Plant Reactome Google Scholar Page | Presentations
Why cite Plant Reactome?
To demonstrate the value of Plant Reactome, we track citations of our publications in the literature. If you reference only the project website (https://plantreactomedev.gramene.org), we cannot track it. We would highly appreciate it if you cite Plant Reactome correctly in your publications.
Please use the following most recent peer-reviewed publication to cite Plant Reactome in your work and websites:
Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis. Gupta P., J. Elser, E. Hooks, P. D’Eustachio, P. Jaiswal and S. Naithani (2024). Nucleic Acids Res.,52 (D1): D1538-D1547. doi:10.1093/nar/gkad1052.
See citations of this article [source: GoogleScholar]
Other Plant Reactome Publications:
2026
Gramene 2025: expanded comparative genomics and pathway resources, integrated search, and pan-genome portals for crop research. Olson A, Kumari S, Wei X, Chougule K, Lu Z, Tello-Ruiz MK, Kumar V, Van Buren P, Olson A, Kim C, Braynen J, Zhang L, Dyer S, Alvarez-Jarreta J, Saraf S, Contreras-Moreira B, Naamati G, Ernst C, Papatheodorou I, George N, Jaiswal P, Naithani S, Gupta P, Elser J, D'Eustachio P, Assmann SM, Ferrero-Serrano Á, Pasha A, Provart N, Gladman N, Ware D (2026). Nucleic Acids Res. 54:D1720-D1732. doi: 10.1093/nar/gkaf1260.
see: citations of this article
The Gene Ontology knowledgebase in 2026. Gene Ontology Consortium. Nucleic Acids Res. 54:D1779-D1792. doi: 10.1093/nar/gkaf1292.
see: citations of this article
2025
Detecting novel plant pathogen threats to food system security by integrating the Plant Reactome and remote sensing. Murray S.C., A. Verhoef, A. Adak, D. Sen, R. Salzman, P. Jaiswal, and S. Naithani (2025). Curr Opin Plant Biol. 83: 102684, doi:10.1016/j.pbi.2024.102684.
see: citations of this article
2023
Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa). Naithani S., B. Mohanty, J. Elser, P. D’Eustachio, and P. Jaiswal (2023). Plants 12: 2146, doi:10.3390/plants12112146.
2022
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. Gupta P., S. Naithani, J. Preece, S. Kim, P. D'Eustachio, J. Elser, E. Bolton, and P. Jaiswal (2022) In: Edwards D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. doi:10.1007/978-1-0716-2067-0_27
Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Tello-Ruiz M.K., Jaiswal P., Ware D. (2022) In: Edwards D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. Doi:10.1007/978-1-0716-2067-0_5
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates, Andrew D Yates, James Allen, Ridwan M Amode, Andrey G Azov, Matthieu Barba, Andrés Becerra, Jyothish Bhai, Lahcen I Campbell, Manuel Carbajo Martinez, Marc Chakiachvili, Kapeel Chougule, Mikkel Christensen, Bruno Contreras-Moreira, Alayne Cuzick, Luca Da Rin Fioretto, Paul Davis, Nishadi H De Silva, Stavros Diamantakis, Sarah Dyer, Justin Elser, Carla V Filippi, Astrid Gall, Dionysios Grigoriadis, Cristina Guijarro-Clarke, Parul Gupta, Kim E Hammond-Kosack, Kevin L Howe, Pankaj Jaiswal, Vinay Kaikala, Vivek Kumar, Sunita Kumari, Nick Langridge, Tuan Le, Manuel Luypaert, Gareth L Maslen, Thomas Maurel, Benjamin Moore, Matthieu Muffato, Aleena Mushtaq, Guy Naamati, Sushma Naithani, Andrew Olson, Anne Parker, Michael Paulini, Helder Pedro, Emily Perry, Justin Preece, Mark Quinton-Tulloch, Faye Rodgers, Marc Rosello, Magali Ruffier, James Seager, Vasily Sitnik, Michal Szpak, John Tate, Marcela K Tello-Ruiz, Stephen J Trevanion, Martin Urban, Doreen Ware, Sharon Wei, Gary Williams, Andrea Winterbottom, Magdalena Zarowiecki, Robert D Finn, Paul Flicek (2022), Nucleic Acids Research, 50 (D1): D996–D1003, doi: 10.1093/nar/gkab1007
2021
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Tello-Ruiz MK, 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 LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, Ware D. (2021) Nucleic Acids Res. 2021 Jan 8;49(D1):D1452-D1463. doi: 10.1093/nar/gkaa979.
Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily. Naithani S, Dikeman D, Garg P, Al-Bader N, Jaiswal P. (2021) PeerJ. 9:e11052. doi:10.7717/peerj.11052.
2020
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Naithani S, Gupta P, Preece J, D’Eustachio P, Elser J, Garg P, Dikeman DA, Kiff J, Cook J, Olson A, Wei S, Tello-Ruiz MK, Mundo AF, Munoz-Pomer A, Mohammed S, Cheng T, Bolton E, Papatheodorou I, Stein L, Ware D, and Jaiswal P. (2020). Nucleic Acids Research, doi: 10.1093/nar/gkz996
Ensembl Genomes 2020-enabling non-vertebrate genomic research. Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, 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 KE, Haskell E, Hunt SE, Jaiswal P, Janacek SH, Kersey PJ, Langridge N, Maheswari U, Maurel T, McDowall MD, 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 DM, Stein J, Tello-Ruiz MK, Trevanion SJ, Urban M, Wei S, Ware D, Williams G, Yates AD, Flicek P. (2020) Nucleic Acids Res. 48(D1):D689-D695. doi: 10.1093/nar/gkz890.
2019
Involving community in genes and pathway curation. Naithani S, Gupta P, Preece J, Garg P, Fraser V, Padgitt-Cobb LK, Martin M, Vining K, Jaiswal P. (2019). Database. 2019:bay146. doi:10.1093/database/bay146
2018
Gramene 2018: unifying comparative genomics and pathway resources for plant research. Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D. Nucleic Acids Res. 2018 Jan 4;46(D1):D1181-D1189. doi: 10.1093/nar/gkx1111.
2017
Plant Reactome: a resource for plant pathways and comparative analysis. Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AM, Petryszak R, Stein LD, Ware D, Jaiswal P. (2017) Nucleic Acids Res. 45(D1):D1029-D1039. doi: 10.1093/nar/gkw932.
Variant Effect Prediction Analysis Using Resources Available at Gramene Database. Naithani S, Geniza M, Jaiswal P. (2017). Methods Mol Biol. 1533:279-297. doi: 10.1007/978-1-4939-6658-5_17.
2016
Gramene 2016: comparative plant genomics and pathway resources. Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D. (2016). Nucleic Acids Res. 44(D1):D1133-40. doi: 10.1093/nar/gkv1179.
Gramene Database: navigating plant comparative genomics resources. Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P. Curr Plant Biol. 2016 Nov;7-8:10-15. doi: 10.1016/j.cpb.2016.12.005.
Expression Atlas update--an integrated database of gene and protein expression in humans, animals, and plants. Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Fuentes AM, 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 HE, Brazma A. Nucleic Acids Res. 2016 Jan 4;44(D1):D746-52. doi: 10.1093/nar/gkv1045.
2014
Gramene 2013: comparative plant genomics resources. Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D. (2014) Nucleic Acids Res ;42:D1193-9. doi: 10.1093/nar/gkt1110.
Collaborative publications with other public genomic resources and on FAIR (Findable, Accessible, Interoperable, and Re-usable) data policy:
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Deng C.H., S. Naithani, S. Kumari, I. Cobo-Simon, E.H. Quezada-Rodriguez, M. Skrabisova, N. Gladman, M.J. Correll, A.B. Sikiru, O.O. Afuwape, A. Marrano, I. Rebollo, W. Zhang, and S. Jung (2023). Database, 2023: baad088, doi:10.1093/database/baad088
Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes. Naithani S., C. H. Deng, S. K. Sahu, and P. Jaiswal (2023). Biomolecules 2023, 13, 1403,doi:10.3390/biom13091403.
Towards an open grapevine information system. A-F Adam-Blondon, M Alaux, C Pommier, D Cantu, Z-M Cheng, GR Cramer, C Davies, S Delrot, L Deluc, G Di Gaspero, J Grimplet, A Fennell, JP Londo, P Kersey, F Mattivi, S Naithani, P Neveu, M Nikolski, M Pezzotti, BI Reisch, R Töpfer, MA Vivier, D Ware & H Quesneville (2016). Horticulture Research, 3:16056
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Harper L, Campbell J, Cannon EKS, Jung S, Poelchau M, Walls R, Andorf C, Arnaud E, Berardini TZ, Birkett C, Cannon S, Carson J, Condon B, Cooper L, Dunn N, Elsik CG, Farmer A, Ficklin SP, Grant D, Grau E, Herndon N, Hu ZL, Humann J, Jaiswal P, Jonquet C, Laporte MA, Larmande P, Lazo G, McCarthy F, Menda N, Mungall CJ, Munoz-Torres MC, Naithani S, Nelson R, Nesdill D, Park C, Reecy J, Reiser L, Sanderson LA, Sen TZ, Staton M, Subramaniam S, Tello-Ruiz MK, Unda V, Unni D, Wang L, Ware D, Wegrzyn J, Williams J, Woodhouse M, Yu J, Main D. Database, Volume 2018, 1 January 2018, bay088, doi:10.1093/database/bay088.
2026
Naithani S., Gupta P., J. Elser, P. D’Eustachio, P. Jaiswal (2026). ‘Plant Reactome Knowledgebase: 2026 Updates and Future Direction’ to be presented in the 19th International Biocuration Conference, scheduled in Cape Town, Western Cape, South Africa from April 20-26th, 2026.
Naithani S. (2026). ‘Plant Reactome Knowledgebase: Identifying Genes and Pathways Involved in Biotic and Abiotic Stress Response and Resilience’, in Climate-Smart Agriculture II Workshop at the Plant and Animal Genome (PAG 33) Conference, San Diego, CA, USA.
2025
Gupta P., S. Naithani, J. Elser, P. D’Eustachio, P. Jaiswal (2025). ‘Plant Reactome: Pathway Knowledgebase and Discovery Platform’ in the Computational Biology/Bioinformatics Concurrent Symposium at ASPB’s Plant Biology 2025 meeting, Milwaukee, WI, USA.
Naithani S. (2025). ‘Plant Reactome: A plant pathway Knowledgebase and discovery platform’ at the 18th annual International Biocuration conference, Kansas City, MO, USA.
Naithani S., J. Preece, P. Gupta, P. D’Eustachio, J.L. Elser, and P. Jaiswal (2025). ‘Plant Reactome: Leveraging Neo4j Knowledge Graphs for Pathway Integration, Visualization, Analysis, and Discovery’ in the PAG 32 conference, San Diego, CA, USA.
2024
Naithani S., S. El-Husseini, A. Ganguli, A. Tongsak, K. Sparks, S. Rao, J. Beasley-Bennett, J. Rosenau, R. Callahan, Q. Beers, G. Michna, O. Worley, M. Goebel, S. Buchanan, I. Ramirez, C. Crofford, J. Elser, P. Gupta, P. D'Eustachio, and P. Jaiswal (2024). ‘Plant Reactome: in silico modeling of reference rice pathways for knowledge discovery and translational research’ at 21st International Symposium on Rice Functional Genomics (ISRFG 2024), held in Little Rock/Stuttgart, Arkansas, USA.
Naithani S., P. Gupta, J. Elser, P. D'Eustachio, and P. Jaiswal (2024). ‘Plant Reactome: Leveraging Neo4j Knowledge Graphs for Pathway Integration, Visualization, Analysis, and Discovery’ in the Plant Biology 2024 meeting organized by ASPB in Hawaii, USA.
Naithani S. (2024). ‘Omics data reuse for synthesizing plant gene-networks and pathways for the Plant Reactome Knowledgebase’ presented online in the International Microbiome and Multi’Omics Standards Alliance (IMMSA; https://www.microbialstandards.org) - Bioinformatics working group’s Year of Data Reuse webinar series.
Naithani S. (2024). ‘Identification of conserved, gravitropic genes and pathways across plant species using the Plant Reactome Knowledgebase’ in the NASA GeneLab Analysis Working Group 2024 virtual symposium.
Naithani S., (2024). ‘Plant Reactome Knowledgebase: Decoding Plant Pathway Networks and Unraveling the Genotype-to-Phenotype Connection’ at 17th Annual International Biocuration Conference organized by International Society for Biocuration (ISB), held at the Indian Biological Data Centre (IBDC), Faridabad, India. (Keynote Lecture).
Naithani S. (2024). ‘Plant Reactome Knowledgebase for plant pathway exploration, OMICS data analysis and candidate gene discovery’ at CQLS 2024 Fall Conference, OSU, Corvallis, Oregon, USA.
Naithani S., (2024). ‘Training Undergraduates in Plant Gene and Pathway Biocuration for the Plant Reactome Knowledgebase’ in the Gramene Workshop at the PAG 31 Conference, San Diego, CA, USA.
Olson A., K. Chougule, N. Gladman, V. Kumar, S. Kumari, Z. Lu, M. K. Tello-Ruiz, S. Wei, J. Elser, P. Gupta, S. Naithani, N. George, G. Naamati, Á. Ferrero-Serrano, S. M. Assmann, S. Dyer, I. Papatheodorou, P. Jaiswal, and D. Ware (2024). ‘Gramene 2024: A Comparative Resource on Plant Reference Genomes, Pan-Genomes and Pathways’ in the Plant and Animal Genome Conference (PAG 31), San Diego, CA, USA.
Naithani S. (2024). ‘Supporting Agricultural Genomics Through Bioinformatics’ in the AG2P Workshop and Panel at the PAG 31 Conference, San Diego, CA, US
2023
Naithani S. (2023). ‘Using OMICs Data for Biocuration of Plant Genes and Pathways for the Plant Reactome’ in the PAG 30 conference, San Diego, CA, USA (Invited talk)
2022
El-Husseini S., E. M. Hooks, Q. Beers, K.A. Sparks, O. J. Worley, M. M. Goebel, G. Michna, A. Ganguli, S. Rao, C. Stowell, B. Mohanty, P. D’Eustachio, P. Jaiswal, and S. Naithani (2022). ‘Biocuration of metabolic pathways and transcription factor networks involved in abiotic stress response in rice by undergraduate researchers for the Plant Reactome.’ presented in ASPB’s Plant Biology 2022 meeting, Portland, USA.
Naithani S.(2022). ‘Plant Reactome: Using OMICs data for biocuration of plant genes and pathways’, presented online in AgBioData consortium’s monthly webinar series.
Naithani S. (2022). ‘Plant Reactome resource for space biologists', presented online in NASA GeneLab’s Analysis Working Group 2022 Symposium.
2021
Naithani S. (2021). ‘Biocuration training for undergraduates: challenges and opportunities’ in the 2nd Session of the 14th Annual Biocuration Conference (virtual) organized by the International Society for Biocuration.
Tello-Ruiz M.K., S. Wei, A. Olson, K. Chougule, S. Kumari, V. Kumar, P. Gupta, S. Naithani, J. Elser, P. D’Eustachio, G. Naanamati, B. Contreras-Moreira, I. Papatheodorou, P. Jaiswal, and D. Ware (2021). ‘Gramene 2021: An online resource for Plant Reference Genomes, Pan-genomes and Plant Reactome Pathways’ in ASPB’s Plant Biology 2021 virtual meeting.
Tello-Ruiz M.K., S. Wei, A. Olson, K. Chougule, P. Gupta, S. Naithani, B. Wang, S. Kumari, V. Kumar, P. D’Eustachio, B. Contreras-Moreira, I. Papatheodorou, P. Jaiswal, and D. Ware (2021). ‘Mining Maize with Gramene’ in Maize Genetics Virtual Conference.