-
1
-
-
78651327629
-
The Sol Genomics Network (solgenomics net): Growing tomatoes using Perl
-
doi: 10. 1093/nar/gkq866
-
Bombarely, A., N. Menda, I. Y. Tecle, R. M. Buels, S. Strickler, T. Fischer-York, A. Pujar, J. Leto, J. Gosselin, and L. A. Mueller. 2011. The Sol Genomics Network (solgenomics. net): Growing tomatoes using Perl. Nucleic Acids Res. 39: D1149-D1155. doi: 10. 1093/nar/gkq866.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Bombarely, A.1
Menda, N.2
Tecle, I.Y.3
Buels, R.M.4
Strickler, S.5
Fischer-York, T.6
Pujar, A.7
Leto, J.8
Gosselin, J.9
Mueller, L.A.10
-
2
-
-
84866976764
-
A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research
-
doi: 10. 1094/MPMI-06-12-0148-TA
-
Bombarely, A., H. G. Rosli, J. Vrebalov, P. Moffett, L. A. Mueller, and G. B. Martin. 2012. A draft genome sequence of Nicotiana benthamiana. to enhance molecular plant-microbe biology research. Mol. Plant Microbe Interact. 25: 1523-1530. doi: 10. 1094/MPMI-06-12-0148-TA.
-
(2012)
Mol. Plant Microbe Interact
, vol.25
, pp. 1523-1530
-
-
Bombarely, A.1
Rosli, H.G.2
Vrebalov, J.3
Moffett, P.4
Mueller, L.A.5
Martin, G.B.6
-
3
-
-
9144252016
-
The Gene Ontology Annotation (GOA) Database: Sharing knowledge in Uniprot with gene ontology
-
doi: 10. 1093/nar/gkh021
-
Camon, E., M. Magrane, D. Barrell, V. Lee, E. Dimmer, J. Maslen, D. Binns, N. Harte, R. Lopez, and R. Apweiler. 2004. The Gene Ontology Annotation (GOA) Database: Sharing knowledge in Uniprot with gene ontology. Nucleic Acids Res. 32: D262-D266. doi: 10. 1093/nar/gkh021.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Camon, E.1
Magrane, M.2
Barrell, D.3
Lee, V.4
Dimmer, E.5
Maslen, J.6
Binns, D.7
Harte, N.8
Lopez, R.9
Apweiler, R.10
-
4
-
-
43349107538
-
Using RepeatMasker to identify repetitive elements in genomic sequences
-
Unit 4. 10, doi: 10. 1002/0471250953. bi0410s05
-
Chen, N. 2004. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics Chapter 4: Unit 4. 10. doi: 10. 1002/0471250953. bi0410s05.
-
(2004)
Curr. Protoc. Bioinformatics Chapter
, vol.4
-
-
Chen, N.1
-
5
-
-
84864041933
-
The Biofuel Feedstock Genomics Resource: A web-based portal and database to enable functional genomics of plant biofuel feedstock species
-
doi: 10.2012.1093/database/bar061
-
Childs, K. L., K. Konganti, and C. R. Buell. 2012. The Biofuel Feedstock Genomics Resource: A web-based portal and database to enable functional genomics of plant biofuel feedstock species. Database (Oxford) 2012. doi: 10. 1093/database/bar061.
-
(2012)
Database (Oxford)
-
-
Childs, K.L.1
Konganti, K.2
Buell, C.R.3
-
6
-
-
40949130394
-
Marker-assisted selection: An approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B
-
doi: 10. 1098/rstb. 2007. 2170
-
Collard, B. C. Y., and D. J. Mackill. 2008. Marker-assisted selection: An approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B. Biological Sciences 363: 557-572. doi: 10. 1098/rstb. 2007. 2170.
-
(2008)
Biological Sciences
, vol.363
, pp. 557-572
-
-
Collard, B.C.Y.1
Mackill, D.J.2
-
7
-
-
73349102837
-
SolEST database: A "one-stop shop" approach to the study of Solanaceae transcriptomes
-
D'Agostino, N., A. Traini, L. Frusciante, and M. Chiusano. 2009. SolEST database: A "one-stop shop" approach to the study of Solanaceae transcriptomes. BMC Plant Biol. 9: 142.
-
(2009)
BMC Plant Biol
, vol.9
, pp. 142
-
-
D'Agostino, N.1
Traini, A.2
Frusciante, L.3
Chiusano, M.4
-
8
-
-
38549166729
-
PlantGDB: A resource for comparative plant genomics
-
doi: 10. 1093/nar/gkm1041
-
Duvick, J., A. Fu, U. Muppirala, M. Sabharwal, M. D. Wilkerson, C. J. Lawrence, C. Lushbough, and V. Brendel. 2008. PlantGDB: A resource for comparative plant genomics. Nucleic Acids Res. 36: D959-D965. doi: 10. 1093/nar/gkm1041.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Duvick, J.1
Fu, A.2
Muppirala, U.3
Sabharwal, M.4
Wilkerson, M.D.5
Lawrence, C.J.6
Lushbough, C.7
Brendel, V.8
-
9
-
-
84860442706
-
Integration of two diploid potato linkage maps with the potato genome sequence
-
doi: 10. 1371/journal. pone. 0036347
-
Felcher, K. J., J. J. Coombs, A. N. Massa, C. N. Hansey, J. P. Hamilton, R. E. Veilleux, C. R. Buell, and D. S. Douches. 2012. Integration of two diploid potato linkage maps with the potato genome sequence. PLoS ONE 7: E36347. doi: 10. 1371/journal. pone. 0036347.
-
(2012)
PLoS ONE
, vol.7
-
-
Felcher, K.J.1
Coombs, J.J.2
Massa, A.N.3
Hansey, C.N.4
Hamilton, J.P.5
Veilleux, R.E.6
Buell, C.R.7
Douches, D.S.8
-
10
-
-
84856585935
-
Phytozome: A comparative platform for green plant genomics
-
doi: 10. 1093/nar/gkr944
-
Goodstein, D. M., S. Shu, R. Howson, R. Neupane, R. D. Hayes, J. Fazo, T. Mitros, W. Dirks, U. Hellsten, N. Putnam, and D. S. Rokhsar. 2012. Phytozome: A comparative platform for green plant genomics. Nucleic Acids Res. 40: D1178-D1186. doi: 10. 1093/nar/gkr944.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Goodstein, D.M.1
Shu, S.2
Howson, R.3
Neupane, R.4
Hayes, R.D.5
Fazo, J.6
Mitros, T.7
Dirks, W.8
Hellsten, U.9
Putnam, N.10
Rokhsar, D.S.11
-
11
-
-
79958071911
-
Single nucleotide polymorphism discovery in elite North American potato germplasm
-
doi: 10. 1186/1471-2164-12-302
-
Hamilton, J. P., C. N. Hansey, B. R. Whitty, K. Stoffel, A. N. Massa, A. Van Deynze, W. S. De Jong, D. S. Douches, and C. R. Buell. 2011. Single nucleotide polymorphism discovery in elite North American potato germplasm. BMC Genomics 12: 302. doi: 10. 1186/1471-2164-12-302.
-
(2011)
BMC Genomics
, vol.12
, pp. 302
-
-
Hamilton, J.P.1
Hansey, C.N.2
Whitty, B.R.3
Stoffel, K.4
Massa, A.N.5
Van Deynze, A.6
De Jong, W.S.7
Douches, D.S.8
Buell, C.R.9
-
12
-
-
84863681911
-
Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis
-
doi: 10. 3835/plantgenome2011. 12. 0033
-
Hamilton, J. P., S.-C. Sim, K. Stoffel, A. Van Deynze, C. R. Buell, and D. M. Francis. 2012. Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. Plant Gen. 5: 17-29. doi: 10. 3835/plantgenome2011. 12. 0033.
-
(2012)
Plant Gen
, vol.5
, pp. 17-29
-
-
Hamilton, J.P.1
Sim, S.-C.2
Stoffel, K.3
Van Deynze, A.4
Buell, C.R.5
Francis, D.M.6
-
13
-
-
84883229068
-
Retrospective view of North American potato (Solanum tuberosum L.) breeding in the 20th and 21st centuries
-
doi: 10. 1534/g3. 113. 005595
-
Hirsch, C. N., C. D. Hirsch, K. Felcher, J. Coombs, D. Zarka, A. Van Deynze, W. De Jong, R. E. Veilleux, S. Jansky, P. Bethke, D. S. Douches, and C. R. Buell. 2013. Retrospective view of North American potato (Solanum tuberosum. L.) breeding in the 20th and 21st centuries. G3 (Bethesda) 3: 1003-1013. doi: 10. 1534/g3. 113. 005595.
-
(2013)
G3 (Bethesda)
, vol.3
, pp. 1003-1013
-
-
Hirsch, C.N.1
Hirsch, C.D.2
Felcher, K.3
Coombs, J.4
Zarka, D.5
Van Deynze, A.6
De Jong, W.7
Veilleux, R.E.8
Jansky, S.9
Bethke, P.10
Douches, D.S.11
Buell, C.R.12
-
14
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
doi: 10. 1186/gb-2009-10-3-r25
-
Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: R25. doi: 10. 1186/gb-2009-10-3-r25.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
15
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
doi: 10. 1093/bioinformatics/btp352
-
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, and R. Durbin. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079. doi: 10. 1093/bioinformatics/btp352.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
16
-
-
80255127234
-
Cutadapt removes adapter sequences from highthroughput sequencing reads
-
Martin, M. 2011. Cutadapt removes adapter sequences from highthroughput sequencing reads. EMBnet. journal 17: 10-12.
-
(2011)
EMBnet. journal
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
17
-
-
33846116032
-
New developments in the InterPro database
-
doi: 10. 1093/nar/gkl841
-
Mulder, N. J., R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bork, V. Buillard, L. Cerutti, R. Copley, E. Courcelle, U. Das, L. Daugherty, M. Dibley, R. Finn, W. Fleischmann, J. Gough, D. Haft, N. Hulo, S. Hunter, D. Kahn, A. Kanapin, A. Kejariwal, A. Labarga, P. S. Langendijk-Genevaux, D. Lonsdale, R. Lopez, I. Letunic, M. Madera, J. Maslen, C. McAnulla, J. McDowall, J. Mistry, A. Mitchell, A. N. Nikolskaya, S. Orchard, C. Orengo, R. Petryszak, J. D. Selengut, C. J. Sigrist, P. D. Thomas, F. Valentin, D. Wilson, C. H. Wu, and C. Yeats. 2007. New developments in the InterPro database. Nucleic Acids Res. 35: D224-D228. doi: 10. 1093/nar/gkl841.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Mulder, N.J.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Bork, P.7
Buillard, V.8
Cerutti, L.9
Copley, R.10
Courcelle, E.11
Das, U.12
Daugherty, L.13
Dibley, M.14
Finn, R.15
Fleischmann, W.16
Gough, J.17
Haft, D.18
Hulo, N.19
Hunter, S.20
Kahn, D.21
Kanapin, A.22
Kejariwal, A.23
Labarga, A.24
Langendijk-Genevaux, P.S.25
Lonsdale, D.26
Lopez, R.27
Letunic, I.28
Madera, M.29
Maslen, J.30
McAnulla, C.31
McDowall, J.32
Mistry, J.33
Mitchell, A.34
Nikolskaya, A.N.35
Orchard, S.36
Orengo, C.37
Petryszak, R.38
Selengut, J.D.39
Sigrist, C.J.40
Thomas, P.D.41
Valentin, F.42
Wilson, D.43
Wu, C.H.44
Yeats, C.45
more..
-
18
-
-
34547844136
-
A Chado case study: An ontologybased modular schema for representing genome-associated biological information
-
doi: 10. 1093/bioinformatics/btm189
-
Mungall, C. J., and D. B. Emmert. 2007. A Chado case study: An ontologybased modular schema for representing genome-associated biological information. Bioinformatics 23: I337-I346. doi: 10. 1093/bioinformatics/btm189.
-
(2007)
Bioinformatics
, vol.23
-
-
Mungall, C.J.1
Emmert, D.B.2
-
19
-
-
79960422847
-
Genome sequence and analysis of the tuber crop potato
-
Potato Genome Sequencing Consortium, doi: 10. 1038/nature10158
-
Potato Genome Sequencing Consortium. 2011. Genome sequence and analysis of the tuber crop potato. Nature 475: 189-195. doi: 10. 1038/nature10158.
-
(2011)
Nature
, vol.475
, pp. 189-195
-
-
-
20
-
-
0033990048
-
Primer3 on the WWW for general users and for biologist programmers
-
Rozen, S., and H. Skaletsky. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132: 365-386.
-
(2000)
Methods Mol. Biol
, vol.132
, pp. 365-386
-
-
Rozen, S.1
Skaletsky, H.2
-
21
-
-
84889019837
-
-
G3 (Bethesda). doi: 10. 1534/g3. 113. 007153
-
Sharma, S. K., D. Bolser, J. de Boer, M. Sønderkær, W. Amoros, M. F. Carboni, J. M. D'Ambrosio, G. de la Cruz, A. Di Genova, D. S. Douches, M. Eguiluz, X. Guo, F. Guzman, C. A. Hackett, J. P. Hamilton, G. Li, Y. Li, R. Lozano, A. Maass, D. Marshall, D. Martinez, K. McLean, N. Mejía, L. Milne, S. Munive, I. Nagy, O. Ponce, M. Ramirez, R. Simon, S. J. Thomson, Y. Torres, R. Waugh, Z. Zhang, S. Huang, R. G. F. Visser, C. W. B. Bachem, B. Sagredo, S. E. Feingold, G. Orjeda, R. E. Veilleux, M. Bonierbale, J. M. E. Jacobs, D. Milbourne, D. M. A. Martin, and G. J. Bryan. 2013. Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps. G3 (Bethesda). doi: 10. 1534/g3. 113. 007153.
-
(2013)
Construction of reference chromosome-scale pseudomolecules for potato: Integrating the potato genome with genetic and physical maps
-
-
Sharma, S.K.1
Bolser, D.2
de Boer, J.3
Sønderkær, M.4
Amoros, W.5
Carboni, M.F.6
D'Ambrosio, J.M.7
de la Cruz, G.8
Di Genova, A.9
Douches, D.S.10
Eguiluz, M.11
Guo, X.12
Guzman, F.13
Hackett, C.A.14
Hamilton, J.P.15
Li, G.16
Li, Y.17
Lozano, R.18
Maass, A.19
Marshall, D.20
Martinez, D.21
McLean, K.22
Mejía, N.23
Milne, L.24
Munive, S.25
Nagy, I.26
Ponce, O.27
Ramirez, M.28
Simon, R.29
Thomson, S.J.30
Torres, Y.31
Waugh, R.32
Zhang, Z.33
Huang, S.34
Visser, R.G.F.35
Bachem, C.W.B.36
Sagredo, B.37
Feingold, S.E.38
Orjeda, G.39
Veilleux, R.E.40
Bonierbale, M.41
Jacobs, J.M.E.42
Milbourne, D.43
Martin, D.M.A.44
Bryan, G.J.45
more..
-
22
-
-
24044447664
-
Automated generation of heuristics for biological sequence comparison
-
doi: 10. 1186/1471-2105-6-31
-
Slater, G. S., and E. Birney. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31. doi: 10. 1186/1471-2105-6-31.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 31
-
-
Slater, G.S.1
Birney, E.2
-
23
-
-
18644378331
-
The generic genome browser: A building block for a model organism system database
-
doi: 10. 1101/gr. 403602
-
Stein, L. D., C. Mungall, S. Shu, M. Caudy, M. Mangone, A. Day, E. Nickerson, J. E. Stajich, T. W. Harris, A. Arva, and S. Lewis. 2002. The generic genome browser: A building block for a model organism system database. Genome Res. 12: 1599-1610. doi: 10. 1101/gr. 403602.
-
(2002)
Genome Res
, vol.12
, pp. 1599-1610
-
-
Stein, L.D.1
Mungall, C.2
Shu, S.3
Caudy, M.4
Mangone, M.5
Day, A.6
Nickerson, E.7
Stajich, J.E.8
Harris, T.W.9
Arva, A.10
Lewis, S.11
-
24
-
-
38549144806
-
The Arabidopsis Information Resource (TAIR): Gene structure and function annotation
-
doi: 10. 1093/nar/gkm965
-
Swarbreck, D., C. Wilks, P. Lamesch, T. Z. Berardini, M. Garcia-Hernandez, H. Foerster, D. Li, T. Meyer, R. Muller, L. Ploetz, A. Radenbaugh, S. Singh, V. Swing, C. Tissier, P. Zhang, and E. Huala. 2008. The Arabidopsis Information Resource (TAIR): Gene structure and function annotation. Nucleic Acids Res. 36: D1009-D1014. doi: 10. 1093/nar/gkm965.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Swarbreck, D.1
Wilks, C.2
Lamesch, P.3
Berardini, T.Z.4
Garcia-Hernandez, M.5
Foerster, H.6
Li, D.7
Meyer, T.8
Muller, R.9
Ploetz, L.10
Radenbaugh, A.11
Singh, S.12
Swing, V.13
Tissier, C.14
Zhang, P.15
Huala, E.16
-
25
-
-
0026482438
-
High density molecular linkage maps of the tomato and potato genomes
-
Tanksley, S. D., M. W. Ganal, J. P. Prince, M. C. de Vicente, M. W. Bonierbale, P. Broun, T. M. Fulton, J. J. Giovannoni, S. Grandillo, G. B. Martin, et al. 1992. High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141-1160.
-
(1992)
Genetics
, vol.132
, pp. 1141-1160
-
-
Tanksley, S.D.1
Ganal, M.W.2
Prince, J.P.3
de Vicente, M.C.4
Bonierbale, M.W.5
Broun, P.6
Fulton, T.M.7
Giovannoni, J.J.8
Grandillo, S.9
Martin, G.B.10
-
26
-
-
0034882994
-
Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential
-
doi: 10. 1101/gr. 184001
-
Temnykh, S., G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour, and S. McCouch. 2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa. L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11: 1441-1452. doi: 10. 1101/gr. 184001.
-
(2001)
Genome Res
, vol.11
, pp. 1441-1452
-
-
Temnykh, S.1
DeClerck, G.2
Lukashova, A.3
Lipovich, L.4
Cartinhour, S.5
McCouch, S.6
-
27
-
-
84863693752
-
The tomato genome sequence provides insights into fleshy fruit evolution
-
Tomato Genome Sequencing Consortium, doi: 10. 1038/nature11119
-
Tomato Genome Sequencing Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641. doi: 10. 1038/nature11119.
-
(2012)
Nature
, vol.485
, pp. 635-641
-
-
-
28
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
doi: 10. 1093/bioinformatics/btp120
-
Trapnell, C., L. Pachter, and S. L. Salzberg. 2009. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111. doi: 10. 1093/bioinformatics/btp120.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
29
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
doi: 10. 1038/nbt. 1621
-
Trapnell, C., B. A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M. J. van Baren, S. L. Salzberg, B. J. Wold, and L. Pachter. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28: 511-515. doi: 10. 1038/nbt. 1621.
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
30
-
-
33745375367
-
Construction of a 10, 000-marker ultradense genetic recombination map of potato: Providing a framework for accelerated gene isolation and a genomewide physical map
-
van Os, H. et al. 2006. Construction of a 10, 000-marker ultradense genetic recombination map of potato: providing a framework for accelerated gene isolation and a genomewide physical map. Genetics 173: 1075-1087.
-
(2006)
Genetics
, vol.173
, pp. 1075-1087
-
-
van Os, H.1
-
31
-
-
43749114275
-
Using Chado to store genome annotation data
-
Unit 9. 6, doi: 10. 1002/0471250953. bi0906s12
-
Zhou, P., D. Emmert, and P. Zhang. 2006. Using Chado to store genome annotation data. Curr. Protoc. Bioinformatics Chapter 9: Unit 9. 6. doi: 10. 1002/0471250953. bi0906s12.
-
(2006)
Curr. Protoc. Bioinformatics Chapter
, vol.9
-
-
Zhou, P.1
Emmert, D.2
Zhang, P.3
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