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Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies
2008
Nucleic Acids Research
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The investigation uses the proteininteraction network for all essential immunome human genes available in the Immunome Knowledge Base and an analysis of their enriched gene ontology annotations. ...
The method can be generalized for any disease group with sufficient information. ...
With an exhaustive analysis of literature and databases, we identified altogether 847 genes and proteins that are crucial for the immune system and thus form the essential human immunome (20) . ...
doi:10.1093/nar/gkn982
pmid:19073697
pmcid:PMC2632920
fatcat:riw2rrqwcfexljyrg5sy7fhbc4
From Functional Genomics to Functional Immunomics: New Challenges, Old Problems, Big Rewards
2006
PLoS Computational Biology
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Based on the recent discovery of regulation mechanisms in T cell responses, we envision the use of immunomic microarrays as a tool for advances in systems biology of cellular immune responses, by means ...
T he development of DNA microarray technology a decade ago led to the establishment of functional genomics as one of the most active and successful scientific disciplines today. ...
Acknowledgments The authors would like to thank J. ...
doi:10.1371/journal.pcbi.0020081
pmid:16863395
pmcid:PMC1523295
fatcat:zimvmtzt3bduzghvx2eprndezy
Computational Approaches and Challenges to Developing Universal Influenza Vaccines
2019
Vaccines
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Understanding the potential of computational vaccine design is necessary before these approaches can be implemented on a broad scale. ...
We propose that with the development of novel technologies that allow the integration of data sources such as protein structural modeling, host antibody repertoire analysis and advanced phylodynamic modeling ...
We also acknowledge the three anonymous reviewers' valuable comments to improve this review.
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/vaccines7020045
pmid:31141933
pmcid:PMC6631137
fatcat:difxw2yy4vdxrg257jytohqfeq
Advances in the development of human protein microarrays
2017
Espert Review of Proteomics
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Areas covered: This review provides an overview of the technological basis, applications and limitations of some of the most commonly used full-length, recombinant protein and protein fragment microarray ...
platforms, including ProtoArray Human Protein Microarrays, HuProt Human Proteome Microarrays, Human Protein Atlas Protein Fragment Arrays, Nucleic Acid Programmable Arrays and Immunome Protein Arrays. ...
Other approaches therefore aim to achieve controlled, oriented immobilization of different recombinant proteins onto the surface via a common affinity tag [2, 12, 14, 17, 20, 21] , which has theoretical ...
doi:10.1080/14789450.2017.1347042
pmid:28644690
fatcat:4a6ddus4ijbnzalvg6yay6lmce
Immunomics in Pediatric Rheumatic Diseases
2019
Frontiers in Medicine
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The inherent complexity in the immune landscape of pediatric rheumatic disease necessitates a holistic system approach. ...
The development and progression of immunomics are well suited to deal with this complexity. ...
One particular study on KD patients, examined the entire white blood population with the Illumina M450K beadchip, in an attempt to identify patterns of DNA methylation of all 10 human toll-like receptors ...
doi:10.3389/fmed.2019.00111
pmid:31231652
pmcid:PMC6558393
fatcat:neoj5zpez5fgtny3saqi76woxy
Designing the Next Generation of Vaccines for Global Public Health
2011
Omics
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Our first project based on omics was initiated in 2000 and was termed reverse vaccinology. At that time, antigen identification was mainly based on bioinformatic analysis of a singular genome. ...
the more traditional licensed vaccines; and finally, (4) the great promise for innovative vaccine design and research with convergence of omics sciences, such as genomics, proteomics, immunomics, and ...
OMICS-DERIVED VACCINES 559 Author Disclosure Statement The authors declare that no conflicting financial interests exist. ...
doi:10.1089/omi.2010.0127
pmid:21682594
fatcat:kelvo65henhtzdrxokql7u5wmq
Vaccinology in the genome era
2009
Journal of Clinical Investigation
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in terms of controlling human pathogens. ...
However, as we discuss in this Review, the arrival of the genome era has revolutionized vaccine development and catalyzed a shift from conventional culture-based approaches to genome-based vaccinology. ...
A limitation of the immunomic approaches is that differentially expressed proteins, such as those dependent on pathogen-host interaction, will not be detected. ...
doi:10.1172/jci38330
pmid:19729849
pmcid:PMC2735939
fatcat:a34ucy22i5dfxabiuyfxed24me
Exploring the Papillomaviral Proteome to Identify Potential Candidates for a Chimeric Vaccine against Cervix Papilloma Using Immunomics and Computational Structural Vaccinology
2019
Viruses
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HPV type-restriction, non-targeted delivery, and the highcost of existing vaccines necessitate continuing research on the HPV vaccine. ...
The human papillomavirus (HPV) 58 is considered to be the second most predominant genotype in cervical cancer incidents in China. ...
Conflicts of Interest: The authors declare no conflict of interest. ...
doi:10.3390/v11010063
pmid:30650527
pmcid:PMC6357041
fatcat:jzhrhb2u7rf4rixnj3kftrwn6a
Cellular immunity and immunotherapy of brain tumors
2004
Frontiers in Bioscience
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A definitive association between the expression of these HSP by CNS tumors and an immune response has not been established, but could theoretically provide an efficient therapeutic target when pulsed with ...
New serotherapy approaches (i.e., antibodybased adoptive immunotherapy) for brain tumors, which Immunomics in Neuro-Oncology. ...
doi:10.2741/1465
pmid:15353342
fatcat:qavbf46nhnhkzfg2y4vbfu56vq
The Fourth International Neonatal and Maternal Immunization Symposium (INMIS 2017): Toward Integrating Maternal and Infant Immunization Programs
2018
mSphere
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Symposium, where presentations focused on the state-of-the-art research on the development and implementation of vaccines given during pregnancy for the protection of mothers and infants. ...
care and pediatric programs for reduction of maternal and infant mortality worldwide.IMPORTANCE This report provides an overview of the proceedings of the 4th International Maternal and Neonatal Immunization ...
The Human Immunome Project (http://www.humanvaccinesproject.org/work/ human-immunome-program/) aims to determine the sequence of every human Ab and T cell receptor. ...
doi:10.1128/msphere.00221-18
pmid:30404933
pmcid:PMC6222055
fatcat:7vdr7s2jlrftxmotnbccn45xqu
Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone
2003
Journal of Biomedicine and Biotechnology
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Finally, we review relevant methods to the prediction of immunome, with special emphasis on quantitative methods, and the subcellular localization of proteins within bacteria. ...
In this disquisition, we evaluate proteomic approaches to the discovery of subunit vaccines, focussing on viral, bacterial, fungal, and parasite systems. ...
Preceding sections have addressed two approaches to the identification of the immunome: experimental proteomic analysis of microbial proteins and mechanistic informatic prediction. ...
doi:10.1155/s1110724303209232
pmid:14688414
pmcid:PMC521502
fatcat:yosbr6vxinhqfn6mywqmbkamea
Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design
2021
Briefings in Bioinformatics
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Immunoinformatics has emerged in the recent decades as a field capable of offering this approach by bridging experimental and theoretical immunology with state-of-the-art computational tools. ...
With the onset of the COVID-19 pandemic, the amount of data on genomic and proteomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stored in various databases has exponentially ...
The support and resources from the Center for High Performance Computing at Shahid Beheshti University of Iran are gratefully acknowledged. The authors appreciate Dr. ...
doi:10.1093/bib/bbab241
pmid:34219142
fatcat:qkrlrtrnt5c6dndo3uv5lkyhae
The Vertebrate Genome Annotation browser 10 years on
2013
Nucleic Acids Research
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ACKNOWLEDGEMENTS We thank the HAVANA team for providing annotation of the reference genomes, and also the immune response annotation group (IRAG) that provided community annotation for the pig immunome ...
Finally, we are grateful for the funding provided for this work by the National Institutes of Health, the Wellcome Trust and the BBSRC. ...
The next challenge for genomic browsers is therefore to condense such information into an informative display, allowing users to interpret what is happening to the expression of their transcript of interest ...
doi:10.1093/nar/gkt1241
pmid:24316575
pmcid:PMC3964964
fatcat:2ut4jvn3kffxzkqnd3ppj7sd2a
Fishing for vaccines against Vibrio cholerae using in silico pan-proteomic reverse vaccinology approach
2019
PeerJ
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N16961) proteome was computationally screened in a sequential prioritization approach that focused on determining the antigenicity of potential vaccine candidates. ...
Cholera, an acute enteric infection, is a serious health challenge in both the underdeveloped and the developing world. ...
COGs analysis was conducted on the basis of protein sequence similarity and conserved domains in comparison to reported proteins in the database. ...
doi:10.7717/peerj.6223
pmid:31249730
pmcid:PMC6589079
fatcat:rf4ukfk5ofchpg5d3ze46nnuvi
Antibody repertoire profiling with mimotope arrays
2016
Human Vaccines & Immunotherapeutics
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Here, the advantages and disadvantages of the major profiling techniques as well as their current and future application in disease prediction and vaccination are discussed. ...
These methods can be combined in a pipeline, which ultimately maps the antibody reactivities onto defined arrays of structures -peptides or carbohydrates. ...
a theoretical abstraction based on the concept of specificity. ...
doi:10.1080/21645515.2017.1264786
pmid:27929733
pmcid:PMC5328411
fatcat:q6dlik65nvesvjsxd7v74qlg2e
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