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Welcome to He Group Webpage

Welcome to hegroup.org! Welcome to the home page of Dr. Yongqun Oliver He. S laboratory research group at the University of Michigan! We do both dry-lab (bioinformatics lab) and wet-lab (microbiology and immunology lab) biomedical research. Our primary bioinformatics research has many topics: (1) Ontology development. Dr He has initiated and led the development of several community-based ontologies, including Vaccine Ontology. VO), Ontology of Adverse Events. OAE), Ontology of Genes and Genomes. Vaccine ...

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CONTACTS AT HEGROUP.ORG

YONGQUN HE

YONGQUN HE

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YONGQUN HE

YONGQUN HE

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Welcome to He Group Webpage | hegroup.org Reviews
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Welcome to hegroup.org! Welcome to the home page of Dr. Yongqun Oliver He. S laboratory research group at the University of Michigan! We do both dry-lab (bioinformatics lab) and wet-lab (microbiology and immunology lab) biomedical research. Our primary bioinformatics research has many topics: (1) Ontology development. Dr He has initiated and led the development of several community-based ontologies, including Vaccine Ontology. VO), Ontology of Adverse Events. OAE), Ontology of Genes and Genomes. Vaccine ...
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2 projects
3 publications
4 faqs
5 links
6 news
7 such as ontofox
8 and ontobee
9 brucella
10 pathogenesis and immunity
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people,projects,publications,faqs,links,news,such as ontofox,and ontobee,brucella,pathogenesis and immunity,strains,b abortus,b suis,he lab,ontobee,ontofox,genomesh,ignet,minituba,phidias,violin,he group,niaid
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Welcome to He Group Webpage | hegroup.org Reviews

https://hegroup.org

Welcome to hegroup.org! Welcome to the home page of Dr. Yongqun Oliver He. S laboratory research group at the University of Michigan! We do both dry-lab (bioinformatics lab) and wet-lab (microbiology and immunology lab) biomedical research. Our primary bioinformatics research has many topics: (1) Ontology development. Dr He has initiated and led the development of several community-based ontologies, including Vaccine Ontology. VO), Ontology of Adverse Events. OAE), Ontology of Genes and Genomes. Vaccine ...

SUBDOMAINS

ontofox.hegroup.org ontofox.hegroup.org

Ontofox

Is a web-based Onto. Logy tool that f. Ntology terms and a x. Ioms Ontofox supports ontology reuse. It allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from source ontologies and save the results using the RDF/XML serialization of the OWL. Ontofox follows and expands the MIREOT. We have now changed the name OntoFox (with capital F) to Ontofox (with low case f) to be consistent with other Ontoanimal tools. 1 Data input using web forms:. Beta Cell Ge...

ignet.hegroup.org ignet.hegroup.org

Ignet

The Ignet (Integrated gene network) project is a centrality- and ontology-based liteature discovery system for analyzing and visualizing biological gene interaction networks using all PubMed literature papers. Currently Ignet focuses on the literature mining of human gene interaction networks. Hur et al, 2012. Then such a CONDL strategy was proposed. Later we used the same CONDL strategy to study the fever and vaccine specific human gene interaction networks (Reference: Hur et al, 2012. Ozgur A, Xiang Z,...

crcview.hegroup.org crcview.hegroup.org

CRCView

CRCView is a web-based microarray data analysis and visualization system. CRCView is powered by CRC. Or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor. 1) CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology ( GO. 2007 Jul 15;23(14):1843-5. To check all the chan...

INTERNAL PAGES

hegroup.org hegroup.org
1

He Group OntoDen

http://www.hegroup.org/ontoden/index.php

Biomedical ontology development and applications form a major research focus in Dr. Oliver He. S group. OntoDen is the web page that summarizes and integrates our ontology research activities. Onto-animal ontology software programs. Development of biomedical ontologies. Tutorial: check out ontology code using SVN: Go to: the section of SVN tutorial on this page. Or directly to the SVN tutorial page. Tutorial: check out ontology code using Git: Go to: the section of Git tutorial on this page. A web-based ...

2

He Group: FAQs

http://www.hegroup.org/faqs.php

1 Who is He Group? He Group is the research group in Dr. Yongqun Oliver He's laboratory located in the University of Michigan Medical School. He Group includes integrated wet-lab group and bioinformatics group. Our primary research interests are pathogen-host interactions ( PHI. And vaccine research and development (R&D). Please look our Projects. 2 What software programs developed in He Group can be used to study infectious diseases? Genomics data integration and literature annotation, and study of.

3

The OneNet Theory of Life

http://www.hegroup.org/onenettheory.html

The OneNet Theory of Life. The author first proposed the One Network (abbreviated as OneNet) Theory of Life (for one organism) in a peer-reviewed article published in the journal. Expert Reviews in Vaccines. In June 2014 ( He, 2014. And the author further extended the theory in another article in. In 2016 ( He, 2016. The OneNet theory theory is targeted to explain and seek the deep mechanisms of various phenotypes and phenomena of the life of an organism (for example, a single cell bacterium like. An org...

4

Yongqun He

http://www.hegroup.org/aboutUs/Oliver.html

Yongqun Oliver He, D.V.M., Ph.D. Unit for Laboratory Animal Medicine. Department of Microbiology and immunology. Center for Comput. Med. and Bioinformatics. Ann Arbor, Michigan, USA. BS in Veterinary Med. (equivalent to DVM in US), Jiangxi Agricultural Univ. Nanchang, China. 1986-1991. Assistant Veterinarian (licensed), Beijing Xijiao Livestock and Poultry Company, Beijing, China. 1991-1993. MS, Infect. Dis. and Veterinary Preventive Med., China Agricultural University. Beijing, China. 1993-1996. Dr He's...

5

He Group Web Links

http://www.hegroup.org/links.html

Links to Dr. He's pages:. In the Unit for Laboratory Animal Medicine (ULAM). In the Department of Microbiology and Immunology. Dr He Research Laboratory. University of Michigan Links:. University of Michigan Medical School. Unit for Laboratory Animal Medicine (ULAM). Department of Microbiology and Immunology. Center for Computational Biology and Medicine. Including UM Taubman Library. Http:/ www.ucsf.edu/news/2014/02/111956/science-policy-team-wins-national-video-content. Ann Arbor, MI 48109.

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ontobee.org ontobee.org

Ontobee

http://www.ontobee.org/ontobeep/index.php

Ontobeep is an ontology alignment and comparison program that aligns, compares, and displays the similarities and differences among selected ontologies available in Ontobee. Ontobeep also provides a Statistics page to summarize the findings out of the ontology alignment and comparison. See more information in Ontobeep Tutorial. Please select two to three ontologies:. Anatomical Entity Ontology (AEO). Adverse Event Reporting Ontology (AERO). Ascomycete phenotype ontology (APO). Basic Formal Ontology (BFO).

asfv.org asfv.org

Panasfv

http://www.asfv.org/structure/index.php

Genome-wide Structure Prediction and Function Annotation of African Swine Fever Virus (ASFV). NOTE: Sorry: the data is currently not available. University of Michigan Medical School. Ann Arbor, MI 48109.

asfv.org asfv.org

Panasfv

http://www.asfv.org/faqs.php

Why the Panasfv query does not work? The Panasfv query function is down due to a maintenance issue. 2 What is Panasfv? Panasfv is a program targeted for systematic analysis of ASFV genomes. University of Michigan Medical School. Ann Arbor, MI 48109.

asfv.org asfv.org

Panasfv

http://www.asfv.org/index.php

Panasfv is a program that generates a master genome annotation covering all genomes for ASFV. Sorry that this query program is currently down. Select an ASFV strain. African swine fever virus BA71V. African swine fever virus Benin 97/1. African swine fever virus E75. African swine fever virus Georgia 2007/1. African swine fever virus KN. African swine fever virus MAL. African swine fever virus MK. African swine fever virus OURT 88/3 (avirulent field isolate). African swine fever virus PR4.

asfv.org asfv.org

Panasfv

http://www.asfv.org/stats.php

NOTE: Sorry: the statistics data is currently not available. University of Michigan Medical School. Ann Arbor, MI 48109.

clo-ontology.org clo-ontology.org

CLO

http://www.clo-ontology.org/links.php

Ontologies in OBO Foundry: http:/ www.obofoundry.org. OBI: Ontology for Biomedical Investigations: http:/ obi-ontology.org. Protege ontology editor: http:/ protege.stanford.edu/. NCBO BioPortal: http:/ bioportal.bioontology.org/. University of Michigan Medical School. Ann Arbor, MI 48109.

clo-ontology.org clo-ontology.org

CLO

http://www.clo-ontology.org/index.php

The Cell Line Ontology (CLO) is a community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. The CLO development has becoming a community effort with international collaborations. Our development consortium includes experts from all over the world: the USA, Europe, and Japan. Journal of Biomedical Semantics. 37 doi:10.1186/2041-1480-5-37. PMID: 25852852. University of Michigan Medical School. Ann Arbor, MI 48109.

ontobee.org ontobee.org

Ontobee

http://www.ontobee.org/index.php

Server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences. And presents individual ontology term URIs to (i). For user-friendly web browsing and navigation, and to (ii). Applications. Ontobee is the default linked data server for most OBO Foundry library ontologies. Ontobee has also been used for many non-OBO ontologies. Please select an ontology (optional). Anatomical Entity Ontology (AEO).

ontobee.org ontobee.org

Ontobee: AEO

http://www.ontobee.org/browser/index.php?o=AEO

Http:/ purl.obolibrary.org/obo/aeo.owl. Http:/ purl.obolibrary.org/obo/aeo.owl. AEO is an ontology of anatomical structures that expands CARO, the Common Anatomy Reference Ontology. This version corrects the namespace and includes some flybase alt IDs. Http:/ purl.obolibrary.org/obo/aeo/releases/2014-12-05/aeo.owl. OBO-Edit 2.1.1-beta7. Has obo format version:. Number of Terms ( including imported terms. Number of SPARQL queries:8. University of Michigan Medical School. Ann Arbor, MI 48109.

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Welcome to He Group Webpage

Welcome to hegroup.org! Welcome to the home page of Dr. Yongqun Oliver He. S laboratory research group at the University of Michigan! We do both dry-lab (bioinformatics lab) and wet-lab (microbiology and immunology lab) biomedical research. Our primary bioinformatics research has many topics: (1) Ontology development. Dr He has initiated and led the development of several community-based ontologies, including Vaccine Ontology. VO), Ontology of Adverse Events. OAE), Ontology of Genes and Genomes. Vaccine ...

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