Citing Gramene
The Gramene database is freely available to its users for conducting comparative plant genomic and pathway analysis. Users can upload their data on both Genome Browser and on the Plant Reactome (https://plantreactome.gramene.org) pathway browser for analysis and visualization. Additional tools available at Gramene include CMap Viewer, Expression Atlas, and Gramene Mart.
When using Gramene or the information derived from Gramene databases, kindly acknowledge the Gramene project (http://www.gramene.org; date accessed and the database version). For information on linking directly to particular data items, see this document.
We appreciate if you cite the relevant references listed below:
Publications:
*Tello-Ruiz MK, Jaiswal P, Ware D. (2022). Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol. 2443:101-131. PMID: 35037202 doi: 10.1007/978-1-0716-2067-0_5.
* 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 DM, D'Eustachio P, Stein LD, Gupta A, Xu W, Regala J, Papatheodorou I, Kersey PJ, Flicek P, Taylor C, Jaiswal P, Ware D. (2021). Gramene 2021: Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res. 49(D1):D1452-D1463. PMID: 33170273, doi:10.1093/nar/gkaa979. Free PDF.
* 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. (2018). Gramene 2018: unifying comparative genomics and pathway resources for plant research. Nucleic Acids Res. 46(D1):D1181-D1189. PMID: 29165610, doi: 10.1093/nar/gkx1111. Free PDF.
* 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. (2016). Gramene Database: Navigating Plant Comparative Genomics Resources. Curr Plant Biol. 7-8:10-15. PMID: 28713666, doi: 10.1016/j.cpb.2016.12.005. Free PDF
* 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). Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Res. 44(D1):D1133-40. PMID: 26553803, doi: 10.1093/nar/gkv1179. Free PDF
* Tello-Ruiz MK, Stein J, Wei S, Youens-Clark K, Jaiswal P, Ware D (2016). Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Plant Bioinformatics: Methods Mol Biol. 1374:141-63. PMID: 26519404, doi: 10.1007/978-1-4939-3167-5_7.
* 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). Gramene 2013: comparative plant genomics resources. Nucleic Acids Res. 42 (D1): D1193-D1199. PMID: 24217918, doi: 10.1093/nar/gkt1110, Free PDF
* Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D (2011). Gramene database in 2010: updates and extensions. Nucleic Acids Research 39: D1085-94. PMID: 21076153, doi: 10.1093/nar/gkq1148, Free PDF
* Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L (2008). Gramene: a growing plant comparative genomics resource. Nucleic Acids Research 36 :D947-53. PMID: 17984077, Free PDF
* Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006). Gramene: a bird's eye view of cereal genomes. Nucleic Acids Research 34: D717-723, PMID: 16381966, doi: 10.1093/nar/gkj154 Free PDF
* Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L (2002). Gramene: a resource for comparative grass genomics. Nucleic Acids Research, 30, 103-105. PMID: 11752266, Free PDF
* Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR (2002). Gramene, a tool for grass genomics. Plant Physiology 130: 1606-1613. PMID: 12481044, doi:10.1104/pp.015248, Free PDF
*Gupta P, Naithani S, Preece J, Kim S, Cheng T, D'Eustachio P, Elser J, Bolton EE, Jaiswal P. (2022). Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. Methods Mol Biol. 2022;2443:511-525. doi: 10.1007/978-1-0716-2067-0_27. PMID: 35037224
* Naithani S, Gupta P, Preece J, D'Eustachio P, Elser J, Kiff J, Garg P, Dikeman DA, Olson AJ, Wei S, Tello-Ruiz MK, Cook J, Fabregat A, Cheng T, Bolton E, Muñoz-Pomer AF, Mohammed S, Papatheodorou I, Stein L, Ware D, and Jaiswal P (2020). Plant Reactome: A knowledgebase and resource for comparative pathway analysis. Nucleic Acids Res. 48(D1): D1093-D1103, PMID: 31680153, doi: 10.1093/nar/gkz996. Free PDF
* 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). Plant Reactome: a resource for plant pathways and comparative analysis. Nucleic Acids Res. PMID: 27799469, doi: 10.1093/nar/gkw932, Free PDF
* Naithani S, Jaiswal P. (2017). Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study. Methods Mol Biol. 1533:241-256. PMID: 27987175, doi: 10.1007/978-1-4939-6658-5_14.
* Dharmawardhana P, Ren L, Amarasinghe V, Monaco M,Thomason J, Ravenscroft D, McCouch S, Ware D, Jaiswal P (2013). A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice 6:1-15. PMID: 24280345, Free PDF
* Monaco MK, Sen TZ, Dharmawardhana PD, Ren L, Schaeffer M, Naithani S, Amarasinghe V, Thomason J, Harper L, Gardiner J, Cannon EKS, Lawrence CJ, Ware D, and Jaiswal P (2012). Maize metabolic network construction and transcriptome analysis. The Plant Genome 6:1-12., Free PDF
* Arnaud E, Laporte MA, Kim S, Aubert C, Leonelli S, Miro B, Cooper L, Jaiswal P, Kruseman G, Shrestha R, Buttigieg PL, Mungall CJ, Pietragalla J, Agbona A, Muliro J, Detras J, Hualla V, Rathore A, Das RR, 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 ED, Mueller LA, Silverstein K, Lafargue A, Antezana E, Devare M, King B. (2020). The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. Patterns (N Y), 1(7):100105. PMID: 33205138, doi: 10.1016/j.patter.2020.100105. Free PDF
* Avraham S, Tung CW, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Zapata F, Ware D (2008). The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res. 36(Database issue):D449-54. PMID: 18194960, doi: 10.1093/nar/gkm908. Free PDF
* Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, Rhee SY (2007). The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol. Feb;143(2):587-99. PMID: 17142475, doi: 10.1104/pp.106.092825. Free PDF
* Jaiswal P, Avraham S, Ilic K, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, Schaeffer M, Stein L, Stevens P, Vincent L, Ware D, Zapata F (2005). Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages. Comp Funct Genomics 2005;6(7-8):388-97. PMID: 18629207, doi: 10.1002/cfg.496. Free PDF
* Jaiswal P, Ware D, Ni J, Chang K, Zhao W, Schmidt S, Pan X, Clark K, Teytelman L, Cartinhour S, Stein L, McCouch S (2002). Gramene: development and integration of trait and gene ontologies for rice. Comparative and Functional Genomics 3: 132-136. (Gramene Reference ID 6902) PMID: 18628886, doi: 10.1002/cfg.156 Free PDF
* Yamazaki Y, Jaiswal P (2005) Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase. Plant Cell Physiol 46: 63-68. (Gramene Reference ID 9505), PMID: 15659431, doi: 10.1093/pcp/pci505, Free PDF
Citing Gene Expression at Gramene:
*Moreno P, Fexova S, George N, Manning JR, Miao Z, Mohammed S, Muñoz-Pomer A, Fullgrabe A, Bi Y, Bush N, Iqbal H, Kumbham U, Solovyev A, Zhao L, Prakash A, García-Seisdedos D, Kundu DJ, Wang S, Walzer M, Clarke L, Osumi-Sutherland D, Tello-Ruiz MK, Kumari S, Ware D, Eliasova J, Arends MJ, Nawijn MC, Meyer K, Burdett T, Marioni J, Teichmann S, Vizcaíno JA, Brazma A, Papatheodorou I. (2022). Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Res. 50(D1):D129-D140. PMID: 34850121, doi: 10.1093/nar/gkab1030, Free PDF
* Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R. (2018). Expression Atlas: gene and protein expression across multiple studies and organisms. Nucleic Acids Res. 46(D1):D246-D251. PMID: 29165655, doi: 10.1093/nar/gkx1158, Free PDF
* Petryszak R, Keays M, Tang YA, Fonseca NA, Barrera E, Burdett T, Füllgrabe A, Muñoz-Pomer Fuentes A, 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 and Brazma A (2016). Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants. Nucleic Acids Res. 2016 Jan 4;44(D1):D746-52. doi: 10.1093/nar/gkv1045. PMID: 26481351, Free PDF
* 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. 2021 Mar 15;9:e11052. PMID: 33777532, doi: 10.7717/peerj.11052, Free PDF
* Tello-Ruiz MK, Marco CF, Hsu FM, Khangura RS, Qiao P, Sapkota S, Stitzer MC, Wasikowski R, Wu H, Zhan J, Chougule K, Barone LC, Ghiban C, Muna D, Olson AC, Wang L, Ware D, Micklos DA (2019). Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS One. 14(10):e0224086, PMID: 31658277, doi: 10.1371/journal.pone.0224086, Free PDF
* Naithani S, Gupta P, Preece J, Garg P, Fraser V, Padgitt-Cobb LK, Martin M, Vining K, Jaiswal P. (2019). Involving community in genes and pathway curation. Database (Oxford). Jan 1;2019:bay146. PMID: 30649295, doi: 10.1093/database/bay146, Free PDF
* Naithani S, Geniza M, Jaiswal P. (2017). Variant Effect Prediction Analysis Using Resources Available at Gramene Database. Methods Mol Biol. 1533:279-297. PMID: 27987178, doi: 10.1007/978-1-4939-6658-5_17.
* Naithani S, Partipilo CM, Raja R, Elser JL, Jaiswal P (2016). FragariaCyc: A Metabolic Pathway Database for Woodland Strawberry Fragaria vesca. Front Plant Sci. 7:242. PMID: 26973684, doi: 10.3389/fpls.2016.00242. Free PDF
* Naithani S, Raja R, Waddell EN, Elser J, Gouthu S, Deluc LG, Jaiswal P (2014). VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera). Front Plant Sci. 5:644. PMID: 25538713, doi: 10.3389/fpls.2014.00644. Free PDF
* Gramene: A Genomics and Genetics Resources for Maize. Maize Genetics Cooperation Newsletter, Volume 80, 2006.
(Full article or PDF Newsletter), pp 99-107]
* Gramene: A genomics and genetics resource for rice. [http://www.shigen.nig.ac.jp/rice/rgn/vol22/v01.html] Rice Genetics Newsletter, 2005, Vol. 22, No. 1. 9-16.
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