College of Agricultural Sciences

A. R. Deans, Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., Balhoff, J. P., Blackburn, D. C., Blake, J. A., J. Burleigh, G., Chanet, B., Cooper, L. D., Courtot, M., Csösz, S., Cui, H., Dahdul, W., Das, S., T. Dececchi, A., 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., R. Squires, B., 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.

F. Lens, Cooper, L., Gandolfo, M. Alejandra, Groover, A., Jaiswal, P., Lachenbruch, B., Spicer, R., Staton, M. E., 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, p. 5, 2012.

V. V. Peremyslov, Mockler, T. C., Filichkin, S. A., Fox, S. E., Jaiswal, P., Makarova, K. S., Koonin, E. V., and Dolja, V. V., “Expression, splicing, and evolution of the myosin gene family in plants.”, Plant physiology, vol. 155, pp. 1191-204, 2011.

R. Petryszak, Keays, M., Y Tang, A., Fonseca, N. A., Barrera, E., Burdett, T., Füllgrabe, A., Fuentes, A. Muñoz- Pom, Jupp, S., Koskinen, S., Mannion, O., Huerta, L., Megy, K., Snow, C., Williams, E., Barzine, M., Hastings, E., Weisser, H., Wright, J., Jaiswal, P., Huber, W., Choudhary, J., Parkinson, H. E., and Brazma, A., “Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants.”, Nucleic acids research, vol. 44, pp. D746-52, 2016.

I. Papatheodorou, Fonseca, N. A., Keays, M., Y Tang, A., Barrera, E., Bazant, W., Burke, M., Füllgrabe, A., Fuentes, A. Muñoz- Pom, George, N., Huerta, L., Koskinen, S., Mohammed, S., Geniza, M., Preece, J., Jaiswal, P., Jarnuczak, A. F., Huber, W., Stegle, O., Vizcaino, J. Antonio, Brazma, A., and Petryszak, R., “Expression Atlas: gene and protein expression across multiple studies and organisms.”, Nucleic acids research, vol. 46, pp. D246-D251, 2018.

S. A. Filichkin, Cumbie, J. S., Dharmawardhana, P., Jaiswal, P., Chang, J. H., Palusa, S. G., Reddy, A. S. N., Megraw, M., and Mockler, T. C., “Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis.”, Molecular plant, vol. 8, pp. 207-27, 2015.

K. L. Howe, Contreras-Moreira, B., De Silva, N., Maslen, G., Akanni, W., Allen, J., Alvarez-Jarreta, J., Barba, M., Bolser, D. M., Cambell, L., Carbajo, M., Chakiachvili, M., Christensen, M., Cummins, C., Cuzick, A., Davis, P., Fexova, S., Gall, A., George, N., Gil, L., Gupta, P., Hammond-Kosack, K. E., Haskell, E., Hunt, S. E., Jaiswal, P., Janacek, S. H., Kersey, P. J., Langridge, N., Maheswari, U., Maurel, T., McDowall, M. D., Moore, B., Muffato, M., Naamati, G., Naithani, S., Olson, A., Papatheodorou, I., Patricio, M., Paulini, M., Pedro, H., Perry, E., Preece, J., Rosello, M., Russell, M., Sitnik, V., Staines, D. M., Stein, J., Tello-Ruiz, M. K., Trevanion, S. J., Urban, M., Wei, S., Ware, D., Williams, G., Yates, A. D., and Flicek, P., “Ensembl Genomes 2020-enabling non-vertebrate genomic research.”, Nucleic acids research, 2019.

A. E. Thessen, Bunker, D. E., Buttigieg, P. Luigi, Cooper, L. D., Dahdul, W. M., Domisch, S., Franz, N. M., Jaiswal, P., Lawrence-Dill, C. J., Midford, P. E., Mungall, C. J., Ramírez, M. J., Specht, C. D., Vogt, L., Vos, R. Aldo, Walls, R. L., White, J. W., Zhang, G., Deans, A. R., Huala, E., Lewis, S. E., and Mabee, P. M., “Emerging semantics to link phenotype and environment.”, PeerJ, vol. 3, p. e1470, 2015.

A. C Quandt, Di, Y., Elser, J., Jaiswal, P., and Spatafora, J. W., “Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides.”, G3 (Bethesda, Md.), 2016.

A. C Quandt, Di, Y., Elser, J., Jaiswal, P., and Spatafora, J. W., “Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides.”, G3 (Bethesda, Md.), vol. 6, pp. 731-41, 2016.

A. C Quandt, Di, Y., Elser, J., Jaiswal, P., and Spatafora, J. W., “Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides.”, G3 (Bethesda, Md.), 2016.

S. E. Fox, Geniza, M., Hanumappa, M., Naithani, S., Sullivan, C. M., Preece, J., Tiwari, V. I. K., Elser, J., Leonard, J. M., Sage, A., Gresham, C., Kerhornou, A., Bolser, D., McCarthy, F., Kersey, P., Lazo, G. R., and Jaiswal, P., “De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum.”, PLoS ONE, vol. 9, 2014.

P. Garg and Jaiswal, P., “Databases and bioinformatics tools for rice research”, Current Plant Biology, vol. 7-8, pp. 39 - 52, 2016.

S. Schaeffer, Harper, A., Raja, R., Jaiswal, P., and Dhingra, A., “Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes.”, PloS one, vol. 9, p. e112870, 2014.

Y. Yamazaki and Jaiswal, P., “Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase.”, Plant & cell physiology, vol. 46, pp. 63-8, 2005.

N. Lingutla, Preece, J., Todorovic, S., Cooper, L., Moore, L., and Jaiswal, P., “AISO: Annotation of Image Segments with Ontologies”, Journal of Biomedical Semantics, vol. 5, p. 50, 2014.

L. Harper, Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., Andorf, C., Arnaud, E., Berardini, T. Z., Birkett, C., Cannon, S., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C. G., Farmer, A., Ficklin, S. P., Grant, D., Grau, E., Herndon, N., Hu, Z. - L., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M. - A., Larmande, P., Lazo, G., McCarthy, F., Menda, N., Mungall, C. J., Munoz-Torres, M. C., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L. - A., Sen, T. Z., Staton, M., Subramaniam, S., Tello-Ruiz, M. Karey, Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M., Yu, J., and Main, D., “AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.”, Database : the journal of biological databases and curation, vol. 2018, 2018.

S. A. Filichkin, Hamilton, M., Dharmawardhana, P. D., Singh, S. K., Sullivan, C., Ben-Hur, A., Reddy, A. S. N., and Jaiswal, P., “Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching.”, Frontiers in plant science, vol. 9, p. 5, 2018.