Biblio

Found 79 results
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Journal Article
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.
Y. Gao, Liu, X., Jin, Y., Wu, J., Li, S., Li, Y., Chen, B., Zhang, Y., Wei, L., Li, W., Li, R., Lin, C., Reddy, A. S. N., Jaiswal, P., and Gu, L., Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa., Plant Physiol, vol. 190, no. 1, pp. 459-479, 2022.
L. K. Padgitt-Cobb, Kingan, S. B., Wells, J., Elser, J., Kronmiller, B., Moore, D., Concepcion, G., Peluso, P., Rank, D., Jaiswal, P., Henning, J., and Hendrix, D. A., A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome., Plant Genome, vol. 14, no. 1, p. e20072, 2021.
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.
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.
C. Warman, Sullivan, C. M., Preece, J., Buchanan, M. E., Vejlupkova, Z., Jaiswal, P., and Fowler, J. E., A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels., Plant J, vol. 106, no. 2, pp. 566-579, 2021.
P. Vangay, Burgin, J., Johnston, A., Beck, K. L., Berrios, D. C., Blumberg, K., Canon, S., Chain, P., Chandonia, J. - M., Christianson, D., Costes, S. V., Damerow, J., Duncan, W. D., Dundore-Arias, J. Pablo, Fagnan, K., Galazka, J. M., Gibbons, S. M., Hays, D., Hervey, J., Hu, B., Hurwitz, B. L., Jaiswal, P., Joachimiak, M. P., Kinkel, L., Ladau, J., Martin, S. L., McCue, L. Ann, Miller, K., Mouncey, N., Mungall, C., Pafilis, E., Reddy, T. B. K., Richardson, L., Roux, S., Schriml, L. M., Shaffer, J. P., Sundaramurthi, J. Chandrabos, Thompson, L. R., Timme, R. E., Zheng, J., Wood-Charlson, E. M., and Eloe-Fadrosh, E. A., Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities"., mSystems, vol. 6, no. 3, 2021.
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.
P. Gupta, Geniza, M., Naithani, S., Phillips, J. L., Haq, E., and Jaiswal, P., Chia () Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development., Front Plant Sci, vol. 12, p. 667678, 2021.
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.
S. Naithani, Dikeman, D., Garg, P., Al-Bader, N., and Jaiswal, P., Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily., PeerJ, vol. 9, p. e11052, 2021.
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.
Conference Paper
B. Qu, Kumar, P., Zhang, E., Jaiswal, P., Cooper, L., Elser, J., and Zhang, Y., Interactive Design and Visualization of N-ary Relationships, in SIGGRAPH Asia 2017 Symposium on Visualization, New York, NY, USA, 2017.