Related Changes in Human Peripheral Blood IGH Repertoire Following Vaccination

(2012) Yu-Chang Bryan Wu et al.   Frontiers in Immunology

Vaccinomics: Current Findings, Challenges and Novel Approaches for Vaccine Development

(2011) Inna G. Ovsyannikova et al.   AAPS Journal

Chronic Virus Infection Enforces Demethylation of the Locus that Encodes PD-1 in Antigen-Specific CD8+ T Cells

(2011) Ben Youngblood et al.   IMMUNITY

BCG Vaccination Induces Different Cytokine Profiles Following Infant BCG Vaccination in the UK and Malawi

(2011) Maeve K. Lalor et al.   JOURNAL OF INFECTIOUS DISEASES

Regression shrinkage and selection via the lasso: a retrospective

(2011) Robert Tibshirani   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Central dogma at the single-molecule level in living cells

(2011) Gene-Wei Li et al.   NATURE

Systems biology of vaccination for seasonal influenza in humans

(2011) Helder I Nakaya et al.   NATURE IMMUNOLOGY

Aberrant Cell Cycle and Apoptotic Changes Characterise Severe Influenza A Infection – A Meta-Analysis of Genomic Signatures in Circulating Leukocytes

(2011) Grant Parnell et al.   PLoS One

Metabolomic Profile of Hepatitis C Virus-Infected Hepatocytes

(2011) Barbara Roe et al.   PLoS One

Structural basis for immunization with postfusion respiratory syncytial virus fusion F glycoprotein (RSV F) to elicit high neutralizing antibody titers

(2011) K. A. Swanson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measurement of antibody responses to Modified Vaccinia virus Ankara (MVA) and Dryvax® using proteome microarrays and development of recombinant protein ELISAs

(2011) Gary Hermanson et al.   VACCINE

Vaccinomics and Personalized Vaccinology: Is Science Leading Us Toward a New Path of Directed Vaccine Development and Discovery?

(2011) Gregory A. Poland et al.   PLoS Pathogens

Correlates of Protection Induced by Vaccination

(2010) S. A. Plotkin   Clinical and Vaccine Immunology

High dimensional flow cytometry for comprehensive leukocyte immunophenotyping (CLIP) in translational research

(2010) Angélique Biancotto et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Expression of Genes Associated with Immunoproteasome Processing of Major Histocompatibility Complex Peptides Is Indicative of Protection with Adjuvanted RTS,S Malaria Vaccine

(2010) Maryanne T. Vahey et al.   JOURNAL OF INFECTIOUS DISEASES

From ‘differential expression’ to ‘differential networking’ – identification of dysfunctional regulatory networks in diseases

(2010) Alberto de la Fuente   TRENDS IN GENETICS

Peak frequencies of circulating human influenza-specific antibody secreting cells correlate with serum antibody response after immunization

(2010) Jessica L. Halliley et al.   VACCINE

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

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

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

Landscape Analysis of Interactions between Nutrition and Vaccine Responses in Children

(2009) Mathilde Savy et al.   JOURNAL OF NUTRITION

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Influence of cytokine gene variations on immunization to childhood vaccines

(2009) Berran Yucesoy et al.   VACCINE

Capturing the Spectrum of Interaction Effects in Genetic Association Studies by Simulated Evaporative Cooling Network Analysis

(2009) Brett A. McKinney et al.   PLoS Genetics

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination

(2008) D M Reif et al.   GENES AND IMMUNITY

Rapid cloning of high-affinity human monoclonal antibodies against influenza virus

(2008) Jens Wrammert et al.   NATURE

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

(2008) Troy D Querec et al.   NATURE IMMUNOLOGY

Molecular and cellular signatures of human vaccine adjuvants

(2008) F. Mosca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Vaccine immunogenetics: Bedside to bench to population

(2008) Gregory A. Poland et al.   VACCINE