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Found 23 results
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Ware, Doreen
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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.
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.
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
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.
2018
L. Harper
,
Campbell, J.
,
Cannon, E. K. S.
,
Jung, S.
,
Poelchau, M.
,
Walls, R.
,
Andorf, C.
,
Arnaud, E.
,
Berardini, T. Z.
,
Birkett, C.
,
Cannon, S.
,
Carson, J.
,
Condon, B.
,
Cooper, L.
,
Dunn, N.
,
Elsik, C. G.
,
Farmer, A.
,
Ficklin, S. P.
,
Grant, D.
,
Grau, E.
,
Herndon, N.
,
Hu, Z. - L.
,
Humann, J.
,
Jaiswal, P.
,
Jonquet, C.
,
Laporte, M. - A.
,
Larmande, P.
,
Lazo, G.
,
McCarthy, F.
,
Menda, N.
,
Mungall, C. J.
,
Munoz-Torres, M. C.
,
Naithani, S.
,
Nelson, R.
,
Nesdill, D.
,
Park, C.
,
Reecy, J.
,
Reiser, L.
,
Sanderson, L. - A.
,
Sen, T. Z.
,
Staton, M.
,
Subramaniam, S.
,
Tello-Ruiz, M. K.
,
Unda, V.
,
Unni, D.
,
Wang, L.
,
Ware, D.
,
Wegrzyn, J.
,
Williams, J.
,
Woodhouse, M.
,
Yu, J.
, and
Main, D.
,
“
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.
”
,
Database : the journal of biological databases and curation
, vol. 2018, 2018.
M. K. Tello-Ruiz
,
Naithani, S.
,
Stein, J. C.
,
Gupta, P.
,
Campbell, M.
,
Olson, A.
,
Wei, S.
,
Preece, J.
,
Geniza, M. J.
,
Jiao, Y.
,
Lee, Y. K.
,
Wang, B.
,
Mulvaney, J.
,
Chougule, K.
,
Elser, J.
,
Al-Bader, N.
,
Kumari, S.
,
Thomason, J.
,
Kumar, V.
,
Bolser, D. M.
,
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, L. D.
,
Petryszak, R.
,
Papatheodorou, I.
,
Kersey, P. J.
,
Lockhart, P.
,
Taylor, C.
,
Jaiswal, P.
, and
Ware, D.
,
“
Gramene 2018: unifying comparative genomics and pathway resources for plant research.
”
,
Nucleic acids research
, vol. 46, no. D1, pp. D1181-D1189, 2018.
S. Naithani
,
Preece, J.
,
D'Eustachio, P.
,
Gupta, P.
,
Amarasinghe, V.
,
Dharmawardhana, P. D.
,
Wu, G.
,
Fabregat, A.
,
Elser, J. L.
,
Weiser, J.
,
Keays, M.
,
Munoz-Pomer Fuentes, A.
,
Petryszak, R.
,
Stein, L. D.
,
Ware, D.
, and
Jaiswal, P.
,
“
Plant Reactome: a resource for plant pathways and comparative analysis.
”
,
Nucleic acids research
, vol. 45, no. D1, pp. D1029-D1039, 2018.
2016
M. K. Tello-Ruiz
,
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, D. M.
,
Kerhornou, A.
,
Walts, B.
,
Fonseca, N. A.
,
Huerta, L.
,
Keays, M.
,
Tang, A. Y.
,
Parkinson, H.
,
Fabregat, A.
,
McKay, S.
,
Weiser, J.
,
D'Eustachio, P.
,
Stein, L.
,
Petryszak, R.
,
Kersey, P. J.
,
Jaiswal, P.
, and
Ware, D.
,
“
Gramene 2016: comparative plant genomics and pathway resources.
”
,
Nucleic acids research
, vol. 44, no. D1, pp. D1133-40, 2016.
M. K. Tello-Ruiz
,
Stein, J.
,
Wei, S.
,
Youens-Clark, K.
,
Jaiswal, P.
, and
Ware, D.
,
“
Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.
”
, in
Methods in molecular biology (Clifton, N.J.)
, vol. 1374, 2016, pp. 141-63.
P. Gupta
,
Naithani, S.
,
Tello-Ruiz, M. K.
,
Chougule, K.
,
D'Eustachio, P.
,
Fabregat, A.
,
Jiao, Y.
,
Keays, M.
,
Lee, Y. K.
,
Kumari, S.
,
Mulvaney, J.
,
Olson, A.
,
Preece, J.
,
Stein, J.
,
Wei, S.
,
Weiser, J.
,
Huerta, L.
,
Petryszak, R.
,
Kersey, P.
,
Stein, L. D.
,
Ware, D.
, and
Jaiswal, P.
,
“
Gramene Database: Navigating Plant Comparative Genomics Resources.
”
,
Current plant biology
, vol. 7-8, pp. 10-15, 2016.
2014
M. K. Monaco
,
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, P. J.
,
Stein, L.
,
Jaiswal, P.
, and
Ware, D.
,
“
Gramene 2013: comparative plant genomics resources.
”
,
Nucleic acids research
, vol. 42, no. Database issue, pp. D1193-9, 2014.
2013
P. Dharmawardhana
,
Ren, L.
,
Amarasinghe, V.
,
Monaco, M.
,
Thomason, J.
,
Ravenscroft, D.
,
McCouch, S.
,
Ware, D.
, and
Jaiswal, P.
,
“
A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress
”
,
Rice
, vol. 6, 2013.
M. K. Monaco
,
Sen, T. Z.
,
Dharmawardhana, P. D.
,
Ren, L.
,
Schaeffer, M.
,
Naithani, S.
,
Amarasinghe, V.
,
Thomason, J.
,
Harper, L.
,
Gardiner, J.
,
Cannon, E. K. S.
,
Lawrence, C. J.
,
Ware, D.
, and
Jaiswal, P.
,
“
Maize Metabolic Network Construction and Transcriptome Analysis
”
,
The Plant Genome
, vol. 6, no. 1, pp. 1-12, 2013.
2011
K. Youens-Clark
,
Buckler, E.
,
Casstevens, T.
,
Chen, C.
,
Declerck, G.
,
Derwent, P.
,
Dharmawardhana, P.
,
Jaiswal, P.
,
Kersey, P.
,
Karthikeyan, A. S.
,
Lu, J.
,
McCouch, S. R.
,
Ren, L.
,
Spooner, W.
,
Stein, J. C.
,
Thomason, J.
,
Wei, S.
, and
Ware, D.
,
“
Gramene database in 2010: updates and extensions.
”
,
Nucleic acids research
, vol. 39, no. Database issue, pp. D1085-94, 2011.
2009
J. Ni
,
Pujar, A.
,
Youens-Clark, K.
,
Yap, I.
,
Jaiswal, P.
,
Tecle, I.
,
Tung, C. - W.
,
Ren, L.
,
Spooner, W.
,
Wei, X.
,
Avraham, S.
,
Ware, D.
,
Stein, L.
, and
McCouch, S.
,
“
Gramene QTL database: development, content and applications.
”
,
Database : the journal of biological databases and curation
, vol. 2009, p. bap005, 2009.
2008
C. Liang
,
Jaiswal, P.
,
Hebbard, C.
,
Avraham, S.
,
Buckler, E. S.
,
Casstevens, T.
,
Hurwitz, B.
,
McCouch, S.
,
Ni, J.
,
Pujar, A.
,
Ravenscroft, D.
,
Ren, L.
,
Spooner, W.
,
Tecle, I.
,
Thomason, J.
,
Tung, C. - W.
,
Wei, X.
,
Yap, I.
,
Youens-Clark, K.
,
Ware, D.
, and
Stein, L.
,
“
Gramene: a growing plant comparative genomics resource.
”
,
Nucleic acids research
, vol. 36, no. Database issue, pp. D947-53, 2008.
S. Avraham
,
Tung, C. - W.
,
Ilic, K.
,
Jaiswal, P.
,
Kellogg, E. A.
,
McCouch, S.
,
Pujar, A.
,
Reiser, L.
,
Rhee, S. Y.
,
Sachs, M. M.
,
Schaeffer, M.
,
Stein, L.
,
Stevens, P.
,
Vincent, L.
,
Zapata, F.
, and
Ware, D.
,
“
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.
”
,
Nucleic acids research
, vol. 36, no. Database issue, pp. D449-54, 2008.
2006
P. Jaiswal
,
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, T. M.
,
Buckler, E. S.
,
Stein, L.
, and
McCouch, S.
,
“
Gramene: a bird's eye view of cereal genomes.
”
,
Nucleic acids research
, vol. 34, no. Database issue, pp. D717-23, 2006.
A. Pujar
,
Jaiswal, P.
,
Kellogg, E. A.
,
Ilic, K.
,
Vincent, L.
,
Avraham, S.
,
Stevens, P.
,
Zapata, F.
,
Reiser, L.
,
Rhee, S. Y.
,
Sachs, M. M.
,
Schaeffer, M.
,
Stein, L.
,
Ware, D.
, and
McCouch, S.
,
“
Whole-plant growth stage ontology for angiosperms and its application in plant biology.
”
,
Plant physiology
, vol. 142, no. 2, pp. 414-28, 2006.
2005
P. Jaiswal
,
Avraham, S.
,
Ilic, K.
,
Kellogg, E. A.
,
McCouch, S.
,
Pujar, A.
,
Reiser, L.
,
Rhee, S. Y.
,
Sachs, M. M.
,
Schaeffer, M.
,
Stein, L.
,
Stevens, P.
,
Vincent, L.
,
Ware, D.
, and
Zapata, F.
,
“
Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages.
”
,
Comparative and functional genomics
, vol. 6, no. 7-8, pp. 388-97, 2005.
2002
D. Ware
,
Jaiswal, P.
,
Ni, J.
,
Pan, X.
,
Chang, K.
,
Clark, K.
,
Teytelman, L.
,
Schmidt, S.
,
Zhao, W.
,
Cartinhour, S.
,
McCouch, S.
, and
Stein, L.
,
“
Gramene: a resource for comparative grass genomics.
”
,
Nucleic acids research
, vol. 30, no. 1, pp. 103-5, 2002.
P. Jaiswal
,
Ware, D.
,
Ni, J.
,
Chang, K.
,
Zhao, W.
,
Schmidt, S.
,
Pan, X.
,
Clark, K.
,
Teytelman, L.
,
Cartinhour, S.
,
Stein, L.
, and
McCouch, S.
,
“
Gramene: development and integration of trait and gene ontologies for rice.
”
,
Comparative and functional genomics
, vol. 3, no. 2, pp. 132-6, 2002.
Major Grants
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