-
1
-
-
34547561588
-
FatiGO+: A functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
-
Al-Shahrour F, Minguez P, Tarraga J, Medina I, Alloza E, Montaner D, Dopazo J (2007) FatiGO+: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res 35: W91-W96
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Al-Shahrour, F.1
Minguez, P.2
Tarraga, J.3
Medina, I.4
Alloza, E.5
Montaner, D.6
Dopazo, J.7
-
2
-
-
33646384941
-
Receptors for auxin: Will it all end in TIRs?
-
Badescu GO, Napier RM (2006) Receptors for auxin: will it all end in TIRs? Trends Plant Sci 11: 217-223
-
(2006)
Trends Plant Sci
, vol.11
, pp. 217-223
-
-
Badescu, G.O.1
Napier, R.M.2
-
3
-
-
34250675590
-
The Arabidopsis EIN3 binding F-box proteins EBF1 and EBF2 have distinct but overlapping roles in ethylene signaling
-
Binder BM, Walker JM, Gagne JM, Emborg TJ, Hemmann G, Bleecker AB, Vierstra RD (2007) The Arabidopsis EIN3 binding F-box proteins EBF1 and EBF2 have distinct but overlapping roles in ethylene signaling. Plant Cell 19: 509-523
-
(2007)
Plant Cell
, vol.19
, pp. 509-523
-
-
Binder, B.M.1
Walker, J.M.2
Gagne, J.M.3
Emborg, T.J.4
Hemmann, G.5
Bleecker, A.B.6
Vierstra, R.D.7
-
4
-
-
33947578710
-
The evolutionarily conserved Arabidopsis thaliana F-box protein AtFBP7 is required for efficient translation during temperature stress
-
Calderon-Villalobos LI, Nill C, Marrocco K, Kretsch T, Schwechheimer C (2007) The evolutionarily conserved Arabidopsis thaliana F-box protein AtFBP7 is required for efficient translation during temperature stress. Gene 392: 106-116
-
(2007)
Gene
, vol.392
, pp. 106-116
-
-
Calderon-Villalobos, L.I.1
Nill, C.2
Marrocco, K.3
Kretsch, T.4
Schwechheimer, C.5
-
5
-
-
34347389905
-
Three distinct modes of intron dynamics in the evolution of eukaryotes
-
Carmel L, Wolf YI, Rogozin IB, Koonin EV (2007) Three distinct modes of intron dynamics in the evolution of eukaryotes. Genome Res 17: 1034-1044
-
(2007)
Genome Res
, vol.17
, pp. 1034-1044
-
-
Carmel, L.1
Wolf, Y.I.2
Rogozin, I.B.3
Koonin, E.V.4
-
6
-
-
10044250974
-
ZOMES III: The interface between signalling and proteolysis. Meeting on the COP9 signalosome, proteasome and eIF3
-
Chang EC, Schwechheimer C (2004) ZOMES III: the interface between signalling and proteolysis. Meeting on the COP9 signalosome, proteasome and eIF3. EMBO Rep 5: 1041-1045
-
(2004)
EMBO Rep
, vol.5
, pp. 1041-1045
-
-
Chang, E.C.1
Schwechheimer, C.2
-
7
-
-
0033692378
-
NOTUNG: A program for dating gene duplications and optimizing gene family trees
-
Chen K, Durand D, Farach-Colton M (2000) NOTUNG: a program for dating gene duplications and optimizing gene family trees. J Comput Biol 7: 429-447
-
(2000)
J Comput Biol
, vol.7
, pp. 429-447
-
-
Chen, K.1
Durand, D.2
Farach-Colton, M.3
-
8
-
-
33846059234
-
The TIGR plant transcript assemblies database
-
Childs KL, Hamilton JP, Zhu W, Ly E, Cheung F, Wu H, Rabinowicz PD, Town CD, Buell CR, Chan AP (2007) The TIGR plant transcript assemblies database. Nucleic Acids Res 35: D846-851
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Childs, K.L.1
Hamilton, J.P.2
Zhu, W.3
Ly, E.4
Cheung, F.5
Wu, H.6
Rabinowicz, P.D.7
Town, C.D.8
Buell, C.R.9
Chan, A.P.10
-
9
-
-
24644503098
-
Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
-
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676
-
(2005)
Bioinformatics
, vol.21
, pp. 3674-3676
-
-
Conesa, A.1
Gotz, S.2
Garcia-Gomez, J.M.3
Terol, J.4
Talon, M.5
Robles, M.6
-
10
-
-
19544379019
-
The F-box protein TIR1 is an auxin receptor
-
Dharmasiri N, Dharmasiri S, Estelle M (2005) The F-box protein TIR1 is an auxin receptor. Nature 435: 441-445
-
(2005)
Nature
, vol.435
, pp. 441-445
-
-
Dharmasiri, N.1
Dharmasiri, S.2
Estelle, M.3
-
11
-
-
0035871316
-
EID1, an F-box protein involved in phytochrome A-specific light signaling
-
Dieterle M, Zhou YC, Schafer E, Funk M, Kretsch T (2001) EID1, an F-box protein involved in phytochrome A-specific light signaling. Genes Dev 15: 939-944
-
(2001)
Genes Dev
, vol.15
, pp. 939-944
-
-
Dieterle, M.1
Zhou, Y.C.2
Schafer, E.3
Funk, M.4
Kretsch, T.5
-
12
-
-
2942633715
-
The Arabidopsis F-box protein SLEEPY1 targets gibberellin signaling repressors for gibberellininduced degradation
-
Dill A, Thomas SG, Hu J, Steber CM, Sun TP (2004) The Arabidopsis F-box protein SLEEPY1 targets gibberellin signaling repressors for gibberellininduced degradation. Plant Cell 16: 1392-1405
-
(2004)
Plant Cell
, vol.16
, pp. 1392-1405
-
-
Dill, A.1
Thomas, S.G.2
Hu, J.3
Steber, C.M.4
Sun, T.P.5
-
13
-
-
0037477611
-
The F-box-containing protein UFO and AGAMOUS participate in antagonistic pathways governing early petal development in Arabidopsis
-
Durfee T, Roe JL, Sessions RA, Inouye C, Serikawa K, Feldmann KA, Weigel D, Zambryski PC (2003) The F-box-containing protein UFO and AGAMOUS participate in antagonistic pathways governing early petal development in Arabidopsis. Proc Natl Acad Sci USA 100: 8571-8576
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 8571-8576
-
-
Durfee, T.1
Roe, J.L.2
Sessions, R.A.3
Inouye, C.4
Serikawa, K.5
Feldmann, K.A.6
Weigel, D.7
Zambryski, P.C.8
-
14
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
15
-
-
33744914841
-
Relaxed neighbor joining: A fast distance-based phylogenetic tree construction method
-
Evans J, Sheneman L, Foster J (2006) Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. J Mol Evol 62: 785-792
-
(2006)
J Mol Evol
, vol.62
, pp. 785-792
-
-
Evans, J.1
Sheneman, L.2
Foster, J.3
-
16
-
-
57749097215
-
-
Felsenstein J (1989) PHYLIP: Phylogeny Inference Package Version 3.2, Cladistics 5: 164-166
-
Felsenstein J (1989) PHYLIP: Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166
-
-
-
-
17
-
-
0141905891
-
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
-
Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, Hannick LI, Maiti R, Ronning CM, Rusch DB, Town CD, et al (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31: 5654-5666
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 5654-5666
-
-
Haas, B.J.1
Delcher, A.L.2
Mount, S.M.3
Wortman, J.R.4
Smith Jr, R.K.5
Hannick, L.I.6
Maiti, R.7
Ronning, C.M.8
Rusch, D.B.9
Town, C.D.10
-
18
-
-
6444243196
-
Formation of an SCF(ZTL) complex is required for proper regulation of circadian timing
-
Han L, Mason M, Risseeuw EP, Crosby WL, Somers DE (2004) Formation of an SCF(ZTL) complex is required for proper regulation of circadian timing. Plant J 40: 291-301
-
(2004)
Plant J
, vol.40
, pp. 291-301
-
-
Han, L.1
Mason, M.2
Risseeuw, E.P.3
Crosby, W.L.4
Somers, D.E.5
-
19
-
-
22044444886
-
FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis
-
Imaizumi T, Schultz TF, Harmon FG, Ho LA, Kay SA (2005) FKF1 F-box protein mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. Science 309: 293-297
-
(2005)
Science
, vol.309
, pp. 293-297
-
-
Imaizumi, T.1
Schultz, T.F.2
Harmon, F.G.3
Ho, L.A.4
Kay, S.A.5
-
20
-
-
34848886909
-
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla
-
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467
-
(2007)
Nature
, vol.449
, pp. 463-467
-
-
Jaillon, O.1
Aury, J.M.2
Noel, B.3
Policriti, A.4
Clepet, C.5
Casagrande, A.6
Choisne, N.7
Aubourg, S.8
Vitulo, N.9
Jubin, C.10
-
23
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33: 511-518
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
24
-
-
33646921186
-
Forward genetic analysis of the circadian clock separates the multiple functions of ZEITLUPE
-
Kevei E, Gyula P, Hall A, Kozma-Bognar L, Kim WY, Eriksson ME, Toth R, Hanano S, Feher B, Southern MM, et al (2006) Forward genetic analysis of the circadian clock separates the multiple functions of ZEITLUPE. Plant Physiol 140: 933-945
-
(2006)
Plant Physiol
, vol.140
, pp. 933-945
-
-
Kevei, E.1
Gyula, P.2
Hall, A.3
Kozma-Bognar, L.4
Kim, W.Y.5
Eriksson, M.E.6
Toth, R.7
Hanano, S.8
Feher, B.9
Southern, M.M.10
-
25
-
-
34247200577
-
The AtGenExpress global stress expression data set: Protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
-
Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 50: 347-363
-
(2007)
Plant J
, vol.50
, pp. 347-363
-
-
Kilian, J.1
Whitehead, D.2
Horak, J.3
Wanke, D.4
Weinl, S.5
Batistic, O.6
D'Angelo, C.7
Bornberg-Bauer, E.8
Kudla, J.9
Harter, K.10
-
26
-
-
0036635467
-
Arabidopsis SON1 is an F-box protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance
-
Kim HS, Delaney TP (2002) Arabidopsis SON1 is an F-box protein that regulates a novel induced defense response independent of both salicylic acid and systemic acquired resistance. Plant Cell 14: 1469-1482
-
(2002)
Plant Cell
, vol.14
, pp. 1469-1482
-
-
Kim, H.S.1
Delaney, T.P.2
-
27
-
-
33746690468
-
The F-box protein family
-
REVIEWS3002
-
Kipreos ET, Pagano M (2000) The F-box protein family. Genome Biol 1: REVIEWS3002
-
(2000)
Genome Biol
, vol.1
-
-
Kipreos, E.T.1
Pagano, M.2
-
28
-
-
27644472372
-
Orthologs, paralogs, and evolutionary genomics
-
Koonin EV (2005) Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet 39: 309-338
-
(2005)
Annu Rev Genet
, vol.39
, pp. 309-338
-
-
Koonin, E.V.1
-
29
-
-
1942469549
-
Molecular analyses of the Arabidopsis TUBBY-like protein gene family
-
Lai CP, Lee CL, Chen PH, Wu SH, Yang CC, Shaw JF (2004) Molecular analyses of the Arabidopsis TUBBY-like protein gene family. Plant Physiol 134: 1586-1597
-
(2004)
Plant Physiol
, vol.134
, pp. 1586-1597
-
-
Lai, C.P.1
Lee, C.L.2
Chen, P.H.3
Wu, S.H.4
Yang, C.C.5
Shaw, J.F.6
-
30
-
-
33749559690
-
F-box proteins everywhere
-
Lechner E, Achard P, Vansiri A, Potuschak T, Genschik P (2006) F-box proteins everywhere. Curr Opin Plant Biol 9: 631-638
-
(2006)
Curr Opin Plant Biol
, vol.9
, pp. 631-638
-
-
Lechner, E.1
Achard, P.2
Vansiri, A.3
Potuschak, T.4
Genschik, P.5
-
31
-
-
33846036895
-
The E3 ubiquitin ligase gene family in plants: Regulation by degradation
-
Mazzucotelli E, Belloni S, Marone D, De Leonardis AM, Guerra D, Fonzo N, Cattivelli L, Mastrangelo AM (2006) The E3 ubiquitin ligase gene family in plants: regulation by degradation. Curr Genomics 7: 509-522
-
(2006)
Curr Genomics
, vol.7
, pp. 509-522
-
-
Mazzucotelli, E.1
Belloni, S.2
Marone, D.3
De Leonardis, A.M.4
Guerra, D.5
Fonzo, N.6
Cattivelli, L.7
Mastrangelo, A.M.8
-
32
-
-
42949157236
-
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
-
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, et al (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991-996
-
(2008)
Nature
, vol.452
, pp. 991-996
-
-
Ming, R.1
Hou, S.2
Feng, Y.3
Yu, Q.4
Dionne-Laporte, A.5
Saw, J.H.6
Senin, P.7
Wang, W.8
Ly, B.V.9
Lewis, K.L.10
-
33
-
-
33846116032
-
New developments in the InterPro database
-
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, et al (2007) New developments in the InterPro database. Nucleic Acids Res 35: D224-228
-
(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
-
34
-
-
33846101405
-
The TIGR rice genome annotation resource: Improvements and new features
-
Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, et al (2007) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35: D883-D887
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Ouyang, S.1
Zhu, W.2
Hamilton, J.3
Lin, H.4
Campbell, M.5
Childs, K.6
Thibaud-Nissen, F.7
Malek, R.L.8
Lee, Y.9
Zheng, L.10
-
35
-
-
4544340842
-
The F-box protein AhSLF-S2 controls the pollen function of S-RNase-based self-incompatibility
-
Qiao H, Wang F, Zhao L, Zhou J, Lai Z, Zhang Y, Robbins TP, Xue Y (2004) The F-box protein AhSLF-S2 controls the pollen function of S-RNase-based self-incompatibility. Plant Cell 16: 2307-2322
-
(2004)
Plant Cell
, vol.16
, pp. 2307-2322
-
-
Qiao, H.1
Wang, F.2
Zhao, L.3
Zhou, J.4
Lai, Z.5
Zhang, Y.6
Robbins, T.P.7
Xue, Y.8
-
36
-
-
0037249498
-
The Arabidopsis Information Resource (TAIR): A model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
-
Rhee SY, Beavis W, Berardini TZ, Chen GH, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, et al (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31: 224-228
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 224-228
-
-
Rhee, S.Y.1
Beavis, W.2
Berardini, T.Z.3
Chen, G.H.4
Dixon, D.5
Doyle, A.6
Garcia-Hernandez, M.7
Huala, E.8
Lander, G.9
Montoya, M.10
-
37
-
-
33845868781
-
Patterns of intron loss and gain in plants: Intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana
-
Roy SW, Penny D (2007) Patterns of intron loss and gain in plants: intron loss-dominated evolution and genome-wide comparison of O. sativa and A. thaliana. Mol Biol Evol 24: 171-181
-
(2007)
Mol Biol Evol
, vol.24
, pp. 171-181
-
-
Roy, S.W.1
Penny, D.2
-
38
-
-
16244362244
-
A gene expression map of Arabidopsis thaliana development
-
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506
-
(2005)
Nat Genet
, vol.37
, pp. 501-506
-
-
Schmid, M.1
Davison, T.S.2
Henz, S.R.3
Pape, U.J.4
Demar, M.5
Vingron, M.6
Scholkopf, B.7
Weigel, D.8
Lohmann, J.U.9
-
39
-
-
2442692997
-
Identification of the pollen determinant of S-RNasemediated self-incompatibility
-
Sijacic P, Wang X, Skirpan AL, Wang Y, Dowd PE, McCubbin AG, Huang S, Kao TH (2004) Identification of the pollen determinant of S-RNasemediated self-incompatibility. Nature 429: 302-305
-
(2004)
Nature
, vol.429
, pp. 302-305
-
-
Sijacic, P.1
Wang, X.2
Skirpan, A.L.3
Wang, Y.4
Dowd, P.E.5
McCubbin, A.G.6
Huang, S.7
Kao, T.H.8
-
40
-
-
33947682757
-
MAX2 participates in an SCF complex which acts locally at the node to suppress shoot branching
-
Stirnberg P, Furner IJ, Ottoline Leyser HM (2007) MAX2 participates in an SCF complex which acts locally at the node to suppress shoot branching. Plant J 50: 80-94
-
(2007)
Plant J
, vol.50
, pp. 80-94
-
-
Stirnberg, P.1
Furner, I.J.2
Ottoline Leyser, H.M.3
-
42
-
-
34547781750
-
-
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599
-
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599
-
-
-
-
43
-
-
33748760611
-
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)
-
Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604
-
(2006)
Science
, vol.313
, pp. 1596-1604
-
-
Tuskan, G.A.1
DiFazio, S.2
Jansson, S.3
Bohlmann, J.4
Grigoriev, I.5
Hellsten, U.6
Putnam, N.7
Ralph, S.8
Rombauts, S.9
Salamov, A.10
-
44
-
-
17744371504
-
Genomewide analysis of S-locus F-box-like genes in Arabidopsis thaliana
-
Wang L, Dong L, Zhang Y, Zhang Y, WuW, Deng X, Xue Y (2004) Genomewide analysis of S-locus F-box-like genes in Arabidopsis thaliana. Plant Mol Biol 56: 929-945
-
(2004)
Plant Mol Biol
, vol.56
, pp. 929-945
-
-
Wang, L.1
Dong, L.2
Zhang, Y.3
Zhang, Y.4
Wu, W.5
Deng, X.6
Xue, Y.7
-
45
-
-
0034867567
-
ORE9, an F-box protein that regulates leaf senescence in Arabidopsis
-
Woo HR, Chung KM, Park JH, Oh SA, Ahn T, Hong SH, Jang SK, Nam HG (2001) ORE9, an F-box protein that regulates leaf senescence in Arabidopsis. Plant Cell 13: 1779-1790
-
(2001)
Plant Cell
, vol.13
, pp. 1779-1790
-
-
Woo, H.R.1
Chung, K.M.2
Park, J.H.3
Oh, S.A.4
Ahn, T.5
Hong, S.H.6
Jang, S.K.7
Nam, H.G.8
-
46
-
-
40449120616
-
Genome structure and emerging evidence of an incipient sex chromosome in Populus
-
Yin T, DiFazio SP, Gunter LE, Zhang X, Sewell MM, Woolbright SA, Allan GJ, Kelleher CT, Douglas CJ, Wang M, et al (2008) Genome structure and emerging evidence of an incipient sex chromosome in Populus. Genome Res 18: 422-430
-
(2008)
Genome Res
, vol.18
, pp. 422-430
-
-
Yin, T.1
DiFazio, S.P.2
Gunter, L.E.3
Zhang, X.4
Sewell, M.M.5
Woolbright, S.A.6
Allan, G.J.7
Kelleher, C.T.8
Douglas, C.J.9
Wang, M.10
|