The Pathogen-Host Interaction Data Integration and Analysis System (PHIDIAS) is a web-based database and analysis system that integrates and analyzes genomic sequences, curated literature information, and gene expression data related to pathogen-host interactions (or called host-pathogen interactions) for those pathogens important in public health.
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University of Michigan
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Yongqun He
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PHIDIAS: Pathogen-Host Interaction Data Integration and Analysis System | phidias.us Reviews
https://phidias.us
The Pathogen-Host Interaction Data Integration and Analysis System (PHIDIAS) is a web-based database and analysis system that integrates and analyzes genomic sequences, curated literature information, and gene expression data related to pathogen-host interactions (or called host-pathogen interactions) for those pathogens important in public health.
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PHIDIAS: Pathogen-Host Interaction Data Integration and Analysis System
http://www.phidias.us/docs/docs.php
Publications of PHIDIAS and PHIDIAS programs:. Lin Y, Xiang Z, He Y. Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology. Journal of Biomedical Semantics. 2011 Oct 31;2(1):9. [Epub ahead of print] PMID: 22041276. Zuoshuang Xiang, Yuying Tian, Yongqun He. PHIDIAS: a pathogen-host interaction data integration and analysis system. 2007 Jul 30;8(7):R150. PMID: 17663773. Zuoshuang Xiang, Wenjie Zheng and Yongqun He. BBP:. Genome annotation with literature mining and curation.
PHIDIAS: Pathogen-Host Interaction Data Integration and Analysis System
http://www.phidias.us/links.php
Here we collect a list of related web links:. PATRIC Specialty Genes: http:/ patricbrc.org/portal/portal/patric/SpecialtyGenes. GBrowse: http:/ www.gmod.org/GBrowse. NCBI Protein RefSeq: http:/ www.ncbi.nlm.nih.gov/RefSeq/. NCBI BLAST download: http:/ www.ncbi.nlm.nih.gov/BLAST/download.shtml. NCBI CDD: http:/ www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. PubMed: http:/ www.pubmed.org. NCBI GEO: http:/ www.ncbi.nlm.nih.gov/geo/. ArrayExpress: http:/ www.ebi.ac.uk/arrayexpress/.
PHIDIAS: Pathogen-Host Interaction Data Integration and Analysis System
http://www.phidias.us/faqs.php
1 What is PHIDIAS? PHIDIAS is the Pathogen-Host Interaction Data integration and Analysis System. 2 Who are primary PHIDIAS users? PHI researchers and bioinformaticians. 3 What are the pathogen and host targets? PHIDIAS is focused on studying NIAID/CDC priority category A, B, and C pathogens, and other priority pathogens with regard to public health. The host targets are mainly human and mouse. 4 What are the relationships among different PHIDIAS components? 5 Can I submit data to PHIDIAS?
PHIDIAS: Pathogen-Host Interaction Data Integration and Analysis System
http://www.phidias.us/stat.php
See the Victors virulence factors statistics on the page Victors Statistics. 36 pathogens, including 2894 references (1384 journal articles,136 book references,1370 websites and 4 theses). PHI networks of 21 pathogens. Thousands of genes important of PHI. The Pacodom module stores 7938 position-specific scoring matrices ( PSSM. Found from 153166 protein sequences. 562990 gene sequences, 527324 protein sequences, and 7938 PSSMs. Pathogen Genomes in PHIDIAS.
PHIDIAS: Pathogen-Host Interaction Data Integration and Analysis System
http://www.phidias.us/blast/index.php
Pathogen specific BLAST Searches. PHIDIAS provides 5 customed, pathogen specific BLAST searches:. Include blastn, blastp, blastx, tblastn, tblastx. Find the target sequences using given forward and reverse primer sequences. Pattern Hit Initiated (PHI) BLAST: Identify proteins that preserve a specified pattern contained within your query. Query includes a protein sequence and a regular expression defining the pattern of interest. Reversed Position Specific (RPS) BLAST: compare a sequence to a collection o...
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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.
Welcome to He Group Webpage
http://www.hegroup.org/index.php
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 ...
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.
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...
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...
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PHIDIAS: Pathogen-Host Interaction Data Integration and Analysis System
PHIDIAS is a web-based database and analysis system that aims to manually curate, computationally analyze, and address different scientific issues in the areas of pathogen-host interactions (PHI, or called host-pathogen interactions or HPI). PHIDIAS has emphasized the study of those pathogens that cause various infectious diseases in humans and animals. Some key features about PHIDIAS:. PHIDIAS was initially generated by expanding our internally developed. Bioinformatics Portal ( BBP. To represent Brucel...
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