Reverse vaccinology in the 21st century: improvements over the original design (Q38092843)

28 August 2017

title

Reverse vaccinology in the 21st century: improvements over the original design (English)

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28 August 2017

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28 August 2017

Rino Rappuoli

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28 August 2017

language of work or name

English

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publication date

25 March 2013

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Annals of the New York Academy of Sciences

28 August 2017

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inferred from page(s)

published in

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28 August 2017

volume

1285

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28 August 2017

page(s)

115-132

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Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

28 August 2017

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Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"

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Comparative genomics: the bacterial pan-genome

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Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

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Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

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Population genetics and evolution of the pan-genome of Streptococcus pneumoniae

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Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

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Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

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Rapid Pneumococcal Evolution in Response to Clinical Interventions

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Ecology drives a global network of gene exchange connecting the human microbiome

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Vaccination against Neisseria meningitidis using three variants of the lipoprotein GNA1870

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Characterization of diverse subvariants of the meningococcal factor H (fH) binding protein for their ability to bind fH, to mediate serum resistance, and to induce bactericidal antibodies

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Variation of the factor H-binding protein of Neisseria meningitidis

21 January 2018

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Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies

21 January 2018

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By-passing in vitro screening—next generation sequencing technologies applied to antibody display and in silico candidate selection

21 January 2018

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Sequencing and genome assembly using next-generation technologies

21 January 2018

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Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies

21 January 2018

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Qualitative and quantitative assessment of meningococcal antigens to evaluate the potential strain coverage of protein-based vaccines

21 January 2018

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The meningococcal vaccine candidate GNA1870 binds the complement regulatory protein factor H and enhances serum resistance

21 January 2018

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Group A Streptococcus produce pilus-like structures containing protective antigens and Lancefield T antigens

21 January 2018

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Comparing microarrays and next-generation sequencing technologies for microbial ecology research.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Identification of novel genomic islands coding for antigenic pilus-like structures in Streptococcus agalactiae.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Multilocus sequence typing

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Multilocus sequence typing of Streptococcus pyogenes and the relationships between emm type and clone

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Determining the genetic structure of the natural population of Staphylococcus aureus: a comparison of multilocus sequence typing with pulsed-field gel electrophoresis, randomly amplified polymorphic DNA analysis, and phage typing

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Database-driven multi locus sequence typing (MLST) of bacterial pathogens

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Basic local alignment search tool

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Improved tools for biological sequence comparison

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Fast and accurate long-read alignment with Burrows-Wheeler transform

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

The Sequence Alignment/Map format and SAMtools

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Evolution of MRSA during hospital transmission and intercontinental spread

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Detection of recombination events in bacterial genomes from large population samples

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Identifying bacterial genes and endosymbiont DNA with Glimmer

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Improved microbial gene identification with GLIMMER

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Microbial gene identification using interpolated Markov models

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Interpolated Markov models for eukaryotic gene finding.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

GeneMark.hmm: new solutions for gene finding

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Large-scale prokaryotic gene prediction and comparison to genome annotation

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Annotating genomes with massive-scale RNA sequencing

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Bacillus anthracis genome organization in light of whole transcriptome sequencing

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Proteogenomic mapping as a complementary method to perform genome annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Methods for predicting bacterial protein subcellular localization

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Sequence conserved for subcellular localization

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Prediction of protein subcellular localization

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Large-scale predictions of gram-negative bacterial protein subcellular locations

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Protein subcellular localization prediction based on compartment-specific features and structure conservation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

A novel representation of protein sequences for prediction of subcellular location using support vector machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Assessing the precision of high-throughput computational and laboratory approaches for the genome-wide identification of protein subcellular localization in bacteria.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Literature mining of host-pathogen interactions: comparing feature-based supervised learning and language-based approaches

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Bacterial proteomics and identification of potential vaccine targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Characterization and identification of vaccine candidate proteins through analysis of the group A Streptococcus surface proteome.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Outer membrane vesicles from group B Neisseria meningitidis delta gna33 mutant: proteomic and immunological comparison with detergent-derived outer membrane vesicles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Proteomics characterization of outer membrane vesicles from the extraintestinal pathogenic Escherichia coli DeltatolR IHE3034 mutant.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Proteomic analysis of cell surface proteins from Clostridium difficile

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

A comprehensive analysis of Bordetella pertussis surface proteome and identification of new immunogenic proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Surfome analysis as a fast track to vaccine discovery: identification of a novel protective antigen for Group B Streptococcus hypervirulent strain COH1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Investigating pathogen biology at the level of the proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Quantitative profile of the uropathogenic Escherichia coli outer membrane proteome during growth in human urine

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Immunoinformatics comes of age

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Benchmarking B cell epitope prediction: underperformance of existing methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Prediction of residues in discontinuous B-cell epitopes using protein 3D structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Reverse Vaccinology: Developing Vaccines in the Era of Genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Immune epitope database analysis resource

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

NadA, a novel vaccine candidate of Neisseria meningitidis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Neisseria meningitidis NadA is a new invasin which promotes bacterial adhesion to and penetration into human epithelial cells.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

A novel phase variation mechanism in the meningococcus driven by a ligand-responsive repressor and differential spacing of distal promoter elements

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Structural insight into the mechanism of DNA-binding attenuation of the Neisserial adhesin repressor NadR by the small natural ligand 4-hydroxyphenylacetic acid

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Gene expression profile in Neisseria meningitidis and Neisseria lactamica upon host-cell contact: from basic research to vaccine development.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Transcriptome analysis of Neisseria meningitidis in human whole blood and mutagenesis studies identify virulence factors involved in blood survival

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Microbial gene expression elucidated by selective capture of transcribed sequences (SCOTS).

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

In vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Toward a genome-wide systems biology analysis of host-pathogen interactions in group A Streptococcus

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

The Listeria transcriptional landscape from saprophytism to virulence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

The primary transcriptome of the major human pathogen Helicobacter pylori

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Pili in Gram-negative and Gram-positive bacteria - structure, assembly and their role in disease.

21 January 2018

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https://api.crossref.org/works/10.1111%2FNYAS.12046

Assembly of pili on the surface of Corynebacterium diphtheriae.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

A pneumococcal pilus influences virulence and host inflammatory responses

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

A second pilus type in Streptococcus pneumoniae is prevalent in emerging serotypes and mediates adhesion to host cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Genome-based approaches to vaccine development

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Streptococcus pneumoniae pilus subunits protect mice against lethal challenge

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Streptococcus pneumoniae contains 3 rlrA pilus variants that are clonally related

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Multi high-throughput approach for highly selective identification of vaccine candidates: the Group A Streptococcus case.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Microbial cell individuality and the underlying sources of heterogeneity

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

The cost of virulence: retarded growth of Salmonella Typhimurium cells expressing type III secretion system 1

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

The epigenetic control of antigenic variation in Plasmodium falciparum

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Genome flexibility in Neisseria meningitidis

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

The Streptococcus pneumoniae pilus-1 displays a biphasic expression pattern

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Stochastic gene expression in a single cell

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Phenotypic variation in bacteria: the role of feedback regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Cellular decision making and biological noise: from microbes to mammals

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

From molecular noise to behavioural variability in a single bacterium.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Stochastic gene expression in fluctuating environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Emergent bistability by a growth-modulating positive feedback circuit

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Single-cell microbiology: tools, technologies, and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Mass cytometry: technique for real time single cell multitarget immunoassay based on inductively coupled plasma time-of-flight mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Decoding human cytomegalovirus

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Transcriptome Complexity in a Genome-Reduced Bacterium

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Genome Analysis Reveals Pili in Group B Streptococcus

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

Sequence Variation in Group AStreptococcusPili and Association of Pilus Backbone Types with Lancefield T Serotypes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FNYAS.12046

21 January 2018

Identifiers

DOI

10.1111/NYAS.12046

1 reference

28 August 2017

1 reference