Items where Subject is "ontology"

Paper

Bruskiewich, R., Coe, E. H., Jaiswal, P., McCouch, S., Polacco, M., Stein, L., Vincent, L., Ware, D. (April 2002) The Plant Ontology (TM) Consortium and plant ontologies. Comparative and Functional Genomics, 3 (2). pp. 137-142. ISSN 1531-6912

Chen, G., Hata, N., Zhang, M. Q. (2004) Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Res, 32 (8). pp. 2362-71. ISSN 1362-4962 (Electronic)

Eilbeck, K., Lewis, S. E., Mungall, C. J., Yandell, M., Stein, L. D., Durbin, R., Ashburner, M. (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biology, 6 (5). R44. ISSN 1465-6914

Fang, H., Wu, Y., Yang, H., Yoon, M., Jimenez-Barron, L. T., Mittelman, D., Robison, R., Wang, K., Lyon, G. J. (February 2017) Whole genome sequencing of one complex pedigree illustrates challenges with genomic medicine. BMC Med Genomics, 10 (1). p. 10. ISSN 1755-8794

Fischer, Stephan, Gillis, Jesse (October 2022) Defining the extent of gene function using ROC curvature. Bioinformatics. btac692. ISSN 1367-4803

Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L. D., Ware, D. H., Zapata, F. (2005) Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comp Funct Genomics, 6 (7-8). pp. 388-97. ISSN 1531-6912 (Print)

Jaiswal, P., Ware, D., Ni, J. J., Chang, K., Zhao, W., Schmidt, S., Pan, X. K., Clark, K., Teytelman, L., Cartinhour, S., Stein, L., McCouch, S. (April 2002) Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics, 3 (2). pp. 132-136. ISSN 1531-6912

Kohler, S., Vasilevsky, N. A., Engelstad, M., Foster, E., McMurry, J., Ayme, S., Baynam, G., Bello, S. M., Boerkoel, C. F., Boycott, K. M., Brudno, M., Buske, O. J., Chinnery, P. F., Cipriani, V., Connell, L. E., Dawkins, H. J., DeMare, L. E., Devereau, A. D., de Vries, B. B., Firth, H. V., Freson, K., Greene, D., Hamosh, A., Helbig, I., Hum, C., Jahn, J. A., James, R., Krause, R., Laulederkind, S. J., Lochmuller, H., Lyon, G. J., Ogishima, S., Olry, A., Ouwehand, W. H., Pontikos, N., Rath, A., Schaefer, F., Scott, R. H., Segal, M., Sergouniotis, P. I., Sever, R., Smith, C. L., Straub, V., Thompson, R., Turner, C., Turro, E., Veltman, M. W., Vulliamy, T., Yu, J., von Ziegenweidt, J., Zankl, A., Zuchner, S., Zemojtel, T., Jacobsen, J. O., Groza, T., Smedley, D., Mungall, C. J., Haendel, M., Robinson, P. N. (January 2016) The Human Phenotype Ontology in 2017. Nucleic Acids Res, 45 (D1). D865-D876. ISSN 1362-4962 (Electronic)0305-1048 (Linking)

O'Meara, M. J., Ballouz, S., Shoichet, B. K., Gillis, J. (2016) Ligand Similarity Complements Sequence, Physical Interaction, and Co-Expression for Gene Function Prediction. PLoS One, 11 (7). e0160098. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Pujar, An., Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, Sh., Stevens, P., Zapata, F., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L. D., Ware, D. H., McCouch, S. (October 2006) Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology, 142 (2). pp. 414-428. ISSN 00320889

Book

Thor, A., Anderson, P., Raschid, L., Navlakha, S., Saha, B., Khuller, S., Zhang, X. N. (October 2011) Link prediction for annotation graphs using graph summarization. Lecture Notes in Computer Science, 7031 L (Part 1). Springer, pp. 714-729. ISBN 03029743 (ISSN); 9783642250729 (ISBN)

Dataset

Gillis, J., Pavlidis, P. (2013) Data from "Assessing identity, redundancy and confounds in Gene Ontology annotations over time". [Dataset]

Gillis, J., Pavlidis, P. (2013) Use case: The postsynaptic proteome, from "Assessing identity, redundancy and confounds in Gene Ontology annotations over time". [Dataset]