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Jaiswal, Pankaj
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K. E. Bushley
,
Raja, R.
,
Jaiswal, P.
,
Cumbie, J. S.
,
Nonogaki, M.
,
Boyd, A. E.
,
C Owensby, A.
,
Knaus, B. J.
,
Elser, J.
,
Miller, D.
,
Di, Y.
,
McPhail, K. L.
, and
Spatafora, J. W.
,
“
The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster
”
,
PLOS Genetics
, vol. 9, 2013.
V. Shulaev
,
Sargent, D. J.
,
Crowhurst, R. N.
,
Mockler, T. C.
,
Folkerts, O.
,
Delcher, A. L.
,
Jaiswal, P.
,
Mockaitis, K.
,
Liston, A.
,
Mane, S. P.
,
Burns, P.
,
Davis, T. M.
,
Slovin, J. P.
,
Bassil, N.
,
Hellens, R. P.
,
Evans, C.
,
Harkins, T.
,
Kodira, C.
,
Desany, B.
,
Crasta, O. R.
,
Jensen, R. V.
,
Allan, A. C.
,
Michael, T. P.
,
Setubal, J. Carlos
,
Celton, J. - M.
,
D Rees, J. G.
,
Williams, K. P.
,
Holt, S. H.
,
Rojas, J. Jairo Ruiz
,
Chatterjee, M.
,
Liu, B.
,
Silva, H.
,
Meisel, L.
,
Adato, A.
,
Filichkin, S. A.
,
Troggio, M.
,
Viola, R.
,
Ashman, T. - L.
,
Wang, H.
,
Dharmawardhana, P.
,
Elser, J.
,
Raja, R.
,
Priest, H. D.
,
Bryant, D. W.
,
Fox, S. E.
,
Givan, S. A.
,
Wilhelm, L. J.
,
Naithani, S.
,
Christoffels, A.
,
Salama, D. Y.
,
Carter, J.
,
Girona, E. Lopez
,
Zdepski, A.
,
Wang, W.
,
Kerstetter, R. A.
,
Schwab, W.
,
Korban, S. S.
,
Davik, J.
,
Monfort, A.
,
Denoyes-Rothan, B.
,
Arus, P.
,
Mittler, R.
,
Flinn, B.
,
Aharoni, A.
,
Bennetzen, J. L.
,
Salzberg, S. L.
,
Dickerman, A. W.
,
Velasco, R.
,
Borodovsky, M.
,
Veilleux, R. E.
, and
Folta, K. M.
,
“
The genome of woodland strawberry(Fragaria vesca).
”
,
Nature genetics
, vol. 43, pp. 109-16, 2011.
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
,
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, pp. D1193-9, 2014.
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.
,
Y Tang, A.
,
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, pp. D1133-40, 2016.
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. Koung
,
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.
,
Fuentes, A. Munoz- Pome
,
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, pp. D1181-D1189, 2018.
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, pp. D717-23, 2006.
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, pp. D947-53, 2008.
M. Karey 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.
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, pp. 103-5, 2002.
D. H. Ware
,
Jaiswal, P.
,
Ni, J.
,
Yap, I. V.
,
Pan, X.
,
Clark, K. Y.
,
Teytelman, L.
,
Schmidt, S. C.
,
Zhao, W.
,
Chang, K.
,
Cartinhour, S.
,
Stein, L. D.
, and
McCouch, S. R.
,
“
Gramene, a tool for grass genomics.
”
,
Plant physiology
, vol. 130, pp. 1606-13, 2002.
P. Jaiswal
,
“
Gramene database: a hub for comparative plant genomics.
”
,
Methods in molecular biology (Clifton, N.J.)
, vol. 678, pp. 247-75, 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, pp. D1085-94, 2011.
P. Gupta
,
Naithani, S.
,
Tello-Ruiz, M. Karey
,
Chougule, K.
,
D’Eustachio, P.
,
Fabregat, A.
,
Jiao, Y.
,
Keays, M.
,
Lee, Y. Koung
,
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.
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, pp. 132-6, 2002.
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.
I
B. Qu
,
Kumar, P.
,
Zhang, E.
,
Jaiswal, P.
,
Cooper, L.
,
Elser, J.
, and
Zhang, Y.
,
“
Interactive Design and Visualization of N-ary Relationships
”
, in
SIGGRAPH Asia 2017 Symposium on Visualization
, New York, NY, USA, 2017.
J. Azevedo
,
Courtois, F.
,
Hakimi, M. - A.
,
Demarsy, E.
,
Lagrange, T.
,
Alcaraz, J. - P.
,
Jaiswal, P.
,
Maréchal-Drouard, L.
, and
Lerbs-Mache, S.
,
“
Intraplastidial trafficking of a phage-type RNA polymerase is mediated by a thylakoid RING-H2 protein.
”
,
Proceedings of the National Academy of Sciences of the United States of America
, vol. 105, pp. 9123-8, 2008.
S. Naithani
,
Gupta, P.
,
Preece, J.
,
Garg, P.
,
Fraser, V.
,
Padgitt-Cobb, L. K.
,
Martin, M.
,
Vining, K.
, and
Jaiswal, P.
,
“
Involving community in genes and pathway curation.
”
,
Database : the journal of biological databases and curation
, vol. 2019, 2019.
M
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, pp. 1-12, 2013.
N
T. A. Beardslee
,
Roy-Chowdhury, S.
,
Jaiswal, P.
,
Buhot, L.
,
Lerbs-Mache, S.
,
Stern, D. B.
, and
Allison, L. A.
,
“
A nucleus-encoded maize protein with sigma factor activity accumulates in mitochondria and chloroplasts.
”
,
The Plant journal : for cell and molecular biology
, vol. 31, pp. 199-209, 2002.
O
R. L. Walls
,
Athreya, B.
,
Cooper, L.
,
Elser, J.
,
Gandolfo, M. A.
,
Jaiswal, P.
,
Mungall, C. J.
,
Preece, J.
,
Rensing, S.
,
Smith, B.
, and
Stevenson, D. W.
,
“
Ontologies as integrative tools for plant science.
”
,
American journal of botany
, vol. 99, pp. 1-13, 2012.
A. Oellrich
,
Walls, R. L.
,
Cannon, E. K. S.
,
Cannon, S. B.
,
Cooper, L.
,
Gardiner, J.
,
Gkoutos, G. V.
,
Harper, L.
,
He, M.
,
Hoehndorf, R.
,
Jaiswal, P.
,
Kalberer, S. R.
,
Lloyd, J. P.
,
Meinke, D.
,
Menda, N.
,
Moore, L.
,
Nelson, R. T.
,
Pujar, A.
,
Lawrence, C. J.
, and
Huala, E.
,
“
An ontology approach to comparative phenomics in plants.
”
,
Plant methods
, vol. 11, p. 10, 2015.
P
S. Naithani
and
Jaiswal, P.
,
“
Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study.
”
,
Methods in molecular biology (Clifton, N.J.)
, vol. 1533, pp. 241-256, 2017.
L. Cooper
and
Jaiswal, P.
,
“
The Plant Ontology: A Tool for Plant Genomics.
”
, in
Methods in molecular biology (Clifton, N.J.)
, vol. 1374, 2016, pp. 89-114.
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