A guide to in silico vaccine discovery for eukaryotic pathogens (Q45003975)

8 December 2017

A guide to in silico vaccine discovery for eukaryotic pathogens (English)

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8 December 2017

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8 December 2017

3

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8 December 2017

Stephen J Goodswen

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8 December 2017

24 October 2012

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Briefings in Bioinformatics

8 December 2017

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8 December 2017

14

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8 December 2017

6

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8 December 2017

753-774

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

8 December 2017

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Search for potential vaccine candidate open reading frames in the Bacillus anthracis virulence plasmid pXO1: in silico and in vitro screening

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Genomic approach for analysis of surface proteins in Chlamydia pneumoniae

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Microbial genomes and vaccine design: refinements to the classical reverse vaccinology approach

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Toxoplasma gondii: the model apicomplexan.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Genetics. Themes and variations in apicomplexan parasite biology

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

WoLF PSORT: protein localization predictor

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

The difficulty of identifying genes in anonymous vertebrate sequences

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

The gene identification problem: an overview for developers.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Finding genes by computer: the state of the art.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

An assessment of gene prediction accuracy in large DNA sequences

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Gene finding in novel genomes

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Current methods of gene prediction, their strengths and weaknesses

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Intrinsic and extrinsic approaches for detecting genes in a bacterial genome

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Powers and pitfalls in sequence analysis: the 70% hurdle

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Identification of coding regions in genomic DNA sequences: an application of dynamic programming and neural networks

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Gene recognition via spliced sequence alignment.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Ab initio gene finding in Drosophila genomic DNA

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Prediction of complete gene structures in human genomic DNA

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

GeneMark.hmm: new solutions for gene finding

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Computational inference of homologous gene structures in the human genome

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

GAZE: a generic framework for the integration of gene-prediction data by dynamic programming

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

The Ensembl genome database project

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

AUGUSTUS: a web server for gene finding in eukaryotes

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Using multiple alignments to improve gene prediction.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Using ESTs to improve the accuracy of de novo gene prediction

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Conrad: gene prediction using conditional random fields.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

mGene.web: a web service for accurate computational gene finding

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

An overview of the current status of eukaryote gene prediction strategies

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

How does eukaryotic gene prediction work?

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Comparative gene prediction in human and mouse

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Predicting protein subcellular localisation from amino acid sequence information

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Locating proteins in the cell using TargetP, SignalP and related tools

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Machine learning approaches for the prediction of signal peptides and other protein sorting signals

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Improved prediction of signal peptides: SignalP 3.0

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Predicting subcellular localization of proteins based on their N-terminal amino acid sequence

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Evaluation of methods for the prediction of membrane spanning regions

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

The RESID Database of Protein Modifications: 2003 developments

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Recent developments in the cell biology and biochemistry of glycosylphosphatidylinositol lipids (review).

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

PredGPI: a GPI-anchor predictor

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Prediction of potential GPI-modification sites in proprotein sequences

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

FragAnchor: a large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

An introduction to epitope prediction methods and software

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Methods and protocols for prediction of immunogenic epitopes

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Prediction of T-cell epitope

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Machine learning competition in immunology - Prediction of HLA class I binding peptides.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Reliable prediction of T-cell epitopes using neural networks with novel sequence representations

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

NetMHCpan, a method for MHC class I binding prediction beyond humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Class I T-cell epitope prediction: improvements using a combination of proteasome cleavage, TAP affinity, and MHC binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Global haplotype partitioning for maximal associated SNP pairs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Discovery of promiscuous HLA-II-restricted T cell epitopes with TEPITOPE.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Benchmarking B cell epitope prediction: underperformance of existing methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Immunomics: discovering new targets for vaccines and therapeutics

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Prediction of linear B-cell epitopes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Antibody-protein interactions: benchmark datasets and prediction tools evaluation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Prediction of linear B-cell epitopes using amino acid pair antigenicity scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Predicting linear B-cell epitopes using string kernels

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

A semi-empirical method for prediction of antigenic determinants on protein antigens

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

The immune epitope database 2.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Comparative genomics - a perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

On Some Principles Governing Molecular Evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Reverse vaccinology: developing vaccines in the era of genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Comparison of immune response in sheep immunized with DNA vaccine encoding Toxoplasma gondii GRA7 antigen in different adjuvant formulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Immunization of mice with plasmid DNA coding for NcGRA7 or NcsHSP33 confers partial protection against vertical transmission of Neospora caninum.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Modulation of immune response to Toxoplasma gondii in sheep by immunization with a DNA vaccine encoding ROP1 antigen as a fusion protein with ovine CD154.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

The MIC3 gene of Toxoplasma gondii is a novel potent vaccine candidate against toxoplasmosis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Vaccination of mice against experimental Neospora caninum infection using NcSAG1- and NcSRS2-based recombinant antigens and DNA vaccines

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Protective efficacy of vaccination with Neospora caninum multiple recombinant antigens against experimental Neospora caninum infection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Biological role of surface Toxoplasma gondii antigen in development of vaccine

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Protective efficacy of vaccination by recombinant vaccinia virus against Neospora caninum infection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Selection of Neospora caninum antigens stimulating bovine CD4+ve T cell responses through immuno-potency screening and proteomic approaches.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Bovine immune response to inoculation with Neospora caninum surface antigen SRS2 lipopeptides mimics immune response to infection with live parasites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Immunization with native surface protein NcSRS2 induces a Th2 immune response and reduces congenital Neospora caninum transmission in mice.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Delivery of Neospora caninum surface protein, NcSRS2 (Nc-p43), to mouse using recombinant vaccinia virus

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Identification of vaccine candidate peptides in the NcSRS2 surface protein of Neospora caninum by using CD4+ cytotoxic T lymphocytes and gamma interferon-secreting T lymphocytes of infected holstein cattle.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Isolation, characterization and expression of a GRA2 homologue from Neospora caninum.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Prevention of lethal experimental infection of C57BL/6 mice by vaccination with Brucella abortus strain RB51 expressing Neospora caninum antigens.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Vaccination with recombinant NcROP2 combined with recombinant NcMIC1 and NcMIC3 reduces cerebral infection and vertical transmission in mice experimentally infected with Neospora caninum tachyzoites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Identification and characterization of Neospora caninum cyclophilin that elicits gamma interferon production

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

Toxoplasma gondii: the vaccine potential of three trivalent antigen-cocktails composed of recombinant ROP2, ROP4, GRA4 and SAG1 proteins against chronic toxoplasmosis in BALB/c mice

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS066

21 January 2018

Identifiers

DOI

10.1093/BIB/BBS066

1 reference

journals/bib/GoodswenKE13

8 December 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PubMed ID

23097412