overview

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.

selected publications
Academic Articles54
  • Xia, J., Chiu, L., Nehring, R. B., Nunez, M., Mei, Q., Perez, M., ... Rosenberg, S. M. (2019). Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage. CELL. 176(1-2), 127-+.
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  • Giglio, M., Tauber, R., Nadendla, S., Munro, J., Olley, D., Ball, S., ... Chibucos, M. C. (2019). ECO, the Evidence & Conclusion Ontology: community standard for evidence information.. Nucleic acids research. 47(D1), D1186-D1194.
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  • Siegele, D. A., LaBonte, S. A., Wu, P., Chibucos, M. C., Nandendla, S., Giglio, M. G., & Hu, J. C. (2019). Phenotype annotation with the ontology of microbial phenotypes (OMP). JOURNAL OF BIOMEDICAL SEMANTICS. 10(1), 13.
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  • The Gene Ontology Consortium, .. (2019). The Gene Ontology Resource: 20 years and still GOing strong.. Nucleic acids research. 47(D1), D330-D338.
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  • Carbon, S., Dietze, H., Lewis, S. E., Mungall, C. J., Munoz-Torres, M. C., Basu, S., ... Consortium, G. O. (2017). Expansion of the Gene Ontology knowledgebase and resources. Nucleic acids research. 45(D1), D331-D338.
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  • Nehring, R. B., Gu, F., Lin, H., Gibson, J. L., Blythe, M. J., Wilson, R., ... Rosenberg, S. M. (2016). An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli. Nucleic acids research. 44(5), e41-e41.
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  • Blake, J. A., Christie, K. R., Dolan, M. E., Drabkin, H. J., Hill, D. P., Ni, L., ... Consortium, G. O. (2015). Gene Ontology Consortium: going forward. Nucleic acids research. 43(D1), D1049-D1056.
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  • Chibucos, M. C., Zweifel, A. E., Herrera, J. C., Meza, W., Eslamfam, S., Uetz, P., ... Giglio, M. G. (2014). An ontology for microbial phenotypes. BMC MICROBIOLOGY. 14(1), 294.
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  • Hu, J. C., Sherlock, G., Siegele, D. A., Aleksander, S. A., Ball, C. A., Demeter, J., ... Thomas, P. D. (2014). PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic acids research. 42(D1), D677-D684.
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  • Hu, J. C., Sherlock, G., Siegele, D. A., Aleksander, S. A., Altman, T., Ball, C. A., ... Thomas, P. D. (2014). PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools (vol 42, pg D677, 2014). Nucleic acids research. 42(19), 12330-12330.
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  • Blake, J. A., Dolan, M., Drabkin, H., Hill, D. P., Ni, L. i., Sitnikov, D., ... Consortium, G. O. (2013). Gene Ontology Annotations and Resources. Nucleic acids research. 41(D1), D530-D535.
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  • McIntosh, B. K., Renfro, D. P., Knapp, G. S., Lairikyengbam, C. R., Liles, N. M., Niu, L., ... Hu, J. C. (2012). EcoliWiki: a wiki-based community resource for Escherichia coli. Nucleic acids research. 40(D1), D1270-D1277.
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  • Renfro, D. P., McIntosh, B. K., Venkatraman, A., Siegele, D. A., & Hu, J. C. (2012). GONUTS: the Gene Ontology Normal Usage Tracking System. Nucleic acids research. 40(D1), D1262-D1269.
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  • Brister, J. R., Le Mercier, P., & Hu, J. C. (2012). Microbial virus genome annotation-Mustering the troops to fight the sequence onslaught. VIROLOGY. 434(2), 175-180.
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  • Blake, J. A., Dolan, M., Drabkin, H., Hill, D. P., Ni, L., Sitnikov, D., ... Consortium, G. O. (2012). The Gene Ontology: enhancements for 2011. Nucleic acids research. 40(D1), D559-D564.
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  • Knapp, G. S., & Hu, J. C. (2010). Specificity of the E-coli LysR-Type Transcriptional Regulators. PLoS ONE. 5(12), e15189-e15189.
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  • Rajagopala, S. V., Yamamoto, N., Zweifel, A. E., Nakamichi, T., Huang, H., Mendez-Rios, J. D., ... Uetz, P. (2010). The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology. BMC GENOMICS. 11(1), 470-470.
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  • Gaudet, P., Chisholm, R., Berardini, T., Dimmer, E., Engel, S. R., Fey, P., ... Consortium, G. O. (2009). The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species. PLoS Comput Biol. 5(7), e1000431-e1000431.
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  • Knapp, G. S., & Hu, J. C. (2009). The oligomerization of CynR in Escherichia coli. Protein Sci. 18(11), 2307-2315.
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  • Knapp, G. S., Tsai, J. W., & Hu, J. C. (2009). The oligomerization of OxyR in Escherichia coli. Protein Sci. 18(1), 101-107.
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  • Hu, J. C., Karp, P. D., Keseler, I. M., Krummenacker, M., & Siegele, D. A. (2009). What we can learn about Escherichia coli through application of Gene Ontology. TRENDS IN MICROBIOLOGY. 17(7), 269-278.
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  • Hu, J. C., Aramayo, R., Bolser, D., Conway, T., Elsik, C. G., Gribskov, M., ... Welch, R. D. (2008). The emerging world of wikis. Science (New York, N.Y.). 320(5881), 1289-1290.
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  • Fischer, T. B., Holmes, J. B., Miller, I. R., Parsons, J. R., Tung, L., Hu, J. C., & Tsai, J. (2006). Assessing methods for identifying pair-wise atomic contacts across binding interfaces. JOURNAL OF STRUCTURAL BIOLOGY. 153(2), 103-112.
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  • Marino-Ramirez, L., Minor, J. L., Reading, N., & Hu, J. C. (2004). Identification and mapping of self-assembling protein domains encoded by the Escherichia coli K-12 genome by use of lambda repressor fusions. JOURNAL OF BACTERIOLOGY. 186(5), 1311-1319.
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  • Champion, M. M., Campbell, C. S., Siegele, D. A., Russell, D. H., & Hu, J. C. (2003). Proteome analysis of Escherichia coli K-12 by two-dimensional native-state chromatography and MALDI-MS. Mol Microbiol. 47(2), 383-396.
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Chapters3
Conference Papers2
chaired theses and dissertations
Email
jimhu@tamu.edu
First Name
James
Last Name
Hu
mailing address
Texas A&M University; Biochemistry & Biophysics; 2128 TAMU
College Station, TX 77843-2128
USA