-
1
-
-
71049115687
-
A snapshot of the emerging tomato genome sequence
-
Mueller, L.A., Lankhorst, R.K., Tanksley, S.D., Giovannoni, J.J., White, R., Vrebalov, J., Fei, Z.J., Eck, J.v., Buels, R., Mills, A.A. et al. (2009) A snapshot of the emerging tomato genome sequence. Plant Genome, 2, 78-92.
-
(2009)
Plant Genome
, vol.2
, pp. 78-92
-
-
Mueller, L.A.1
Lankhorst, R.K.2
Tanksley, S.D.3
Giovannoni, J.J.4
White, R.5
Vrebalov, J.6
Fei, Z.J.7
Eck, J.V.8
Buels, R.9
Mills, A.A.10
-
2
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.J., Chen, Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
-
(2005)
Nature
, vol.437
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
Berka, J.7
Braverman, M.S.8
Chen, Y.J.9
Chen, Z.10
-
3
-
-
40249111689
-
A new class of cleavable fluorescent nucleotides: Synthesis and optimization as reversible terminators for DNA sequencing by synthesis
-
Turcatti, G., Romieu, A., Fedurco, M. and Tairi, A.P. (2008) A new class of cleavable fluorescent nucleotides: Synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res., 36, e25.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Turcatti, G.1
Romieu, A.2
Fedurco, M.3
Tairi, A.P.4
-
4
-
-
24644462173
-
Accurate multiplex polony sequencing of an evolved bacterial genome
-
Shendure, J., Porreca, G.J., Reppas, N.B., Lin, X., McCutcheon, J.P., Rosenbaum, A.M., Wang, M.D., Zhang, K., Mitra, R.D. and Church, G.M. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309, 1728-1732.
-
(2005)
Science
, vol.309
, pp. 1728-1732
-
-
Shendure, J.1
Porreca, G.J.2
Reppas, N.B.3
Lin, X.4
McCutcheon, J.P.5
Rosenbaum, A.M.6
Wang, M.D.7
Zhang, K.8
Mitra, R.D.9
Church, G.M.10
-
5
-
-
41749104588
-
Single-molecule DNA sequencing of a viral genome
-
Harris, T.D., Buzby, P.R., Babcock, H., Beer, E., Bowers, J., Braslavsky, I., Causey, M., Colonell, J., Dimeo, J., Efcavitch, J.W. et al. (2008) Single-molecule DNA sequencing of a viral genome. Science, 320, 106-109.
-
(2008)
Science
, vol.320
, pp. 106-109
-
-
Harris, T.D.1
Buzby, P.R.2
Babcock, H.3
Beer, E.4
Bowers, J.5
Braslavsky, I.6
Causey, M.7
Colonell, J.8
Dimeo, J.9
Efcavitch, J.W.10
-
6
-
-
77956125365
-
A flexible and efficient template format for circular consensus sequencing and SNP detection
-
Travers, K.J., Chin, C.S., Rank, D.R., Eid, J.S. and Turner, S.W. (2010) A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res., 38, e159.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Travers, K.J.1
Chin, C.S.2
Rank, D.R.3
Eid, J.S.4
Turner, S.W.5
-
7
-
-
75549087626
-
Saccharomyces genome database provides mutant phenotype data
-
Engel, S.R., Balakrishnan, R., Binkley, G., Christie, K.R., Costanzo, M.C., Dwight, S.S., Fisk, D.G., Hirschman, J.E., Hitz, B.C., Hong, E.L. et al. (2010) Saccharomyces genome database provides mutant phenotype data. Nucleic Acids Res., 38, D433-D436.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Engel, S.R.1
Balakrishnan, R.2
Binkley, G.3
Christie, K.R.4
Costanzo, M.C.5
Dwight, S.S.6
Fisk, D.G.7
Hirschman, J.E.8
Hitz, B.C.9
Hong, E.L.10
-
8
-
-
38549144806
-
The arabidopsis information resource (TAIR): Gene structure and function annotation
-
Swarbreck, D., Wilks, C., Lamesch, P., Berardini, T.Z., Garcia- Hernandez, M., Foerster, H., Li, D., Meyer, T., Muller, R., Ploetz, L. et al. (2008) The arabidopsis information resource (TAIR): Gene structure and function annotation. Nucleic Acids Res., 36, D1009-D1014.
-
(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
-
9
-
-
53749107455
-
A community-based annotation framework for linking solanaceae genomes with phenomes
-
Menda, N., Buels, R.M., Tecle, I. and Mueller, L.A. (2008) A community-based annotation framework for linking solanaceae genomes with phenomes. Plant Physiol., 147, 1788-1799.
-
(2008)
Plant Physiol.
, vol.147
, pp. 1788-1799
-
-
Menda, N.1
Buels, R.M.2
Tecle, I.3
Mueller, L.A.4
-
10
-
-
75549084998
-
Archiving next generation sequencing data
-
Shumway, M., Cochrane, G. and Sugawara, H. (2010) Archiving next generation sequencing data. Nucleic Acids Res., 38, D870-D871.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Shumway, M.1
Cochrane, G.2
Sugawara, H.3
-
11
-
-
34547844136
-
A chado case study: An ontology-based modular schema for representing genome-associated biological information
-
FlyBase Consortium.
-
Mungall, C.J. and Emmert, D.B. (2007). FlyBase Consortium. (2007) A chado case study: An ontology-based modular schema for representing genome-associated biological information. Bioinformatics, 23, i337-i346.
-
(2007)
Bioinformatics
, vol.23
-
-
Mungall, C.J.1
Emmert, D.B.2
-
12
-
-
58149182724
-
NCBI GEO: Archive for high-throughput functional genomic data
-
Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A., Tomashevsky, M., Marshall, K.A. et al. (2009) NCBI GEO: Archive for high-throughput functional genomic data. Nucleic Acids Res., 37, D885-D890.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Rudnev, D.5
Evangelista, C.6
Kim, I.F.7
Soboleva, A.8
Tomashevsky, M.9
Marshall, K.A.10
-
13
-
-
58149204055
-
ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression
-
Parkinson, H., Kapushesky, M., Kolesnikov, N., Rustici, G., Shojatalab, M., Abeygunawardena, N., Berube, H., Dylag, M., Emam, I., Farne, A. et al. (2009) ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res., 37, D868-D872.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Parkinson, H.1
Kapushesky, M.2
Kolesnikov, N.3
Rustici, G.4
Shojatalab, M.5
Abeygunawardena, N.6
Berube, H.7
Dylag, M.8
Emam, I.9
Farne, A.10
-
14
-
-
0034839588
-
Photolithographic synthesis of high-density oligonucleotide probe arrays
-
Barone, A.D., Beecher, J.E., Bury, P.A., Chen, C., Doede, T., Fidanza, J.A. and McGall, G.H. (2001) Photolithographic synthesis of high-density oligonucleotide probe arrays. Nucleosides Nucleotides Nucleic Acids, 20, 525-531.
-
(2001)
Nucleosides Nucleotides Nucleic Acids
, vol.20
, pp. 525-531
-
-
Barone, A.D.1
Beecher, J.E.2
Bury, P.A.3
Chen, C.4
Doede, T.5
Fidanza, J.A.6
McGall, G.H.7
-
15
-
-
77949368165
-
TobEA: An atlas of tobacco gene expression from seed to senescence
-
Edwards, K.D., Bombarely, A., Story, G.W., Allen, F., Mueller, L.A., Coates, S.A. and Jones, L. (2010) TobEA: An atlas of tobacco gene expression from seed to senescence. BMC Genomics, 11, 142.
-
(2010)
BMC Genomics
, vol.11
, pp. 142
-
-
Edwards, K.D.1
Bombarely, A.2
Story, G.W.3
Allen, F.4
Mueller, L.A.5
Coates, S.A.6
Jones, L.7
-
16
-
-
77951137933
-
Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module
-
Ozaki, S., Ogata, Y., Suda, K., Kurabayashi, A., Suzuki, T., Yamamoto, N., Iijima, Y., Tsugane, T., Fujii, T., Konishi, C. et al. (2010) Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res., 17, 105-116.
-
(2010)
DNA Res.
, vol.17
, pp. 105-116
-
-
Ozaki, S.1
Ogata, Y.2
Suda, K.3
Kurabayashi, A.4
Suzuki, T.5
Yamamoto, N.6
Iijima, Y.7
Tsugane, T.8
Fujii, T.9
Konishi, C.10
-
17
-
-
77954247251
-
Studies of a biochemical factory: Tomato trichome deep expressed sequence tag sequencing and proteomics
-
Schilmiller, A.L., Miner, D.P., Larson, M., McDowell, E., Gang, D.R., Wilkerson, C. and Last, R.L. (2010) Studies of a biochemical factory: Tomato trichome deep expressed sequence tag sequencing and proteomics. Plant Physiol., 153, 1212-1223.
-
(2010)
Plant Physiol.
, vol.153
, pp. 1212-1223
-
-
Schilmiller, A.L.1
Miner, D.P.2
Larson, M.3
McDowell, E.4
Gang, D.R.5
Wilkerson, C.6
Last, R.L.7
-
18
-
-
38549134393
-
The plant ontology database: A community resource for plant structure and developmental stages controlled vocabulary and annotations
-
Avraham, S., Tung, C.W., Ilic, K., Jaiswal, P., Kellogg, E.A., McCouch, S., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M. et al. (2008) The plant ontology database: A community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res., 36, D449-D454.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Avraham, S.1
Tung, C.W.2
Ilic, K.3
Jaiswal, P.4
Kellogg, E.A.5
McCouch, S.6
Pujar, A.7
Reiser, L.8
Rhee, S.Y.9
Sachs, M.M.10
-
19
-
-
75549089545
-
The proteomics identifications database: 2010 update
-
Vizcaino, J.A., Cote, R., Reisinger, F., Barsnes, H., Foster, J.M., Rameseder, J., Hermjakob, H. and Martens, L. (2010) The proteomics identifications database: 2010 update. Nucleic Acids Res., 38, D736-D742.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Vizcaino, J.A.1
Cote, R.2
Reisinger, F.3
Barsnes, H.4
Foster, J.M.5
Rameseder, J.6
Hermjakob, H.7
Martens, L.8
-
20
-
-
0043122944
-
ExPASy: The proteomics server for in-depth protein knowledge and analysis
-
Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R.D. and Bairoch, A. (2003) ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res., 31, 3784-3788.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3784-3788
-
-
Gasteiger, E.1
Gattiker, A.2
Hoogland, C.3
Ivanyi, I.4
Appel, R.D.5
Bairoch, A.6
-
21
-
-
40549114019
-
-
James, N., Graham, N., Clements, D., Schildknecht, B. and May, S. (2007) AtEnsEMBL. Methods Mol. Biol., 406, 213-227.
-
(2007)
AtEnsEMBL. Methods Mol. Biol.
, vol.406
, pp. 213-227
-
-
James, N.1
Graham, N.2
Clements, D.3
Schildknecht, B.4
May, S.5
-
22
-
-
77950613788
-
From protein sequences to 3D-structures and beyond: The example of the UniProt knowledgebase
-
UniProt Consortium
-
Hinz, U. and UniProt Consortium (2010) From protein sequences to 3D-structures and beyond: The example of the UniProt knowledgebase. Cell Mol. Life Sci., 67, 1049-1064.
-
(2010)
Cell Mol. Life Sci.
, vol.67
, pp. 1049-1064
-
-
Hinz, U.1
-
23
-
-
0037246063
-
The protein information resource
-
Wu, C.H., Yeh, L.S., Huang, H., Arminski, L., Castro-Alvear, J., Chen, Y., Hu, Z., Kourtesis, P., Ledley, R.S., Suzek, B.E. et al. (2003) The protein information resource. Nucleic Acids Res., 31, 345-347.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 345-347
-
-
Wu, C.H.1
Yeh, L.S.2
Huang, H.3
Arminski, L.4
Castro-Alvear, J.5
Chen, Y.6
Hu, Z.7
Kourtesis, P.8
Ledley, R.S.9
Suzek, B.E.10
-
24
-
-
69149102637
-
Data deposition and annotation at the worldwide protein data bank
-
Dutta, S., Burkhardt, K., Young, J., Swaminathan, G.J., Matsuura, T., Henrick, K., Nakamura, H. and Berman, H.M. (2009) Data deposition and annotation at the worldwide protein data bank. Mol. Biotechnol., 42, 1-13.
-
(2009)
Mol. Biotechnol.
, vol.42
, pp. 1-13
-
-
Dutta, S.1
Burkhardt, K.2
Young, J.3
Swaminathan, G.J.4
Matsuura, T.5
Henrick, K.6
Nakamura, H.7
Berman, H.M.8
-
25
-
-
0033290515
-
ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences
-
Iseli, C., Jongeneel, C.V. and Bucher, P. (1999) ESTScan: A program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 138-148.
-
(1999)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, pp. 138-148
-
-
Iseli, C.1
Jongeneel, C.V.2
Bucher, P.3
-
26
-
-
0030627982
-
Neural network prediction of translation initiation sites in eukaryotes: Perspectives for EST and genome analysis
-
Pedersen, A.G. and Nielsen, H. (1997) Neural network prediction of translation initiation sites in eukaryotes: Perspectives for EST and genome analysis. Proc. Int. Conf. Intell. Syst. Mol. Biol., 5, 226-233.
-
(1997)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.5
, pp. 226-233
-
-
Pedersen, A.G.1
Nielsen, H.2
-
27
-
-
0027286502
-
MASCOT: Multiple alignment system for protein sequences based on three-way dynamic programming
-
Hirosawa, M., Hoshida, M., Ishikawa, M. and Toya, T. (1993) MASCOT: Multiple alignment system for protein sequences based on three-way dynamic programming. Comput. Appl. Biosci., 9, 161-167.
-
(1993)
Comput. Appl. Biosci.
, vol.9
, pp. 161-167
-
-
Hirosawa, M.1
Hoshida, M.2
Ishikawa, M.3
Toya, T.4
-
28
-
-
0034800374
-
InterProScan-an integration platform for the signature-recognition methods in InterPro
-
Zdobnov, E.M. and Apweiler, R. (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-848.
-
(2001)
Bioinformatics
, vol.17
, pp. 847-848
-
-
Zdobnov, E.M.1
Apweiler, R.2
-
29
-
-
3042521098
-
Improved prediction of signal peptides: SignalP 3.0
-
Bendtsen, J.D., Nielsen, H., von Heijne, G. and Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol., 340, 783-795.
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 783-795
-
-
Bendtsen, J.D.1
Nielsen, H.2
Von Heijne, G.3
Brunak, S.4
-
30
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
Enright, A.J., Van Dongen, S. and Ouzounis, C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
31
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar, R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
33
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
34
-
-
18644378331
-
The generic genome browser: A building block for a model organism system database
-
Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A. et al. (2002) The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610.
-
(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
-
35
-
-
40049105704
-
A comparative analysis into the genetic bases of morphology in tomato varieties exhibiting elongated fruit shape
-
Gonzalo, M.J. and van der Knaap, E. (2008) A comparative analysis into the genetic bases of morphology in tomato varieties exhibiting elongated fruit shape. Theor. Appl. Genet., 116, 647-656.
-
(2008)
Theor. Appl. Genet.
, vol.116
, pp. 647-656
-
-
Gonzalo, M.J.1
Van Der Knaap, E.2
-
36
-
-
0026482438
-
High density molecular linkage maps of the tomato and potato genomes
-
Tanksley, S.D., Ganal, M.W., Prince, J.P., de Vicente, M.C., Bonierbale, M.W., Broun, P., Fulton, T.M., Giovannoni, J.J., Grandillo, S. and Martin, G.B. (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
-
37
-
-
33845887199
-
A microsatellite marker based linkage map of tobacco
-
Bindler, G., van der Hoeven, R., Gunduz, I., Plieske, J., Ganal, M., Rossi, L., Gadani, F. and Donini, P. (2007) A microsatellite marker based linkage map of tobacco. Theor. Appl. Genet., 114, 341-349.
-
(2007)
Theor. Appl. Genet.
, vol.114
, pp. 341-349
-
-
Bindler, G.1
Van Der Hoeven, R.2
Gunduz, I.3
Plieske, J.4
Ganal, M.5
Rossi, L.6
Gadani, F.7
Donini, P.8
-
38
-
-
27244454556
-
The SOL genomics network: A comparative resource for solanaceae biology and beyond
-
Mueller, L.A., Solow, T.H., Taylor, N., Skwarecki, B., Buels, R., Binns, J., Lin, C., Wright, M.H., Ahrens, R., Wang, Y. et al. (2005) The SOL genomics network: A comparative resource for solanaceae biology and beyond. Plant Physiol., 138, 1310-1317.
-
(2005)
Plant Physiol.
, vol.138
, pp. 1310-1317
-
-
Mueller, L.A.1
Solow, T.H.2
Taylor, N.3
Skwarecki, B.4
Buels, R.5
Binns, J.6
Lin, C.7
Wright, M.H.8
Ahrens, R.9
Wang, Y.10
-
39
-
-
11244328060
-
The pathway tools software
-
Karp, P.D., Paley, S. and Romero, P. (2002) The pathway tools software. Bioinformatics, 18(Suppl. 1), S225-S232.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Karp, P.D.1
Paley, S.2
Romero, P.3
-
40
-
-
0037958742
-
R/qtl: QTL mapping in experimental crosses
-
Broman, K.W., Wu, H., Sen, S. and Churchill, G.A. (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics, 19, 889-890.
-
(2003)
Bioinformatics
, vol.19
, pp. 889-890
-
-
Broman, K.W.1
Wu, H.2
Sen, S.3
Churchill, G.A.4
-
41
-
-
34548424412
-
Morphological variation in tomato: A comprehensive study of quantitative trait oci controlling fruit shape and development
-
Brewer, M.T., Moyseenko, J.B., Monforte, A.J. and van der Knaap, E. (2007) Morphological variation in tomato: A comprehensive study of quantitative trait loci controlling fruit shape and development. J. Exp. Bot., 58, 1339-1349.
-
(2007)
J. Exp. Bot.
, vol.58
, pp. 1339-1349
-
-
Brewer, M.T.1
Moyseenko, J.B.2
Monforte, A.J.3
Van Der Knaap, E.4
-
42
-
-
78651325016
-
-
PostgreSQL Global Development Group. PostgreSQL documentation
-
PostgreSQL Global Development Group. (2010) PostgreSQL documentation. (http://www.postgresql.org/docs/9.0/static/introwhatis. html).
-
(2010)
-
-
-
43
-
-
0038635256
-
Test-driven development by example
-
xvii. Addison Wesley Longman Publishing Co., Reading, Massachusetts
-
Beck, K. (2003) Test-driven development by example, Introduction, xvii. Addison Wesley Longman Publishing Co., Reading, Massachusetts.
-
(2003)
Introduction
-
-
Beck, K.1
|