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Found 20 results
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Elser, Justin
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2023
S. Naithani
,
Mohanty, B.
,
Elser, J.
,
D’Eustachio, P.
, and
Jaiswal, P.
,
“
Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)
”
,
Plants
, vol. 12, p. 2146, 2023.
A. E. Thessen
,
Jaiswal, P.
,
Cooper, L.
,
Swetnam, T. L.
,
Hegde, H.
,
Resse, J.
, and
Elser, J.
,
“
Using knowledge graphs to infer gene expression in plants
”
. 2023.
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.
P. Gupta
,
Naithani, S.
,
Preece, J.
,
Kim, S.
,
Cheng, T.
,
D'Eustachio, P.
,
Elser, J.
,
Bolton, E. E.
, and
Jaiswal, P.
,
“
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases.
”
,
Methods Mol Biol
, vol. 2443, pp. 511-525, 2022.
2021
L. K. Padgitt-Cobb
,
Kingan, S. B.
,
Wells, J.
,
Elser, J.
,
Kronmiller, B.
,
Moore, D.
,
Concepcion, G.
,
Peluso, P.
,
Rank, D.
,
Jaiswal, P.
,
Henning, J.
, and
Hendrix, D. A.
,
“
A draft phased assembly of the diploid Cascade hop (Humulus lupulus) genome.
”
,
Plant Genome
, vol. 14, no. 1, p. e20072, 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.
2019
R. L. Walls
,
Cooper, L.
,
Elser, J.
,
Gandolfo, M. A.
,
Mungall, C. J.
,
Smith, B.
,
Stevenson, D. W.
, and
Jaiswal, P.
,
“
The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.
”
,
Frontiers in plant science
, vol. 10, p. 631, 2019.
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.
2017
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, pp. 15:1–15:8.
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, no. 3, pp. 731-41, 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.
2014
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, no. 5, 2014.
A. A. Myburg
,
Grattapaglia, D.
,
Tuskan, G. A.
,
Hellsten, U.
,
Hayes, R. D.
,
Grimwood, J.
,
Jenkins, J.
,
Lindquist, E.
,
Tice, H.
,
Bauer, D.
,
Goodstein, D. M.
,
Dubchak, I.
,
Poliakov, A.
,
Mizrachi, E.
,
Kullan, A. R. K.
,
Hussey, S. G.
,
Pinard, D.
,
van der Merwe, K.
,
Singh, P.
,
van Jaarsveld, I.
,
Silva-Junior, O. B.
,
Togawa, R. C.
,
Pappas, M. R.
,
Faria, D. A.
,
Sansaloni, C. P.
,
Petroli, C. D.
,
Yang, X.
,
Ranjan, P.
,
Tschaplinski, T. J.
,
Ye, C. - Y.
,
Li, T.
,
Sterck, L.
,
Vanneste, K.
,
Murat, F.
,
Soler, M.
,
Clemente, H. S.
,
Saidi, N.
,
Cassan-Wang, H.
,
Dunand, C.
,
Hefer, C. A.
,
Bornberg-Bauer, E.
,
Kersting, A. R.
,
Vining, K.
,
Amarasinghe, V.
,
Ranik, M.
,
Naithani, S.
,
Elser, J.
,
Boyd, A. E.
,
Liston, A.
,
Spatafora, J. W.
,
Dharmwardhana, P.
,
Raja, R.
,
Sullivan, C.
,
Romanel, E.
,
Alves-Ferreira, M.
,
Külheim, C.
,
Foley, W.
,
Carocha, V.
,
Paiva, J.
,
Kudrna, D.
,
Brommonschenkel, S. H.
,
Pasquali, G.
,
Byrne, M.
,
Rigault, P.
,
Tibbits, J.
,
Spokevicius, A.
,
Jones, R. C.
,
Steane, D. A.
,
Vaillancourt, R. E.
,
Potts, B. M.
,
Joubert, F.
,
Barry, K.
,
Pappas, G. J.
,
Strauss, S. H.
,
Jaiswal, P.
,
Grima-Pettenati, J.
,
Salse, J.
,
Van de Peer, Y.
,
Rokhsar, D. S.
, and
Schmutz, J.
,
“
The genome of Eucalyptus grandis.
”
,
Nature
, vol. 510, no. 7505, pp. 356-62, 2014.
S. Naithani
,
Raja, R.
,
Waddell, E. N.
,
Elser, J.
,
Gouthu, S.
,
Deluc, L. G.
, and
Jaiswal, P.
,
“
VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera).
”
,
Frontiers in plant science
, vol. 5, p. 644, 2014.
2013
K. E. Bushley
,
Raja, R.
,
Jaiswal, P.
,
Cumbie, J. S.
,
Nonogaki, M.
,
Boyd, A. E.
,
Owensby, A. C.
,
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, no. 6, 2013.
M. Hanumappa
,
Preece, J.
,
Elser, J.
,
Nemeth, D.
,
Bono, G.
,
Wu, K.
, and
Jaiswal, P.
,
“
WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks
”
,
Rice
, vol. 6, 2013.
2012
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, no. 8, pp. 1-13, 2012.
L. Cooper
,
Walls, R. L.
,
Elser, J.
,
Gandolfo, M. A.
,
Stevenson, D. W.
,
Smith, B.
,
Preece, J.
,
Athreya, B.
,
Mungall, C. J.
,
Rensing, S.
,
Hiss, M.
,
Lang, D.
,
Reski, R.
,
Berardini, T. Z.
,
Li, D.
,
Huala, E.
,
Schaeffer, M.
,
Menda, N.
,
Arnaud, E.
,
Shrestha, R.
,
Yamazaki, Y.
, and
Jaiswal, P.
,
“
The Plant Ontology As A Tool For Comparative Plant Anatomy And Genomic Analyses.
”
,
Plant & Cell Physiology
, 2012.
2011
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. C.
,
Celton, J. - M.
,
Rees, J. D. G.
,
Williams, K. P.
,
Holt, S. H.
,
Ruiz Rojas, J. J.
,
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.
,
Lopez Girona, E.
,
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, no. 2, pp. 109-16, 2011.
Major Grants
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