Biblio

Found 90 results

2023

S. Naithani, Mohanty, B., Elser, J., Dâ€™Eustachio, P., and Jaiswal, P., “Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)”, Plants, vol. 12, p. 2146, 2023.

D. Manzella, Marsella, M., Jaiswal, P., Arnaud, E., and King, B., “Digital Sequence Information and Plant Genetic Resources: Global Policy Meets Interoperability”, in Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development, H. F. Williamson and Leonelli, S., Eds. Cham: Springer International Publishing, 2023, pp. 183–200.

“The Gene Ontology Knowledgebase in 2023.”, Genetics, 2023.

R. Barker, Kruse, C. P. S., Johnson, C., Saravia-Butler, A., Fogle, H., Chang, H. - S., Trane, R. Møller, Kinscherf, N., Villacampa, A., Manzano, A., Herranz, R., Davin, L. B., Lewis, N. G., Perera, I., Wolverton, C., Gupta, P., Jaiswal, P., Reinsch, S. S., Wyatt, S., and Gilroy, S., “Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome.”, NPJ Microgravity, vol. 9, no. 1, p. 21, 2023.

A. E. Thessen, Jaiswal, P., Cooper, L., Swetnam, T. L., Hegde, H., Resse, J., and Elser, J., “Using knowledge graphs to infer gene expression in plants”. 2023.

2022

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.

A. D. Yates, Allen, J., Amode, R. M., Azov, A. G., Barba, M., Becerra, A., Bhai, J., Campbell, L. I., Martinez, M. Carbajo, Chakiachvili, M., Chougule, K., Christensen, M., Contreras-Moreira, B., Cuzick, A., Fioretto, L. Da Rin, Davis, P., De Silva, N. H., Diamantakis, S., Dyer, S., Elser, J., Filippi, C. V., Gall, A., Grigoriadis, D., Guijarro-Clarke, C., Gupta, P., Hammond-Kosack, K. E., Howe, K. L., Jaiswal, P., Kaikala, V., Kumar, V., Kumari, S., Langridge, N., Le, T., Luypaert, M., Maslen, G. L., Maurel, T., Moore, B., Muffato, M., Mushtaq, A., Naamati, G., Naithani, S., Olson, A., Parker, A., Paulini, M., Pedro, H., Perry, E., Preece, J., Quinton-Tulloch, M., Rodgers, F., Rosello, M., Ruffier, M., Seager, J., Sitnik, V., Szpak, M., Tate, J., Tello-Ruiz, M. K., Trevanion, S. J., Urban, M., Ware, D., Wei, S., Williams, G., Winterbottom, A., Zarowiecki, M., Finn, R. D., and Flicek, P., “Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.”, Nucleic Acids Res, vol. 50, no. D1, pp. D996-D1003, 2022.

M. K. Tello-Ruiz, Jaiswal, P., and Ware, D., “Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.”, Methods Mol Biol, vol. 2443, pp. 101-131, 2022.

P. Gupta, Naithani, S., Preece, J., Kim, S., Cheng, T., D'Eustachio, P., Elser, J., Bolton, E. E., and Jaiswal, P., “Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases.”, Methods Mol Biol, vol. 2443, pp. 511-525, 2022.

2021

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.

P. Gupta, Geniza, M., Naithani, S., Phillips, J. L., Haq, E., and Jaiswal, P., “Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development.”, Front Plant Sci, vol. 12, p. 667678, 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.

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.

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.

“The Gene Ontology resource: enriching a GOld mine.”, Nucleic Acids Res, vol. 49, no. D1, pp. D325-D334, 2021.

M. K. Tello-Ruiz, Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D., D'Eustachio, P., Stein, L. D., Gupta, A., Xu, W., Regala, J., Papatheodorou, I., Kersey, P. J., Flicek, P., Taylor, C., Jaiswal, P., and Ware, D., “Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.”, Nucleic Acids Res, vol. 49, no. D1, pp. D1452-D1463, 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., “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities.”, mSystems, vol. 6, no. 1, 2021.

H. Wang, Liu, S., Dai, X., Yang, Y., Luo, Y., Gao, Y., Liu, X., Wei, W., Wang, H., Xu, X., Reddy, A. S. N., Jaiswal, P., Li, W., Liu, B., and Gu, L., “PSDX: A Comprehensive Multi-Omics Association Database of With a Focus on the Secondary Growth in Response to Stresses.”, Front Plant Sci, vol. 12, p. 655565, 2021.

2020

G. Parry, Provart, N. J., Brady, S. M., and Uzilday, B., “Current status of the multinational Arabidopsis community.”, Plant Direct, vol. 4, no. 7, p. e00248, 2020.

E. Arnaud, Laporte, M. - A., Kim, S., Aubert, C., Leonelli, S., Miro, B., Cooper, L., Jaiswal, P., Kruseman, G., Shrestha, R., Buttigieg, P. L., Mungall, C. J., Pietragalla, J., Agbona, A., Muliro, J., Detras, J., Hualla, V., Rathore, A., Das, R. Rani, Dieng, I., Bauchet, G., Menda, N., Pommier, C., Shaw, F., Lyon, D., Mwanzia, L., Juarez, H., Bonaiuti, E., Chiputwa, B., Obileye, O., Auzoux, S., Yeumo, E. Dzalé, Mueller, L. A., Silverstein, K., Lafargue, A., Antezana, E., Devare, M., and King, B., “The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems.”, Patterns (N Y), vol. 1, no. 7, p. 100105, 2020.

A. Kashyap, Rhodes, A., Kronmiller, B., Berger, J., Champagne, A., Davis, E. W., Finnegan, M. V., Geniza, M., Hendrix, D. A., Löhr, C. V., Petro, V. M., Sharpton, T. J., Wells, J., Epps, C. W., Jaiswal, P., Tyler, B. M., and Ramsey, S. A., “Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis.”, BMC Genomics, vol. 21, no. 1, p. 153, 2020.

S. Naithani, Gupta, P., Preece, J., D'Eustachio, P., Elser, J. L., Garg, P., Dikeman, D. A., Kiff, J., Cook, J., Olson, A., Wei, S., Tello-Ruiz, M. K., Mundo, A. Fabregat, Munoz-Pomer, A., Mohammed, S., Cheng, T., Bolton, E., Papatheodorou, I., Stein, L., Ware, D., and Jaiswal, P., “Plant Reactome: a knowledgebase and resource for comparative pathway analysis.”, Nucleic Acids Res, vol. 48, no. D1, pp. D1093-D1103, 2020.

2019

“Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future.”, Plant direct, vol. 3, no. 1, p. e00109, 2019.

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.

S. Naithani, Gupta, P., Preece, J., Garg, P., Fraser, V., Padgitt-Cobb, L. K., Martin, M., Vining, K., and Jaiswal, P., “Involving community in genes and pathway curation.”, Database : the journal of biological databases and curation, vol. 2019, 2019.

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