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.
- 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.
- 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-+.
- 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.
- Carbon, S., Douglass, E., Dunn, N., Good, B., Harris, N. L., Lewis, S. E., ... Consortium, G. O. (2019). The Gene Ontology Resource: 20 years and still GOing strong. Nucleic acids research. 47(D1), D330-D338.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Gaudet, P., Škunca, N., Hu, J. C., & Dessimoz, C. (2017). Primer on the Gene Ontology.. Methods in molecular biology (Clifton, N.J.). Methods in Molecular Biology. (pp. 25-37). Springer New York.
- Chibucos, M. C., Siegele, D. A., Hu, J. C., & Giglio, M. (2017). The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.. Methods in molecular biology (Clifton, N.J.). Methods in Molecular Biology. (pp. 245-259). Springer New York.
- Siegele, D. A., Campbell, L., & Hu, J. C. (2000). Green fluorescent protein as a reporter of transcriptional activity in a prokaryotic system. GUIDE TO TECHNIQUES IN MOUSE DEVELOPMENT, PT A: MICE, EMBRYOS, AND CELLS, 2ND EDITION. Bioluminescence and Chemiluminescence Part C. (pp. 499-513). Academic Press.
- Chibucos, M., Zweifel, A., Siegele, D., Uetz, P., Giglio, M., & Hu, J. (2011). The ontology of microbial phenotypes (OMP): A precomposed ontology based on cross products from multiple external ontologies that is used for guiding microbial phenotype annotation. CEUR Workshop Proceedings. 833, 237-239.
- Champion, M. M., Campbell, C. S., Siegele, D. A., Russell, D. H., & Hu, J. C. (2002). Proteome analysis of Escherichia coli K-12 by two-dimensional native-state chromatography and MALDI-MS. 59-60.
- Bonde, Aniket Sanjiv (2018-12). Identifying Expert Reviews in the Crowd: Linking Curated and Noisy Domains. (Master's Thesis)
- Huo, Zepeng (2017-12). Link Prediction with Personalized Social Influence. (Master's Thesis)
- Zweifel, Adrienne Elizabeth (2010-05). Phenotypic Characterization of Self- Assembling Protein Fragments Using Negative Dominance. (Doctoral Dissertation)
- Venkatraman, Anand (2008-12). Validation of a novel expressed sequence tag (EST) clustering method and development of a phylogenetic annotation pipeline for livestock gene families. (Doctoral Dissertation)
- Diaz Vazquez, Arnaldo Joel (2008-05). Solid-supported phospholipid bilayers: separation matrix for proteomics applications. (Doctoral Dissertation)
- Knapp, Gwendowlyn Sue (2008-05). Oligomerization of the lysr-type transcriptional regulators in Escherichia Coli. (Doctoral Dissertation)
- Niu, Lili (2007-05). Escherichia coli proteomics and bioinformatics. (Doctoral Dissertation)
- Champion, Matthew Maurice (2005-12). Functional proteomics in Escherichia coli. (Doctoral Dissertation)