College of Agricultural Sciences

L. Cooper, Walls, R. L., Elser, J., Gandolfo, M. A., Stevenson, D. W., Smith, B., Preece, J., Athreya, B., Mungall, C. J., Rensing, S., Hiss, M., Lang, D., Reski, R., Berardini, T. Z., Li, D., Huala, E., Schaeffer, M., Menda, N., Arnaud, E., Shrestha, R., Yamazaki, Y., and Jaiswal, P., “The Plant Ontology As A Tool For Comparative Plant Anatomy And Genomic Analyses.”, Plant & Cell Physiology, 2012.

S. Avraham, Tung, C. - W., Ilic, K., Jaiswal, P., Kellogg, E. A., McCouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L., Zapata, F., and Ware, D., “The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.”, Nucleic acids research, vol. 36, pp. D449-54, 2008.

R. L. Walls, Cooper, L., Elser, J., Gandolfo, M. Alejandra, Mungall, C. J., Smith, B., Stevenson, D. W., and Jaiswal, P., “The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.”, Frontiers in plant science, vol. 10, p. 631, 2019.

P. Jaiswal, 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., Ware, D., and Zapata, F., “Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.”, Comparative and functional genomics, vol. 6, pp. 388-97, 2005.

P. Jaiswal and Usadel, B., “Plant Pathway Databases.”, in Methods in molecular biology (Clifton, N.J.), vol. 1374, 2016, pp. 71-87.

S. Naithani, Preece, J., D’Eustachio, P., Gupta, P., Amarasinghe, V., Dharmawardhana, P. D., Wu, G., Fabregat, A., Elser, J. L., Weiser, J., Keays, M., Fuentes, A. Munoz- Pome, Petryszak, R., Stein, L. D., Ware, D., and Jaiswal, P., “Plant Reactome: a resource for plant pathways and comparative analysis.”, Nucleic acids research, vol. 45, pp. D1029-D1039, 2018.

K. Ilic, Kellogg, E. A., Jaiswal, P., Zapata, F., Stevens, P. F., Vincent, L. P., Avraham, S., Reiser, L., Pujar, A., Sachs, M. M., Whitman, N. T., McCouch, S. R., Schaeffer, M. L., Ware, D. H., Stein, L. D., and Rhee, S. Y., “The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant.”, Plant physiology, vol. 143, pp. 587-99, 2007.

L. Cooper, Meier, A., Laporte, M. - A., Elser, J. L., Mungall, C., Sinn, B. T., Cavaliere, D., Carbon, S., Dunn, N. A., Smith, B., Qu, B., Preece, J., Zhang, E., Todorovic, S., Gkoutos, G., Doonan, J. H., Stevenson, D. W., Arnaud, E., and Jaiswal, P., “The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.”, Nucleic acids research, vol. 46, pp. D1168-D1180, 2018.

S. Smita, Lenka, S. Keshari, Katiyar, A., Jaiswal, P., Preece, J., and Bansal, K. Chander, “QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice.”, Database : the journal of biological databases and curation, vol. 2011, p. bar037, 2011.

R. C. Graebner, Wise, M., Cuesta-Marcos, A., Geniza, M., Blake, T., Blake, V. C., Butler, J., Chao, S., Hole, D. J., Horsley, R., Jaiswal, P., Obert, D., Smith, K. P., Ullrich, S., and Hayes, P. M., “Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley.”, PloS one, vol. 10, p. e0133767, 2015.

R. C. Graebner, Wise, M., Cuesta-Marcos, A., Geniza, M., Blake, T. K., Blake, V. C., Butler, J., Chao, S., Hole, D. J., Horsley, R., Jaiswal, P., Obert, D. E., Smith, K. P., Ullrich, S., and Hayes, P. M., “Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley”, PLOS ONE, vol. 10, no. 7, p. e0133767, 2015.

S. E. Fox, Preece, J., Kimbrel, J. A., Marchini, G. L., Sage, A., Youens-Clark, K., Cruzan, M. B., and Jaiswal, P., “SEQUENCING AND DE NOVO TRANSCRIPTOME ASSEMBLY OF BRACHYPODIUM SYLVATICUM (POACEAE )”, Applications in Plant Sciences, vol. 1, 2013.

M. Geniza and Jaiswal, P., “Tools for building de novo transcriptome assembly”, Current Plant Biology, vol. 11-12, pp. 41 - 45, 2017.

S. Naithani, Geniza, M., and Jaiswal, P., “Variant Effect Prediction Analysis Using Resources Available at Gramene Database.”, Methods in molecular biology (Clifton, N.J.), vol. 1533, pp. 279-297, 2017.

S. Naithani, Raja, R., Waddell, E. N., Elser, J., Gouthu, S., Deluc, L. G., and Jaiswal, P., “VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera).”, Frontiers in plant science, vol. 5, p. 644, 2014.

S. Naithani, Raja, R., Waddell, E. N., Elser, J., Gouthu, S., Deluc, L. G., and Jaiswal, P., “VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera)”, Frontiers in Plant Science, no. 79198, 2014.

A. Pujar, Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, S., Stevens, P., Zapata, F., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Ware, D., and McCouch, S., “Whole-plant growth stage ontology for angiosperms and its application in plant biology.”, Plant physiology, vol. 142, pp. 414-28, 2006.

M. Hanumappa, Preece, J., Elser, J., Nemeth, D., Bono, G., Wu, K., and Jaiswal, P., “WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks”, Rice, vol. 6, 2013.