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Jaiswal, Pankaj
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A. R. Deans
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Lewis, S. E.
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Huala, E.
,
Anzaldo, S. S.
,
Ashburner, M.
,
Balhoff, J. P.
,
Blackburn, D. C.
,
Blake, J. A.
,
J. Burleigh, G.
,
Chanet, B.
,
Cooper, L. D.
,
Courtot, M.
,
Csösz, S.
,
Cui, H.
,
Dahdul, W.
,
Das, S.
,
T. Dececchi, A.
,
Dettai, A.
,
Diogo, R.
,
Druzinsky, R. E.
,
Dumontier, M.
,
Franz, N. M.
,
Friedrich, F.
,
Gkoutos, G. V.
,
Haendel, M.
,
Harmon, L. J.
,
Hayamizu, T. F.
,
He, Y.
,
Hines, H. M.
,
Ibrahim, N.
,
Jackson, L. M.
,
Jaiswal, P.
,
James-Zorn, C.
,
Köhler, S.
,
Lecointre, G.
,
Lapp, H.
,
Lawrence, C. J.
,
Le Novère, N.
,
Lundberg, J. G.
,
Macklin, J.
,
Mast, A. R.
,
Midford, P. E.
,
Mikó, I.
,
Mungall, C. J.
,
Oellrich, A.
,
Osumi-Sutherland, D.
,
Parkinson, H.
,
Ramírez, M. J.
,
Richter, S.
,
Robinson, P. N.
,
Ruttenberg, A.
,
Schulz, K. S.
,
Segerdell, E.
,
Seltmann, K. C.
,
Sharkey, M. J.
,
Smith, A. D.
,
Smith, B.
,
Specht, C. D.
,
R. Squires, B.
,
Thacker, R. W.
,
Thessen, A.
,
Fernandez-Triana, J.
,
Vihinen, M.
,
Vize, P. D.
,
Vogt, L.
,
Wall, C. E.
,
Walls, R. L.
,
Westerfeld, M.
,
Wharton, R. A.
,
Wirkner, C. S.
,
Woolley, J. B.
,
Yoder, M. J.
,
Zorn, A. M.
, and
Mabee, P.
,
“
Finding Our Way through Phenotypes
”
,
PLoS Biol
, vol. 13, p. e1002033, 2015.
E
F. Lens
,
Cooper, L.
,
Gandolfo, M. Alejandra
,
Groover, A.
,
Jaiswal, P.
,
Lachenbruch, B.
,
Spicer, R.
,
Staton, M. E.
,
Stevenson, D. W.
,
Walls, R. L.
, and
Wegrzyn, J.
,
“
An extension of the Plant Ontology project supporting wood anatomy and development research
”
,
IAWA Journal
, vol. 33, p. 5, 2012.
V. V. Peremyslov
,
Mockler, T. C.
,
Filichkin, S. A.
,
Fox, S. E.
,
Jaiswal, P.
,
Makarova, K. S.
,
Koonin, E. V.
, and
Dolja, V. V.
,
“
Expression, splicing, and evolution of the myosin gene family in plants.
”
,
Plant physiology
, vol. 155, pp. 1191-204, 2011.
R. Petryszak
,
Keays, M.
,
Y Tang, A.
,
Fonseca, N. A.
,
Barrera, E.
,
Burdett, T.
,
Füllgrabe, A.
,
Fuentes, A. Muñoz- Pom
,
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, H. E.
, and
Brazma, A.
,
“
Expression Atlas update-an integrated database of gene and protein expression in humans, animals and plants.
”
,
Nucleic acids research
, vol. 44, pp. D746-52, 2016.
I. Papatheodorou
,
Fonseca, N. A.
,
Keays, M.
,
Y Tang, A.
,
Barrera, E.
,
Bazant, W.
,
Burke, M.
,
Füllgrabe, A.
,
Fuentes, A. Muñoz- Pom
,
George, N.
,
Huerta, L.
,
Koskinen, S.
,
Mohammed, S.
,
Geniza, M.
,
Preece, J.
,
Jaiswal, P.
,
Jarnuczak, A. F.
,
Huber, W.
,
Stegle, O.
,
Vizcaino, J. Antonio
,
Brazma, A.
, and
Petryszak, R.
,
“
Expression Atlas: gene and protein expression across multiple studies and organisms.
”
,
Nucleic acids research
, vol. 46, pp. D246-D251, 2018.
S. A. Filichkin
,
Cumbie, J. S.
,
Dharmawardhana, P.
,
Jaiswal, P.
,
Chang, J. H.
,
Palusa, S. G.
,
Reddy, A. S. N.
,
Megraw, M.
, and
Mockler, T. C.
,
“
Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis.
”
,
Molecular plant
, vol. 8, pp. 207-27, 2015.
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.
A. E. Thessen
,
Bunker, D. E.
,
Buttigieg, P. Luigi
,
Cooper, L. D.
,
Dahdul, W. M.
,
Domisch, S.
,
Franz, N. M.
,
Jaiswal, P.
,
Lawrence-Dill, C. J.
,
Midford, P. E.
,
Mungall, C. J.
,
Ramírez, M. J.
,
Specht, C. D.
,
Vogt, L.
,
Vos, R. Aldo
,
Walls, R. L.
,
White, J. W.
,
Zhang, G.
,
Deans, A. R.
,
Huala, E.
,
Lewis, S. E.
, and
Mabee, P. M.
,
“
Emerging semantics to link phenotype and environment.
”
,
PeerJ
, vol. 3, p. e1470, 2015.
D
A. C Quandt
,
Di, Y.
,
Elser, J.
,
Jaiswal, P.
, and
Spatafora, J. W.
,
“
Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides.
”
,
G3 (Bethesda, Md.)
, 2016.
A. C Quandt
,
Di, Y.
,
Elser, J.
,
Jaiswal, P.
, and
Spatafora, J. W.
,
“
Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides.
”
,
G3 (Bethesda, Md.)
, 2016.
A. C Quandt
,
Di, Y.
,
Elser, J.
,
Jaiswal, P.
, and
Spatafora, J. W.
,
“
Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides.
”
,
G3 (Bethesda, Md.)
, vol. 6, pp. 731-41, 2016.
S. E. Fox
,
Geniza, M.
,
Hanumappa, M.
,
Naithani, S.
,
Sullivan, C. M.
,
Preece, J.
,
Tiwari, V. I. K.
,
Elser, J.
,
Leonard, J. M.
,
Sage, A.
,
Gresham, C.
,
Kerhornou, A.
,
Bolser, D.
,
McCarthy, F.
,
Kersey, P.
,
Lazo, G. R.
, and
Jaiswal, P.
,
“
De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum.
”
,
PLoS ONE
, vol. 9, 2014.
P. Garg
and
Jaiswal, P.
,
“
Databases and bioinformatics tools for rice research
”
,
Current Plant Biology
, vol. 7-8, pp. 39 - 52, 2016.
C
S. Schaeffer
,
Harper, A.
,
Raja, R.
,
Jaiswal, P.
, and
Dhingra, A.
,
“
Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes.
”
,
PloS one
, vol. 9, p. e112870, 2014.
B
Y. Yamazaki
and
Jaiswal, P.
,
“
Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase.
”
,
Plant & cell physiology
, vol. 46, pp. 63-8, 2005.
A
N. Lingutla
,
Preece, J.
,
Todorovic, S.
,
Cooper, L.
,
Moore, L.
, and
Jaiswal, P.
,
“
AISO: Annotation of Image Segments with Ontologies
”
,
Journal of Biomedical Semantics
, vol. 5, p. 50, 2014.
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. Karey
,
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.
S. A. Filichkin
,
Hamilton, M.
,
Dharmawardhana, P. D.
,
Singh, S. K.
,
Sullivan, C.
,
Ben-Hur, A.
,
Reddy, A. S. N.
, and
Jaiswal, P.
,
“
Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching.
”
,
Frontiers in plant science
, vol. 9, p. 5, 2018.
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