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Identification of candidate disease genes by integrating Gene Ontologies and protein-interaction networks: case study of primary immunodeficiencies

Csaba Ortutay, Mauno Vihinen
2008 Nucleic Acids Research  
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

Ulisses M. Braga-Neto, Ernesto T. A. Marques
2006 PLoS Computational Biology  
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

Qiu, Duvvuri, Bahl
2019 Vaccines  
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

Jessica G. Duarte, Jonathan M. Blackburn
2017 Espert Review of Proteomics  
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

Shi Huan Tay, Katherine Nay Yaung, Jing Yao Leong, Joo Guan Yeo, Thaschawee Arkachaisri, Salvatore Albani
2019 Frontiers in Medicine  
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

Fabio Bagnoli, Barbara Baudner, Ravi P.N. Mishra, Erika Bartolini, Luigi Fiaschi, Paolo Mariotti, Vincenzo Nardi-Dei, Phil Boucher, Rino Rappuoli
2011 Omics  
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

C. Daniela Rinaudo, John L. Telford, Rino Rappuoli, Kate L. Seib
2009 Journal of Clinical Investigation  
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

Satyavani Kaliamurthi, Gurudeeban Selvaraj, Sathishkumar Chinnasamy, Qiankun Wang, Asma Nangraj, William Cho, Keren Gu, Dong-Qing Wei
2019 Viruses  
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

Robert, M. Prins
2004 Frontiers in Bioscience  
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

Flor M Munoz, Pierre Van Damme, Ener Dinleyici, Ed Clarke, Beate Kampmann, Paul T Heath, Ofer Levy, Elke Leuridan, Clare Cutland, Ajoke Sobanjo-Ter Meulen, Arnaud Marchant
2018 mSphere  
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

Irini A. Doytchinova, Paul Taylor
2003 Journal of Biomedicine and Biotechnology  
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

Shokouh Rezaei, Yahya Sefidbakht, Vuk Uskoković
2021 Briefings in Bioinformatics  
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

Jennifer L. Harrow, Charles A. Steward, Adam Frankish, James G. Gilbert, Jose M. Gonzalez, Jane E. Loveland, Jonathan Mudge, Dan Sheppard, Mark Thomas, Stephen Trevanion, Laurens G. Wilming
2013 Nucleic Acids Research  
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

Muhammad I. Rashid, Sammia Rehman, Amjad Ali, Saadia Andleeb
2019 PeerJ  
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

Shina Pashova, Christoph Schneider, Stephan von Gunten, Anastas Pashov
2016 Human Vaccines & Immunotherapeutics  
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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