Citing Gramene

The Gramene database is freely available for download and use as long as Gramene is cited as the source. This includes the tools available at Gramene including but not limited to RiceCyc, CMap Viewer, Gramene Mart and the Genome Browser. When using Gramene or the information derived from Gramene databases, kindly acknowledge the Gramene project by citing the web address (http://www.gramene.org) and identifying the version of Gramene being used (identified on the Home page) and the date accessed.
 
For information on linking directly to particular data items, see this document.

Publications:

Citing the Gramene Project:

When citing the Gramene project for other purposes, please refer to any one of the following papers:

* 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. 2016 Jan 4;44(D1):D1133-40. PMID: 26553803. doi: 10.1093/nar/gkv1179.

* 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. Methods Mol Biol. 2016;1374:141-63. PMID: 26519404. doi: 10.1007/978-1-4939-3167-5_7.

* 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. In press in Current Plant Biology. Available online 14 December 2016. doi: 10.1016/j.cpb.2016.12.005

* 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.

* 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

* 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.

* 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.

* 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.

*  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.

 

Citing Pathways at Gramene:

* 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 (2016) Plant Reactome: a resource for plant pathways and comparative analysis. Nucleic Acids Res. 2016 Oct 30. PMID: 27799469. doi: 10.1093/nar/gkw932.

* 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.

* 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.

 

Citing Ontologies at Gramene:

* 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)

* 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. Epub 2005 Jan 2019. (Gramene Reference ID 9505)

Citing Gene Expression at Gramene:

* 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. Abstract. PMID: 26481351

 

Other Publications

* 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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