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2018
I. Braun, Balhoff, J., Berardini, T. Z., Cooper, L. D., Gkoutos, G., Harper, L., Huala, E., Jaiswal, P., Kazic, T., Lapp, H., Macklin, J. A., Specht, C. D., Vision, T. J., Walls, R. L., and Lawerence-Dill, C. J., 'Computable' phenotypes enable comparative and predictive phenomics among plant species across domains of life, in Application of Semantic Technologies in Biodiversity Science, vol. 33, A. E. Thessen, Ed. Berlin: OS Press/AKA Verlag, 2018, pp. 187-205.
N. Matentzoglu, Balhoff, J. P., Bello, S. M., Boerkoel, C., Bradford, Y. M., Carmody, L. C., Cooper, L. D., Grove, C. A., Harris, N. L., Köhler, S., Laporte, M. - A., Laulederkind, S. L. F., Lee, R., Mazandu, G. K., McMurry, J. A., Mungall, C., Osumi-Sutherland, D., Pilgrim, C., Rageth, K., Robb, S. M. C., Robinson, P. N., Segerdell, E., Thessen, A., Vasilevsky, N., Zhang, X. A., and Haendel, M. A., Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species, 2018.
N. Matentzoglu, Balhoff, J. P., Bello, S. M., Boerkoel, C., Bradford, Y. M., Carmody, L. C., Cooper, L. D., Grove, C. A., Harris, N. L., Köhler, S., Laporte, M. - A., Laulederkind, S. L. F., Lee, R., Mazandu, G. K., McMurry, J. A., Mungall, C., Osumi-Sutherland, D., Pilgrim, C., Rageth, K., Robb, S. M. C., Robinson, P. N., Segerdell, E., Thessen, A., Vasilevsky, N., Zhang, X. A., and Haendel, M. A., Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species, 2018.
N. Matentzoglu, Balhoff, J. P., Bello, S. M., Boerkoel, C., Bradford, Y. M., Carmody, L. C., Cooper, L. D., Grove, C. A., Harris, N. L., Köhler, S., Laporte, M. - A., Laulederkind, S. L. F., Lee, R., Mazandu, G. K., McMurry, J. A., Mungall, C., Osumi-Sutherland, D., Pilgrim, C., Rageth, K., Robb, S. M. C., Robinson, P. N., Segerdell, E., Thessen, A., Vasilevsky, N., Zhang, X. A., and Haendel, M. A., Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species, 2018.
N. Matentzoglu, Balhoff, J. P., Bello, S. M., Boerkoel, C., Bradford, Y. M., Carmody, L. C., Cooper, L. D., Grove, C. A., Harris, N. L., Köhler, S., Laporte, M. - A., Laulederkind, S. L. F., Lee, R., Mazandu, G. K., McMurry, J. A., Mungall, C., Osumi-Sutherland, D., Pilgrim, C., Rageth, K., Robb, S. M. C., Robinson, P. N., Segerdell, E., Thessen, A., Vasilevsky, N., Zhang, X. A., and Haendel, M. A., Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species, 2018.
D. Trigkakis, Preece, J., Meier, A., Elser, J., Kvilekval, K., Fedorov, D., Manjunath, B. S., Jaiswal, P., and Todorovic, S., Planteome & BisQue: Automating Image Annotation with Ontologies using Deep-Learning Networks, in 9th International Conference on Biological Ontology (ICBO 2018) , Corvallis, OR, 2018.
L. Cooper, Meier, A., Laporte, M. - A., Elser, J. L., Mungall, C., Sinn, B. T., Cavaliere, D., Dunn, N. A., Smith, B., Qu, B., Preece, J., Zhang, E., Todorovic, S., Gkoutos, G., Doonan, J., Stevenson, D. W., Arnaud, E., and Jaiswal, P., The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics, Nucleic Acids Research, 2018.
2015
A. R. Deans, Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., Blackburn, D. C., Blake, J. A., Burleigh, G. J., Chanet, B., Cooper, L. D., Courtot, M., Csösz, S., Cui, H., Dahdul, W., Das, S., Dececchi, A. T., Dettai, A., Diogo, R., Druzinsky, R. E., Dumontier, M., Franz, N. M., Friedrich, F., Gkoutos, G. V., Haendel, M., Harmon, L. J., Hayamizu, T. F., He, Y., Hines, H. M., Ibrahim, N., Jackson, L. M., Jaiswal, P., James-Zorn, C., Köhler, S., Lecointre, G., Lapp, H., Lawrence, C. J., Le Novère, N., Lundberg, J. G., Macklin, J., Mast, A. R., Midford, P. E., Mikó, I., Mungall, C. J., Oellrich, A., Osumi-Sutherland, D., Parkinson, H., Ramírez, M. J., Richter, S., Robinson, P. N., Ruttenberg, A., Schulz, K. S., Segerdell, E., Seltmann, K. C., Sharkey, M. J., Smith, A. D., Smith, B., Specht, C. D., Squires, B. R., Thacker, R. W., Thessen, A., Fernandez-Triana, J., Vihinen, M., Vize, P. D., Vogt, L., Wall, C. E., Walls, R. L., Westerfeld, M., Wharton, R. A., Wirkner, C. S., Woolley, J. B., Yoder, M. J., Zorn, A. M., and Mabee, P., Finding Our Way through Phenotypes, PLoS Biol, vol. 13, p. e1002033, 2015.
A. R. Deans, Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., Blackburn, D. C., Blake, J. A., Burleigh, G. J., Chanet, B., Cooper, L. D., Courtot, M., Csösz, S., Cui, H., Dahdul, W., Das, S., Dececchi, A. T., Dettai, A., Diogo, R., Druzinsky, R. E., Dumontier, M., Franz, N. M., Friedrich, F., Gkoutos, G. V., Haendel, M., Harmon, L. J., Hayamizu, T. F., He, Y., Hines, H. M., Ibrahim, N., Jackson, L. M., Jaiswal, P., James-Zorn, C., Köhler, S., Lecointre, G., Lapp, H., Lawrence, C. J., Le Novère, N., Lundberg, J. G., Macklin, J., Mast, A. R., Midford, P. E., Mikó, I., Mungall, C. J., Oellrich, A., Osumi-Sutherland, D., Parkinson, H., Ramírez, M. J., Richter, S., Robinson, P. N., Ruttenberg, A., Schulz, K. S., Segerdell, E., Seltmann, K. C., Sharkey, M. J., Smith, A. D., Smith, B., Specht, C. D., Squires, B. R., Thacker, R. W., Thessen, A., Fernandez-Triana, J., Vihinen, M., Vize, P. D., Vogt, L., Wall, C. E., Walls, R. L., Westerfeld, M., Wharton, R. A., Wirkner, C. S., Woolley, J. B., Yoder, M. J., Zorn, A. M., and Mabee, P., Finding Our Way through Phenotypes, PLoS Biol, vol. 13, p. e1002033, 2015.
2012
L. D. Cooper, Annotating Gene Expression in Physcomitrella patens using the Plant Ontology: Facilitating Cross-Taxa Comparisons. San Diego, CA, 2012.
L. D. Cooper, Annotating the Maize B73 Gene Expression Atlas – A Plant Ontology Use Case for Genomics Data Curation. Washington DC, USA, 2012.
P. Jaiswal, Annotating the Maize B73 Gene Expression Atlas in the Plant Ontology- A Tool for Plant Genomics.. Portland, OR, 2012.
F. Lens, Cooper, L., Gandolfo, M. A., Groover, P., Jaiswal, P., Lachenbruch, R., Spicer, R., Staton, D., Stevenson, D. W., Walls, R. L., and Wegrzyn, J., An extension of the Plant Ontology project supporting wood anatomy and development research, IAWA Journal, vol. 33, pp. 113-117, 2012.
R. L. Walls, Mapping of glossary terms from the Flora of North America to the Plant Ontology enhances both resources, in 3rd International Conference on Biomedical Ontology (ICBO 2012), Graz, Austria, 2012.
R. L. Walls, Athreya, B., Cooper, L., Elser, J., Gandolfo, M. A., Jaiswal, P., Mungall, C. J., Preece, J., Rensing, S., Smith, B., and Stevenson, D. W., Ontologies as Integrative Tools for Plant Science, American Journal of Botany, vol. 99, no. 8, pp. 1263-75, 2012.
J. Preece, The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa. Robinson College, Cambridge, UK, 2012.
L. Cooper, The Plant Ontology: A Tool for Linking Plant Anatomy and Development to Genomics Across Plant Taxa, Plant Biology 2012. Austin, Tx, 2012.
L. D. Cooper, The Plant Ontology: Linking Genomic and Phenomic Data Across Plant Taxa, Plant and Animal Genome XX Conference. San Diego, CA, 2012.
2011
V. Shulaev, Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O. R., Jensen, R. V., Allan, A. C., Michael, T. P., Setubal, J. C., Celton, J. - M., Rees, J. D. G., Williams, K. P., Holt, S. H., Rojas, J. J. R., Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S. A., Troggio, M., Viola, R., Ashman, T. - L., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H. D., Bryant, D. W., Fox, S. E., Givan, S. A., Wilhelm, L. J., Naithani, S., Christoffels, A., Salama, D. Y., Carter, J., Girona, E. L., Zdepski, A., Wang, W., Kerstetter, R. A., Schwab, W., Korban, S. S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J. L., Salzberg, S. L., Dickerman, A. W., Velasco, R., Borodovsky, M., Veilleux, R. E., and Folta, K. M., The genome of woodland strawberry (Fragaria vesca), Nat Genet, vol. 43, pp. 109 - 116, 2011.
V. Shulaev, Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O. R., Jensen, R. V., Allan, A. C., Michael, T. P., Setubal, J. C., Celton, J. - M., Rees, J. D. G., Williams, K. P., Holt, S. H., Rojas, J. J. R., Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S. A., Troggio, M., Viola, R., Ashman, T. - L., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H. D., Bryant, D. W., Fox, S. E., Givan, S. A., Wilhelm, L. J., Naithani, S., Christoffels, A., Salama, D. Y., Carter, J., Girona, E. L., Zdepski, A., Wang, W., Kerstetter, R. A., Schwab, W., Korban, S. S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J. L., Salzberg, S. L., Dickerman, A. W., Velasco, R., Borodovsky, M., Veilleux, R. E., and Folta, K. M., The genome of woodland strawberry (Fragaria vesca), Nat Genet, vol. 43, pp. 109 - 116, 2011.
V. Shulaev, Sargent, D. J., Crowhurst, R. N., Mockler, T. C., Folkerts, O., Delcher, A. L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S. P., Burns, P., Davis, T. M., Slovin, J. P., Bassil, N., Hellens, R. P., Evans, C., Harkins, T., Kodira, C., Desany, B., Crasta, O. R., Jensen, R. V., Allan, A. C., Michael, T. P., Setubal, J. C., Celton, J. - M., Rees, J. D. G., Williams, K. P., Holt, S. H., Rojas, J. J. R., Chatterjee, M., Liu, B., Silva, H., Meisel, L., Adato, A., Filichkin, S. A., Troggio, M., Viola, R., Ashman, T. - L., Wang, H., Dharmawardhana, P., Elser, J., Raja, R., Priest, H. D., Bryant, D. W., Fox, S. E., Givan, S. A., Wilhelm, L. J., Naithani, S., Christoffels, A., Salama, D. Y., Carter, J., Girona, E. L., Zdepski, A., Wang, W., Kerstetter, R. A., Schwab, W., Korban, S. S., Davik, J., Monfort, A., Denoyes-Rothan, B., Arus, P., Mittler, R., Flinn, B., Aharoni, A., Bennetzen, J. L., Salzberg, S. L., Dickerman, A. W., Velasco, R., Borodovsky, M., Veilleux, R. E., and Folta, K. M., The genome of woodland strawberry (Fragaria vesca), Nat Genet, vol. 43, pp. 109 - 116, 2011.

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