Here is a list of selected news from the He Lab over the past years. It is noted that the news website is not regularly updated.
- 12/20/2016: Oliver presented a LINCS Data Science Research (DSR) Webinar presentation titled "Cell Line Ontology-based Standardization, Integration and Analysis of LINCS Cell Lines". Available on YouTube: https://www.youtube.com/watch?v=mKQNUyHDeG8. In this presentation, Oliver presented his research progress in a funded BD2K-LINCS external DSR (eDSR) project with the project title: "Ontology-based Cell Line Standardization, Integration, and LINCS applications".
- 4/23/2016: Rebecca (Becca) Racz graduation ceremony. Oliver was invited to attend the ceremony. Becca officially joined th PharmD club (Congratulations!). Becca will soon join the FDA as an ORISE fellow. Good luck, Becca, with your future career!
- 9/30/2015: Oliver He was invited to the School of Bioinformatics Informatics (SBMI) at University of Texas Health Science Center at Houston (UTHealth) and presented a seminar talk "Ontology development and applications for clinical and biological adverse event data integration and analysis".
- 9/28-30/2015: Oliver He attended the 4th Immunology Summit 2015 at Houston, USA. As a keynote speaker, on 9/28/2015 he presented a talk titled "Rational vaccine design using reverse vaccinology, database data analysis, and literature mining".
- 7/27-30/2015: Oliver He attended the VDOS-2015 workshop and ICBO-2015 conference held at Lisbon, Portugal, on July 27-30. Oliver co-organized the VDOS-2015 workshop and he presented two full length articles as well. In the general ICBO-2015 conference, Oliver presented two posters and two software demostrations. See the details of these articles, posters, and demos, see the Publication page.
- 6/22/2015: Asiyah Yu Lin, who was a postdoctoral fellow in He lab, started her new job at FDA as a ORISE fellow. Congratulations, Asiyah!
- 5/13/2015: Guerlain Ulysse, a previous UROP student in He lab, emailed Oliver He that he got a final offer for the Drug Investigator role at the U.S Food and Drug Administration (FDA). Congratulations, Guerlain!
- April 2015: Rebecca Racz, a UM Pharmacy school student and a research assistant in He lab, was awarded with a Joseph D. Williams Leadership Scholarship. Congratulations, Becca!
- 4/21/2015: Abra Guo, a previous research volunteer in He lab, informed Oliver He that out of several admissions, she decided to attend the M.D. program at the University of Virginia. Congratulations, Abra!
- 3/27/2015: Ms. Denise Bronner, a PhD student in Microbiology and Immunology, defended her PhD thesis on March 27, 2015. Oliver He is her PhD research co-mentor. Congratulations, Denise!
- 10/22/2014: As shown on this web page, Oliver will present a Special Topic Lecture titled "Database Development and Bioinformatics Analysis of Laboratory Animal Responses to Vaccinations" on the 65th AALAS national meeting at San Antonio, Texas, on Oct 22 (Wed), 2014. AALAS represents for the American Association for Laboratory Animal Science, an association of professionals aimed for advancing responsible laboratory animal care and use to benefit people and animals.
- 10/06-10/09/2014: Oliver will attend the International Conference on Biomedical Ontologies (ICBO 2014) conference in Houston, TX. He is also a co-organizer of the Vaccine and Drug Ontology Studies (VDOS 2014) workshop to be held on Oct 7, 2014, prior to the general meeting of the ICBO-2014.
- 09/29-10/01/2014: Oliver He will attend the Immunology Summit - 2014 conference. Oliver is the president of the conference. He will talk in the conference open ceremony, and present a keynote presentation. The final program of the conference is Here.
- 9/9/2014: Oliver He presented a seminar presentation in the Computer Science Department of the Wayne State University. Check Here for detail.
- 08/12/2014: Oliver was invited on 2/5/2014 to speak at the Cambridge Healthtech Institute’s Ninth Annual "Novel Vaccines" conference, as part of the ImVacS (The Immunotherapies and Vaccine Summit), on August 12, 2014, at the Marriott Long Wharf Hotel, Boston, MA. Oliver's presentation talk is: "Databases and in silico Tools for Vaccine Design".
- 6/7/2014: Oliver's Expert Reviews in Vaccines paper (PMID: 24909153) was published. In this paper, Oliver proposed a so-called “One Network (OneNet) Theory of Life”, and proposed ontology-based strategies to study the OneNet interaction network mechanisms of individual organisms including humans.
- 5/23/2014: Dr. Shunzhou Deng arrived at the USA and formally joined the He lab in the University of Michigan as a visiting Scholar since May 27, 2014. Dr. Deng is an associate professor in Jiangxi Agricultural University, Nanchang, Jiangxi, China. He will conduct research in the He lab for one full year.
- 2013-2014: Oliver co-organized the Frontier Microbiology Research Topic "Microbial Modulation of Host Apoptosis and Pyroptosis". All papers are published in the journal Frontiers in Cellular and Infection Microbiology.
- 12/7-8/2013: Oliver attended the 66th International Research Conference (Brucellosis-2013) in Chicago. His presentation talk title was "Caspase-2 mediates a Brucella abortus vaccine strain RB51-induced hybrid cell death having features of apoptosis and pyroptosis". Omar Tibi from He lab also presented an oral presentation titled "Systematic Collection and Meta-analysis of Brucella and Host Gene Expression Data from High Throughput Omics Studies".
- 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.
- 9/27/2013: Oliver presented a talk in Soochow University. His talk title was "Development and applications of biomedical ontologies for data integration, data analysis, and literature mining". His talk was invited by Dr. Bairong Shen (沈百荣), Professor, Director, Center for Systems Biology, Soochow University, China. Dr. Shen was the local organizer of the InCoB2013 conference.
- 9/20-22/2013: Oliver attended the 12th International Conference on Bioinformatics (InCoB2013). He presented a talk on Genomesh (a genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks).
- 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".
- 7/8-9/2013: Oliver presented in the ICBO-2013 a poster titled "HINO: BFO-aligned ontology representation of human molecular interactions and pathways". Based on this project, Oliver later submitted an article to arXive.org.
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).
- 3/8/2013: The supplement “ICoVaX” was published on BMC Bioinformatics. The full content of the supplement can be found at: http://www.biomedcentral.com/bmcbioinformatics/supplements/14/S4 .
- 2/11-12/2013: Oliver He will attend the CTSA Ontology Workshop in Orlando, FL. Oliver will present the Vaccine Ontology (VO) and the Ontology of Adverse Events (OAE) in the workshop. He will also introduce the ontology research in the Univerisity of Michigan.
- 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 and its associated VDOSME workshop were co-organized by Oliver. Oliver and his collaborators also presented talks and papers for the workshop and thematic series. 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.
- 10/12/2012: Invited by Dr. Luonan Chen, Oliver presented a talk in the Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. Oliver's presentation title was: "Analysis of Biological Regulatory Networks using Bayesian Network & Ontology-based Literature Mining Algorithms".
- 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.
- 6/16-19/2012: Oliver from He Group attended the 2012 ASM General Meeting in San Francisco, CA.
- 6/10-13/2012: Oliver and Asiyah from He Group attended a workshop in Buffalo: Immunology Ontologies and Their Applications in Processing Clinical Data.
- 5/30-6/1/2012: Oliver and He lab ontology team hosted a Face-2-Face workshop of the Ontology of Biomedical Investigations (OBI) at Ann Arbor, MI.
- 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. In his talk, Oliver introduced Vaxign reverse vaccinology program and how it has been used for vaccine design.
- 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 the Vaccine Ontology (VO).
- 5/19/2011: The University of Michigan Board of Regents approved Dr. Yongqun "Oliver" He's promotion to an Associate Professor in the Medical School with tenure (effective September 1, 2011).
- 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".
- 4/4/2011: He laboratory published a finding in the journal Infection and Immunity, with an article titled "Proinflammatory Caspase-2-Mediated Macrophage Cell Death Induced by a Rough Attenuated Brucella suis Strain". In this article, we discovered a unique proinflammatory caspase-2-mediated programmed cell death induced by a rough attenuated Brucella suis vaccine candidate strain VTRS1, but inhibited by virulent smooth Brucella strains. This unique cell death differs from apoptosis (which is not proinflammatory). It is also different from classical pyroptosis (which is caspase-1 mediated). In the discussion of this paper, we propose to name this type of cell death a "caspase-2-mediated pyroptosis".
- 12/8-9/2010: Oliver, Allen, and Asiyah (Yu Lin) attended the IDO Workshop 2010. In the workshop, Asiyah presented Brucellosis Ontology, Allen presented OntoBee, and Oliver updated the development of Vaccine Ontology (VO).
- 12/4-5/2010: Xinna, Charlie, Denise, and Oliver attended the annual international Brucellosis meeting in Chicago, USA.,
- 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. Andrew attended the general ISMB 2010 meeting and presented his work on Bayesian network modeling.
- 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: 1R01AI081062-01A1). 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 development and application.
- 5/27/2009: A "Special Issue on Vaccine Informatics" is now open for manuscript submissions
in the Journal of BioMedicine and Biotechnology. Oliver He is the Lead Guest Editor for this special issue. The manuscript due day is October 1, 2009.
- 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 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.
- 12/9/2008: Oliver He presented an oral presentation in the 2nd Vaccine Congress in Boston. His presentation title was "Vaxign: a web-based vaccine target design program for reverse vaccinology".
- 8/12-14/08: Oliver 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".
- 10/17/07: Oliver presented a talk to ~30 UROP undergraduate students in Mason Hall about his lab research. Oliver also discussed with UROP students on bioethical issues.
- 10/10/07: Oliver is accepted as a member of the University of Michigan Comprehensive Cancer Center in the research program of Tumor Immunology & Host Response. Oliver's key research focus is to study programmed cell death (PCD) pathways due to host-pathogen interactions, particularly, macrophage PCD due to the interaction between macrophages and Brucella. The PCD pathway is also critical for cancer research.
- 9/19-21/07: Oliver attended the Workshop on Infectious Disease Ontology at the Cold Spring Harbor Laboratory, and joined a community effort of developing an Infectious disease ontology, led by Drs. Lindsay Cowell and Barry Smith. See more detail on the Infectious Disease Ontology NCBO Wiki.
- 7/14/07: Oliver received his acceptance for attending the Workshop on Infectious Disease Ontology being held at Cold Spring Harbor Laboratory on September 19-21, 2007. Oliver has also been awarded a tuition and travel grant covering full tuition and travel expenses.
- 8/4/06: Alicia finished her summer research internship in the lab.
- 8/1/06: Andrew and Zuoshuang presented their MARIMBA and miniTUBA projects, respectively, in the 5th Great Lakes Bioinformatics Retreat in Grand Rapids, MI.
- 7/18/2006: Thom Todd joined our lab.
- 7/16/2006: A new paper is published in BMC Bioinformatics: BBP: Brucella Genome Annotation with Literature Mining and Curation.
- 7/1/2005: Oliver He officially joined the University of Michigan.
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