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B
A. R. Borneman
,
Zeppel, R.
,
Chambers, P. J.
, and
Curtin, C. D.
,
“
Insights into the Dekkera bruxellensis genomic landscape: comparative genomics reveals variations in ploidy and nutrient utilisation potential amongst wine isolates.
”
,
PLoS Genet
, vol. 10, no. 2, p. e1004161, 2014.
C
C. D. Curtin
and
Pretorius, I. S.
,
“
Genomic insights into the evolution of industrial yeast species Brettanomyces bruxellensis.
”
,
FEMS Yeast Res
, vol. 14, no. 7, pp. 997-1005, 2014.
H
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.
J
P. Jaiswal
,
“
Gramene database: a hub for comparative plant genomics.
”
,
Methods in molecular biology (Clifton, N.J.)
, vol. 678, pp. 247-75, 2011.
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.
L
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.
J. J. Loor
,
Bionaz, M.
, and
Drackley, J. K.
,
“
Systems physiology in dairy cattle: nutritional genomics and beyond.
”
,
Annu Rev Anim Biosci
, vol. 1, pp. 365-92, 2013.
N
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.
,
Fuentes, A. Munoz- Pome
,
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, pp. D1029-D1039, 2018.
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.
S. Naithani
,
Geniza, M.
, and
Jaiswal, P.
,
“
Variant Effect Prediction Analysis Using Resources Available at Gramene Database.
”
,
Methods in molecular biology (Clifton, N.J.)
, vol. 1533, pp. 279-297, 2017.
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.
P
A. Planchart
,
Mattingly, C. J.
,
Allen, D.
,
Ceger, P.
,
Casey, W.
,
Hinton, D.
,
Kanungo, J.
,
Kullman, S. W.
,
Tal, T.
,
Bondesson, M.
,
Burgess, S. M.
,
Sullivan, C.
,
Kim, C.
,
Behl, M.
,
Padilla, S.
,
Reif, D. M.
,
Tanguay, R. L.
, and
Hamm, J.
,
“
Advancing toxicology research using in vivo high throughput toxicology with small fish models.
”
,
ALTEX
, vol. 33, no. 4, pp. 435-452, 2016.
S
S. Smita
,
Lenka, S. Keshari
,
Katiyar, A.
,
Jaiswal, P.
,
Preece, J.
, and
Bansal, K. Chander
,
“
QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice.
”
,
Database : the journal of biological databases and curation
, vol. 2011, p. bar037, 2011.
V
R. VanBuren
,
Bryant, D.
,
Bushakra, J. M.
,
Vining, K. J.
,
Edger, P. P.
,
Rowley, E. R.
,
Priest, H. D.
,
Michael, T. P.
,
Lyons, E.
,
Filichkin, S. A.
,
Dossett, M.
,
Finn, C. E.
,
Bassil, N. V.
, and
Mockler, T. C.
,
“
The genome of black raspberry (Rubus occidentalis).
”
,
Plant J
, vol. 87, no. 6, pp. 535-47, 2016.
W
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.
G. Winter
,
Cordente, A. G.
, and
Curtin, C. D.
,
“
Formation of hydrogen sulfide from cysteine in Saccharomyces cerevisiae BY4742: genome wide screen reveals a central role of the vacuole.
”
,
PLoS One
, vol. 9, no. 12, p. e113869, 2014.
Y
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.