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VIOLIN News

  • 3/19/2014: The full content of the supplement "ICoVax 2013" were released at http://www.biomedcentral.com/bmcbioinformatics/supplements/15/S4.
  • 1/2014: VIOLIN update paper was published in NAR. PMID: 24259431.
  • 10/26/2013: “The 3rd ISV Pre-conference Computational Vaccinology Workshop” (ICoVax 2013: http://www.violinet.org/icovax2013/). ICoVax 2013 was a satellite workshop of the 7th Vaccine & ISV Annual Global Congress (http://www.vaccinecongress.com/). ICoVax 2012 was held on Oct 26, 2013, at Barcelona, Spain. Oliver is a co-organizer and co-chair of the conference.
  • 7/29-31/2013: Oliver presented a talk on the Vaccines-2013, with the talk title "Applications of the Vaccine Ontology (VO) in vaccine data integration and computer-assisted automated reasoning".
  • 7/7/2013: The workshop “Vaccine and Drug Ontology Studies (VDOS-2013)”, International Conference on Biomedical Ontologies (ICBO), Montreal, Qc, Canada, July 7, 2013. URL: http://informatics.mayo.edu/CNTRO/index.php/Events/VDOS_2013. Oliver was a co-organizer and co-chair of the conference. This workshop occurred before the ICBO-2013. Oliver and Asiyah each presented an oral presentaiton.
  • 3/13/2013: Oliver presented a talk at FDA with the title "The Ontology of Adverse Events". This visit was invited and organized by Drs. Darrell Abernethy and Jane Bai at the FDA Office of Clinical Pharmacology (OCP).
  • 2/11-12/2013: Oliver will attend the CTSA Ontology Workshop in Orlando, FL. He will present the Vaccine Ontology (VO) in the workshop.
  • 12/20/2012: A thematic series titled Vaccine and drug ontology in the study of mechanism and effect (VDOSME) was published in the Journal of Biomedical Semantics (JBMS). The thematic series was co-organized by Oliver. VO-related papers were presented. Also, check a related BioMed Central blog.
  • 10/24/2012: Allen and Oliver's algorithm for predicting eluted protein epitopes was announced by Vladmir Brusic as one of the winners in the 2nd Machine Learning Competition in Immunology 2012.
  • 10/16/2012:Oliver presented an oral presentation in the general Vaccine & ISV Annual Global Congress. His presentation title is: Systematic annotation and analysis of "virmugens" - virulence factors whose mutants can be used as live attenuated vaccines.
  • 10/13/2012: Oliver co-organized the 2nd ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2012), a satellite workshop of the general Vaccine & ISV Annual Global Congress. Oliver also presented an oral presentation. Allen also attended the workshop and presented Vaxign software demo.
  • 7/21/2012: Oliver co-organized an ICBO 2012 workshop entitled "Vaccine and Drug Ontology in the Study of Mechanism and Effect" (VDOSME 2012), in the Medical University of Graz, Austria. Oliver presented two talks in the workshop as well. Here is the workshop final program.
  • 5/2/2012: Oliver presented a Webinar presentation in NCBO Webinar Series. His presentation title is: "Vaccine Ontology (VO) and its application in literature mining of vaccine-gene interaction networks".
  • 1/6/2012: Oliver and Allen attended the "African Swine Fever Reverse Vaccinology Project" kickoff meeting in the National Center for Foreign Animal and Zoonotic Disease Defense (FAZD) in Texas. In this meeting, Allen presented our Vaxign vaccine candidate prediction program, and Oliver introduced the prediction results using the Vaxign reverse vaccinology tool.
  • 10/17-19/2011: Oliver attended the 5th Annual Vaccine Renaissance Conference (Vax-Ren-5) at Providence, RI, USA. He presented a talk "Genome-wide vaccine target prediction based on Vaxign reverse vaccinology".
  • 10/2-4/2011: Oliver and Allen presented two posters in the 5th Vaccine and ISV Annual Global Congress in Seattle. Oliver's poster title is "VIOLIN: an integrative vaccine research database and analysis system". Allen's poster title is: "Bioinformatics analysis of protective antigens in manually curated Protegen database".
  • 10/1/2011: Oliver presented a talk "Genome-wide vaccine target prediction using Vaxign reverse vaccinology" in the 1st Computational Vaccinology workshop prior to the 5th Vaccine and ISV Annual Global Congress. Oliver and Allen has also organized a 1.5-hour Vaxign hands-on exercise.
  • 6/20/2011: A comprehensive 26-page review article titled "Emerging Vaccine Informatics" in the Journal of Biomedicine and Biotechnology 2010 special issue on vaccine informatics was published. Oliver is a co-author of this article. This review also introduces VIOLIN and VO.
  • 4/23-25/2011: Oliver attended the BIT 3rd World Vaccine Congress. He gave a talk on Vaxign vaccine design and co-chaired the section "Section 2-2-1: Bioinformatics, Antigen Design, and Vaccine Development".
  • 12/8-9/2010: Oliver, Allen, and Asiyah (Yu Lin) attended the IDO Workshop 2010. Asiyah presented Brucellosis Ontology, Allen presented OntoBee, and Oliver updated the development of Vaccine Ontology (VO).
  • 9/28/2010: A new paper about the application of VIOLIN in analysis/prediction of Brucella vaccines and vaccine targets was published. The PubMed ID is: 20875156.
  • 9/26-28/2010: Oliver He attended InCoB2010 in Tokyo, Japan. He presented a talk on how to use VIOLIN to analyze and predict Brucella vaccines and vaccine targets.
  • 7/9-13/2010: Oliver and Sira attended the Bio-Ontologies 2010 meeting, which is an ISMB SIG meeting. Arzucan Ozgur and Junguk Hur also presented research out of the collaborations between them and He Lab. In total, two oral presentations and two poster presentations were given by He Lab in the conference.
  • 3/22-25/2010: Allen Xiang attended the OBI Spring 2010 Workshop at Vancouver, Canada. He presented a use case on vaccine protection investigation using ontology (OBI and VO)-based ANOVA analysis of literature mined data.
  • 11/10-12/2009: Dr. Oliver He and Allen Xiang attended the “UTMB Sealy Center for Vaccine Development Symposium” in Galveston, Texas. Dr. He presented a talk in how to use VIOLIN and VO to analyze Brucella vaccines (http://www.utmb.edu/scvd/2009Symposium.pdf).
  • 9/21/2009: An Notice of Award (NoA) was issued by NIH-NIAID to officially award Oliver He (PI) and his team and collaborators an R01 grant with the title: "Ontology-based Information Network to Support Vaccine Research" (Grant Number: R01AI081062). This is a four-year grant with an aim to develop VO and apply it for ontology-based literature mining and analysis of vaccine-induced protective immune networks.
  • 7/24-26/2009: Oliver and two lab members (Allen and Sira) attended the 1st International Conference on Biomedical Ontology (ICBO) conference in Buffalo, NY. Two posters and one software demo were presented, all related to Vaccine Ontology (VO) development and application. One poster is introduction of VO, the other is on using VO for literature mining. The software demo is about OntoFox, which a side project derived from the VO development. OntoFox is used for VO development. More details can be seen in the I CBO proceedings.
  • 5/17-21/2009: Oliver attended the 109th ASM General Meeting in Philadelphia, PA. He presented a poster titled "Development of a Community-based Vaccine Ontology".
  • 2/2-6/2009: Oliver attended the OBI 2009 Vancouver Workshop. Oliver discussed with the OBI development team on how to improving VO with the help from OBI and how to update OBI using vaccine-related terms and term relationships. Oliver presented a talk to discuss the relationships between VO and OBI. Oliver has also joined the OBI Consortium and represents the vaccine community in the OBI development.
  • 12/07-09/2008: Dr. Oliver He presented an oral presentation in the 2nd Vaccine Congress organized by the International Society for Vaccines (ISV) and the journal Vaccine. His presentation title is: "Vaxign: a web-based vaccine target design program for reverse vaccinology". In his talk, Oliver focused on introducing the first web-based vaccine design system based on the reverse vaccinology concept originally pioneered by Dr. Rino Rappuoli. Oliver received very positive feedback and encouragements from the vaccine community, including Dr. Rappuoli, the founder of this novel approach for vaccine development. After Dr. He's talk, many groups contacted him for instructions and possible collaborations.
  • 09/16-17/2008: Oliver He attended the Infectious Disease Ontology (IDO) 2008 workshop. In the workshop Oliver presented a talk on the progress of the Vaccine Ontology.
  • Aug 14, 2008: Dr. Oliver He gave a speaker presentation in the Cambridge Healthtech Institute (CHI) conference "Novel Vaccines: Bridging Research, Development & Production". His presentation title is "An Ontology-based Information Network to Support Vaccine Research".
  • July 19, 2008: We presented the VIOLIN and Vaccine Ontology project in ISMB2008 and here is a PDF version.
  • April 12-13, 2008: Both Dr. Oliver He and Zuoshuang (Allen) Xiang attended the training course by Dr. Barry Smith: "An Introduction to Biomedical Ontology" in Buffalo, NY, USA. Dr. Smith introduced ontology with special reference to applications in biomedical research, including Vaccine Ontology.
  • March 19, 2008: Dr. Oliver He was awarded to give a speaker presentation in August 2008 in the Cambridge Healthtech Institute (CHI) conference "Novel Vaccines: Bridging Research, Development & Production", which is part of the Immunotherapeutics& Vaccine Summit--ImVacS. His presentation title is "An Ontology-based Information Network to Support Vaccine Research".
  • Jan 10, 2008: VIOLIN Wiki was created. The collaborative effort of Vaccine Ontology development was described in the Wiki site.
  • Nov 19, 2007: The VIOLIN manuscript was published in the Nucleic Acid Research Database issue as an Epub version (PMID: 18025042).
  • Mar 23, 2007: VIOLIN website was online and had its first show.