2023

Thessen, A. E., Jaiswal, P., Cooper, L., Swetnam, T. L., Hegde, H., Resse, J., & Elser, J. (2023). Using knowledge graphs to infer gene expression in plants. https://doi.org/10.5281/zenodo.7764762
Naithani, S., Mohanty, B., Elser, J., D’Eustachio, P., & Jaiswal, P. (2023). Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa). Plants, 12, 2146. https://doi.org/10.3390/plants12112146
Barker, R., Kruse, C. P. S., Johnson, C., Saravia-Butler, A., Fogle, H., Chang, H. -S., et al. (2023). Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome. Npj Microgravity, 9(1), 21. https://doi.org/10.1038/s41526-023-00247-6 (Original work published 2023 Mar 20 C.E.)
Manzella, D., Marsella, M., Jaiswal, P., Arnaud, E., King, B., Williamson, H. F., & Leonelli, S. (2023). Digital Sequence Information and Plant Genetic Resources: Global Policy Meets Interoperability. In Towards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development (pp. 183–200). Cham: Springer International Publishing. https://doi.org/10.1007/978-3-031-13276-6_10
Consortium, G. O. (2023). The Gene Ontology Knowledgebase in 2023. Genetics. https://doi.org/10.1093/genetics/iyad031 (Original work published 2023 Mar 03 C.E.)

2022

Gupta, P., Naithani, S., Preece, J., Kim, S., Cheng, T., D'Eustachio, P., et al. (2022). Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. Methods Mol Biol, 2443, 511-525. https://doi.org/10.1007/978-1-0716-2067-0_27 (Original work published 2022)
Yates, A. D., Allen, J., Amode, R. M., Azov, A. G., Barba, M., Becerra, A., et al. (2022). Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Res, 50(D1), D996-D1003. https://doi.org/10.1093/nar/gkab1007 (Original work published 2022 Jan 07 C.E.)
Tello-Ruiz, M. K., Jaiswal, P., & Ware, D. (2022). Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol, 2443, 101-131. https://doi.org/10.1007/978-1-0716-2067-0_5 (Original work published 2022)
Gao, Y., Liu, X., Jin, Y., Wu, J., Li, S., Li, Y., et al. (2022). Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa. Plant Physiol, 190(1), 459-479. https://doi.org/10.1093/plphys/kiac272 (Original work published 2022 Aug 29 C.E.)

2021

Padgitt-Cobb, L. K., Kingan, S. B., Wells, J., Elser, J., Kronmiller, B., Moore, D., et al. (2021). A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome. Plant Genome, 14(1), e20072. https://doi.org/10.1002/tpg2.20072 (Original work published 2021 Mar C.E.)
Consortium, G. O. (2021). The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res, 49(D1), D325-D334. https://doi.org/10.1093/nar/gkaa1113 (Original work published 2021 Jan 08 C.E.)
Tello-Ruiz, M. K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., et al. (2021). Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res, 49(D1), D1452-D1463. https://doi.org/10.1093/nar/gkaa979 (Original work published 2021 Jan 08 C.E.)
Vangay, P., Burgin, J., Johnston, A., Beck, K. L., Berrios, D. C., Blumberg, K., et al. (2021). Correction for Vangay et al., "Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities". Msystems, 6(3). https://doi.org/10.1128/mSystems.00273-21 (Original work published 2021 May 04 C.E.)
Gupta, P., Geniza, M., Naithani, S., Phillips, J. L., Haq, E., & Jaiswal, P. (2021). Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development. Front Plant Sci, 12, 667678. https://doi.org/10.3389/fpls.2021.667678 (Original work published 2021)
Wang, H., Liu, S., Dai, X., Yang, Y., Luo, Y., Gao, Y., et al. (2021). PSDX: A Comprehensive Multi-Omics Association Database of With a Focus on the Secondary Growth in Response to Stresses. Front Plant Sci, 12, 655565. https://doi.org/10.3389/fpls.2021.655565 (Original work published 2021)
Naithani, S., Dikeman, D., Garg, P., Al-Bader, N., & Jaiswal, P. (2021). Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily. Peerj, 9, e11052. https://doi.org/10.7717/peerj.11052 (Original work published 2021)
Vangay, P., Burgin, J., Johnston, A., Beck, K. L., Berrios, D. C., Blumberg, K., et al. (2021). Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative's Workshop and Follow-On Activities. Msystems, 6(1). https://doi.org/10.1128/mSystems.01194-20 (Original work published 2021 Feb 23 C.E.)
Warman, C., Sullivan, C. M., Preece, J., Buchanan, M. E., Vejlupkova, Z., Jaiswal, P., & Fowler, J. E. (2021). A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels. Plant J, 106(2), 566-579. https://doi.org/10.1111/tpj.15166 (Original work published 2021 Apr C.E.)

2020

Parry, G., Provart, N. J., Brady, S. M., Uzilday, B., & Committee, M. A. S. (2020). Current status of the multinational Arabidopsis community. Plant Direct, 4(7), e00248. https://doi.org/10.1002/pld3.248 (Original work published 2020 Jul C.E.)
Naithani, S., Gupta, P., Preece, J., D'Eustachio, P., Elser, J. L., Garg, P., et al. (2020). Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res, 48(D1), D1093-D1103. https://doi.org/10.1093/nar/gkz996 (Original work published 2020 Jan 08 C.E.)
Kashyap, A., Rhodes, A., Kronmiller, B., Berger, J., Champagne, A., Davis, E. W., et al. (2020). Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis. Bmc Genomics, 21(1), 153. https://doi.org/10.1186/s12864-019-6432-4 (Original work published 2020 Feb 12 C.E.)
Arnaud, E., Laporte, M. -A., Kim, S., Aubert, C., Leonelli, S., Miro, B., et al. (2020). The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. Patterns (N Y), 1(7), 100105. https://doi.org/10.1016/j.patter.2020.100105 (Original work published 2020 Oct 09 C.E.)

2019

Walls, R. L., Cooper, L., Elser, J., Gandolfo, M. A., Mungall, C. J., Smith, B., et al. (2019). The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species. Frontiers In Plant Science, 10, 631. https://doi.org/10.3389/fpls.2019.00631 (Original work published 2019)
Naithani, S., Gupta, P., Preece, J., Garg, P., Fraser, V., Padgitt-Cobb, L. K., et al. (2019). Involving community in genes and pathway curation. Database : The Journal Of Biological Databases And Curation, 2019. https://doi.org/10.1093/database/bay146 (Original work published 2019 01 01 C.E.)
Howe, K. L., Contreras-Moreira, B., De Silva, N., Maslen, G., Akanni, W., Allen, J., et al. (2019). Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz890 (Original work published 2019 Oct 10 C.E.)
Consortium, I. A. I. (2019). Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future. Plant Direct, 3(1), e00109. https://doi.org/10.1002/pld3.109 (Original work published 2019 Jan C.E.)

2018

Tello-Ruiz, M. K., Naithani, S., Stein, J. C., Gupta, P., Campbell, M., Olson, A., et al. (2018). Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Research, 46(D1), D1181-D1189. https://doi.org/10.1093/nar/gkx1111 (Original work published 2018 Jan 04 C.E.)
Papatheodorou, I., Fonseca, N. A., Keays, M., Tang, A., Barrera, E., Bazant, W., et al. (2018). Expression Atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Research, 46(D1), D246-D251. https://doi.org/10.1093/nar/gkx1158 (Original work published 2018 Jan 04 C.E.)
Naithani, S., Preece, J., D'Eustachio, P., Gupta, P., Amarasinghe, V., Dharmawardhana, P. D., et al. (2018). Plant Reactome: a resource for plant pathways and comparative analysis. Nucleic Acids Research, 45(D1), D1029-D1039. https://doi.org/10.1093/nar/gkw932 (Original work published 2017 Jan 04 C.E.)
Cooper, L., Meier, A., Laporte, M. -A., Elser, J. L., Mungall, C., Sinn, B. T., et al. (2018). The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Research, 46(D1), D1168-D1180. https://doi.org/10.1093/nar/gkx1152 (Original work published 2018 01 04 C.E.)
Harper, L., Campbell, J., Cannon, E. K. S., Jung, S., Poelchau, M., Walls, R., et al. (2018). AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database : The Journal Of Biological Databases And Curation, 2018. https://doi.org/10.1093/database/bay088 (Original work published 2018 01 01 C.E.)
Filichkin, S. A., Hamilton, M., Dharmawardhana, P. D., Singh, S. K., Sullivan, C., Ben-Hur, A., et al. (2018). Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching. Frontiers In Plant Science, 9, 5. https://doi.org/10.3389/fpls.2018.00005 (Original work published 2018)

2017

Naithani, S., & Jaiswal, P. (2017). Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study. Methods In Molecular Biology (Clifton, N.j.), 1533, 241-256. https://doi.org/10.1007/978-1-4939-6658-5_14 (Original work published 2017)
Qu, B., Kumar, P., Zhang, E., Jaiswal, P., Cooper, L., Elser, J., & Zhang, Y. (2017). Interactive Design and Visualization of N-ary Relationships. SIGGRAPH Asia 2017 Symposium on Visualization, 15:1–15:8. New York, NY, USA: ACM. https://doi.org/10.1145/3139295.3139314
Geniza, M., & Jaiswal, P. (2017). Tools for building de novo transcriptome assembly. Current Plant Biology, 11-12, 41 - 45. https://doi.org/https://doi.org/10.1016/j.cpb.2017.12.004
Naithani, S., Geniza, M., & Jaiswal, P. (2017). Variant Effect Prediction Analysis Using Resources Available at Gramene Database. Methods In Molecular Biology (Clifton, N.j.), 1533, 279-297. https://doi.org/10.1007/978-1-4939-6658-5_17 (Original work published 2017)

2016

Petryszak, R., Keays, M., Tang, A., Fonseca, N. A., Barrera, E., Burdett, T., et al. (2016). Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Research, 44(D1), D746-52. https://doi.org/10.1093/nar/gkv1045 (Original work published 2016 Jan 4 C.E.)
Tello-Ruiz, M. K., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., et al. (2016). Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Research, 44(D1), D1133-40. https://doi.org/10.1093/nar/gkv1179 (Original work published 2016 Jan 4 C.E.)
Tello-Ruiz, M. K., Stein, J., Wei, S., Youens-Clark, K., Jaiswal, P., & Ware, D. (2016). Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. In Methods in molecular biology (Clifton, N.J.) (Vol. 1374, pp. 141-63). https://doi.org/10.1007/978-1-4939-3167-5_7 (Original work published 2016)
Cooper, L., & Jaiswal, P. (2016). The Plant Ontology: A Tool for Plant Genomics. In Methods in molecular biology (Clifton, N.J.) (Vol. 1374, pp. 89-114). https://doi.org/10.1007/978-1-4939-3167-5_5 (Original work published 2016)
Jaiswal, P., & Usadel, B. (2016). Plant Pathway Databases. In Methods in molecular biology (Clifton, N.J.) (Vol. 1374, pp. 71-87). https://doi.org/10.1007/978-1-4939-3167-5_4 (Original work published 2016)
Gupta, P., Naithani, S., Tello-Ruiz, M. K., Chougule, K., D'Eustachio, P., Fabregat, A., et al. (2016). Gramene Database: Navigating Plant Comparative Genomics Resources. Current Plant Biology, 7-8, 10-15. https://doi.org/10.1016/j.cpb.2016.12.005 (Original work published 2016 Nov C.E.)
Naithani, S., Partipilo, C. M., Raja, R., Elser, J. L., & Jaiswal, P. (2016). FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca. Frontiers In Plant Science, 7, 242. https://doi.org/10.3389/fpls.2016.00242 (Original work published 2016)
Quandt, A., Di, Y., Elser, J., Jaiswal, P., & Spatafora, J. W. (2016). Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides. G3 (Bethesda, Md.), 6(3), 731-41. https://doi.org/10.1534/g3.116.027045 (Original work published 2016 Jan 22 C.E.)
Garg, P., & Jaiswal, P. (2016). Databases and bioinformatics tools for rice research. Current Plant Biology, 7-8, 39 - 52. https://doi.org/https://doi.org/10.1016/j.cpb.2016.12.006
Quandt, A., Di, Y., Elser, J., Jaiswal, P., & Spatafora, J. W. (2016). Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides. G3 (Bethesda, Md.). https://doi.org/10.1534/g3.116.027045 (Original work published 2016 Jan 22 C.E.)

2015

Thessen, A. E., Bunker, D. E., Buttigieg, P. L., Cooper, L. D., Dahdul, W. M., Domisch, S., et al. (2015). Emerging semantics to link phenotype and environment. Peerj, 3, e1470. https://doi.org/10.7717/peerj.1470 (Original work published 2015)
Graebner, R. C., Wise, M., Cuesta-Marcos, A., Geniza, M., Blake, T., Blake, V. C., et al. (2015). Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley. Plos One, 10(7), e0133767. https://doi.org/10.1371/journal.pone.0133767 (Original work published 2015)
Oellrich, A., Walls, R. L., Cannon, E. K. S., Cannon, S. B., Cooper, L., Gardiner, J., et al. (2015). An ontology approach to comparative phenomics in plants. Plant Methods, 11, 10. https://doi.org/10.1186/s13007-015-0053-y (Original work published 2015)
Filichkin, S. A., Cumbie, J. S., Dharmawardhana, P., Jaiswal, P., Chang, J. H., Palusa, S. G., et al. (2015). Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis. Molecular Plant, 8(2), 207-27. https://doi.org/10.1016/j.molp.2014.10.011 (Original work published 2015 Feb C.E.)