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James C. Hu

Hu, James C.
James C. Hu
BioBio / Room 443A
Undergraduate Education
B.S. Stanford University (1975)
Graduate Education
Ph.D. University of Wisconson (1987)

Microbial Genomics and Annotation

The value of society’s investment in science is strongly dependent on the ability of future scientists to build on the results of previous results. As the pace of scientific productivity has accelerated through genomics and other Big Data technologies, the ability of scientist to master the literature is increasingly dependent on computational tools. One important aspect of making data more reusable is the association of data with annotations that can be used in computer-based data mining and analyses.

My group works on the development and use of biological ontologies, which are sets of standardized controlled vocabularies for annotation. Our current focus is on the Ontology for Microbial Phenotypes, which is being constructed to facilitate the reuse and analysis of data from the awesome power of microbial genetics. We also work with the Gene Ontology Consortium on the annotation of gene functions, an have developed systems for integrating annotation with education in the Community Assessment of Community Annotation with Ontologies (CACAO)

We have also worked on developing systems for building model organism databases for community annotation, including EcoliWiki, which reuses and modifies the open source software built for Wikipedia to provide more specialized scientific data resources.

Recent Publications

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  1. Siegele, DA, LaBonte, SA, Wu, PI, Chibucos, MC, Nandendla, S, Giglio, MG et al.. Phenotype annotation with the ontology of microbial phenotypes (OMP). J Biomed Semantics. 2019;10 (1):13.
    doi: 10.1186/s13326-019-0205-5. PubMed PMID:31307550. PubMed Central PMC6631659.

  2. Xia, J, Chiu, LY, Nehring, RB, Bravo Núñez, MA, Mei, Q, Perez, M et al.. Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage. Cell. 2019;176 (1-2):127-143.e24.
    doi: 10.1016/j.cell.2018.12.008. PubMed PMID:30633903. PubMed Central PMC6344048.

  3. Giglio, M, Tauber, R, Nadendla, S, Munro, J, Olley, D, Ball, S et al.. ECO, the Evidence & Conclusion Ontology: community standard for evidence information. Nucleic Acids Res. 2019;47 (D1):D1186-D1194.
    doi: 10.1093/nar/gky1036. PubMed PMID:30407590. PubMed Central PMC6323956.

  4. Chibucos, MC, Siegele, DA, Hu, JC, Giglio, M. The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. Methods Mol. Biol. 2017;1446 :245-259.
    doi: 10.1007/978-1-4939-3743-1_18. PubMed PMID:27812948. PubMed Central PMC6377151.

  5. Gaudet, P, Škunca, N, Hu, JC, Dessimoz, C. Primer on the Gene Ontology. Methods Mol. Biol. 2017;1446 :25-37.
    doi: 10.1007/978-1-4939-3743-1_3. PubMed PMID:27812933. PubMed Central PMC6377150.

  6. Nehring, RB, Gu, F, Lin, HY, Gibson, JL, Blythe, MJ, Wilson, R et al.. An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli. Nucleic Acids Res. 2016;44 (5):e41.
    doi: 10.1093/nar/gkv1131. PubMed PMID:26578563. PubMed Central PMC4797258.

  7. Chibucos, MC, Zweifel, AE, Herrera, JC, Meza, W, Eslamfam, S, Uetz, P et al.. An ontology for microbial phenotypes. BMC Microbiol. 2014;14 :294.
    doi: 10.1186/s12866-014-0294-3. PubMed PMID:25433798. PubMed Central PMC4287307.

  8. Hu, JC, Sherlock, G, Siegele, DA, Aleksander, SA, Ball, CA, Demeter, J et al.. PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res. 2014;42 (Database issue):D677-84.
    doi: 10.1093/nar/gkt1203. PubMed PMID:24285306. PubMed Central PMC3965092.

  9. Brister, JR, Le Mercier, P, Hu, JC. Microbial virus genome annotation-mustering the troops to fight the sequence onslaught. Virology. 2012;434 (2):175-80.
    doi: 10.1016/j.virol.2012.09.027. PubMed PMID:23084289. PubMed Central PMC3518702.

  10. Renfro, DP, McIntosh, BK, Venkatraman, A, Siegele, DA, Hu, JC. GONUTS: the Gene Ontology Normal Usage Tracking System. Nucleic Acids Res. 2012;40 (Database issue):D1262-9.
    doi: 10.1093/nar/gkr907. PubMed PMID:22110029. PubMed Central PMC3245169.

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