-
1
-
-
77949507309
-
Robust biomarker identification for cancer diagnosis with ensemble feature selection methods
-
Abeel, T., Helleputte, T., Van de Peer, Y., Dupont, P., and Saeys, Y. (2010). Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics 26: 392-398.
-
(2010)
Bioinformatics
, vol.26
, pp. 392-398
-
-
Abeel, T.1
Helleputte, T.2
de Peer, Y.V.3
Dupont, P.4
Saeys, Y.5
-
2
-
-
74249116441
-
Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12-regulated transcriptional network
-
Adato, A., et al. (2009). Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12-regulated transcriptional network. PLoS Genet. 5: e1000777.
-
(2009)
PLoS Genet
, vol.5
-
-
Adato, A.1
-
3
-
-
2942572926
-
Quantifying the relationship between co-expression, co-regulation and gene function
-
Allocco, D.J., Kohane, I.S., and Butte, A.J. (2004). Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics 5: 18.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 18
-
-
Allocco, D.J.1
Kohane, I.S.2
Butte, A.J.3
-
4
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
5
-
-
84857780876
-
Evidence for network evolution in an Arabidopsis interactome map
-
Arabidopsis Interactome Mapping Consortium
-
Arabidopsis Interactome Mapping Consortium (2011). Evidence for network evolution in an Arabidopsis interactome map. Science 333: 601-607.
-
(2011)
Science
, vol.333
, pp. 601-607
-
-
-
6
-
-
2942552459
-
An automated method for finding molecular complexes in large protein interaction networks
-
Bader, G.D., and Hogue, C.W. (2003). An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 4.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 4
-
-
Bader, G.D.1
Hogue, C.W.2
-
7
-
-
58149182724
-
NCBI GEO: Archive for high-throughput functional genomic data
-
(Database issue)
-
Barrett, T., et al. (2009). NCBI GEO: Archive for high-throughput functional genomic data. Nucleic Acids Res. 37(Database issue): D885-D890.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Barrett, T.1
-
8
-
-
84863561742
-
Lycopene cyclase paralog CruP protects against reactive oxygen species in oxygenic photosyn-thetic organisms
-
Bradbury, L.M.T., Shumskaya, M., Tzfadia, O., Wu, S.-B., Kennelly, E.J., and Wurtzel, E.T. (2012). Lycopene cyclase paralog CruP protects against reactive oxygen species in oxygenic photosyn-thetic organisms. Proc. Natl. Acad. Sci. USA 109: E1888-E1897.
-
(2012)
Proc. Natl. Acad. Sci.
, vol.109
-
-
Bradbury, L.M.T.1
Shumskaya, M.2
Tzfadia, O.3
Wu, S.B.4
Kennelly, E.J.5
Wurtzel, E.T.6
-
9
-
-
0035183643
-
Bleaching herbicide norflurazon inhibits phytoene desaturase by competition with the cofactors
-
Breitenbach, J., Zhu, C., and Sandmann, G. (2001). Bleaching herbicide norflurazon inhibits phytoene desaturase by competition with the cofactors. J. Agric. Food Chem. 49: 5270-5272.
-
(2001)
J. Agric. Food Chem
, vol.49
, pp. 5270-5272
-
-
Breitenbach, J.1
Zhu, C.2
Sandmann, G.3
-
10
-
-
33745035630
-
Predicting genes for orphan metabolic activities using phylogenetic profiles
-
Chen, L., and Vitkup, D. (2006). Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biol. 7: R17.
-
(2006)
Genome Biol
, vol.7
-
-
Chen, L.1
Vitkup, D.2
-
11
-
-
0347968038
-
NASCArrays: A repository for microarray data generated by NASC's transcriptomics service
-
(Database issue)
-
Craigon, D.J., James, N., Okyere, J., Higgins, J., Jotham, J., and May, S. (2004). NASCArrays: A repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res. 32(Database issue): D575-D577.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Craigon, D.J.1
James, N.2
Okyere, J.3
Higgins, J.4
Jotham, J.5
May, S.6
-
12
-
-
80051571790
-
Carotenoids
-
F. Rébeillé and R. Douce, eds (Amsterdam: Elsevier
-
Cuttriss, A.J., Cazzonelli, C.I., Wurtzel, E.T., and Pogson, B.J. (2011). Carotenoids. In Biosynthesis of Vitamins in Plants (Advances in Botanical Research, Part A), F. Rébeillé and R. Douce, eds (Amsterdam: Elsevier), pp. 1-36.
-
(2011)
Biosynthesis of Vitamins In Plants (Advances In Botanical Research, Part A)
, pp. 1-36
-
-
Cuttriss, A.J.1
Cazzonelli, C.I.2
Wurtzel, E.T.3
Pogson, B.J.4
-
13
-
-
0742304254
-
Prediction of protein function using protein-protein interaction data
-
Deng, M.H., Zhang, K., Mehta, S., Chen, T., and Sun, F.Z. (2003). Prediction of protein function using protein-protein interaction data. J. Comput. Biol. 10: 947-960.
-
(2003)
J. Comput. Biol.
, vol.10
, pp. 947-960
-
-
Deng, M.H.1
Zhang, K.2
Mehta, S.3
Chen, T.4
Sun, F.Z.5
-
14
-
-
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
-
15
-
-
84859336922
-
Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches
-
Fukushima, A., Nishizawa, T., Hayakumo, M., Hikosaka, S., Saito, K., Goto, E., and Kusano, M. (2012). Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. Plant Physiol. 158: 1487-1502.
-
(2012)
Plant Physiol
, vol.158
, pp. 1487-1502
-
-
Fukushima, A.1
Nishizawa, T.2
Hayakumo, M.3
Hikosaka, S.4
Saito, K.5
Goto, E.6
Kusano, M.7
-
16
-
-
79958850343
-
Synergistic use of plant-prokaryote comparative genomics for functional annotations
-
Gerdes, S., et al. (2011). Synergistic use of plant-prokaryote comparative genomics for functional annotations. BMC Genomics 12 (suppl. 1): S2.
-
(2011)
BMC Genomics
, vol.12
, Issue.1 SUPPL.
-
-
Gerdes, S.1
-
17
-
-
33646140795
-
Integrative analysis of transcript and metabolite profiling data sets to evaluate the regulation of biochemical pathways during photomorphogenesis. Arch. Biochem
-
Ghassemian, M., Lutes, J., Tepperman, J.M., Chang, H.S., Zhu, T., Wang, X., Quail, P.H., and Lange, B.M. (2006). Integrative analysis of transcript and metabolite profiling data sets to evaluate the regulation of biochemical pathways during photomorphogenesis. Arch. Biochem. Biophys. 448: 45-59.
-
(2006)
Biophys
, vol.448
, pp. 45-59
-
-
Ghassemian, M.1
Lutes, J.2
Tepperman, J.M.3
Chang, H.S.4
Zhu, T.5
Wang, X.6
Quail, P.H.7
Lange, B.M.8
-
18
-
-
76749118521
-
Model selection: Beyond the Bayesian/frequentist divide
-
Guyon, I., Saffari, A., Dror, G., and Cawley, G. (2010). Model selection: Beyond the Bayesian/frequentist divide. J. Mach. Learn. Res. 11: 61-87.
-
(2010)
J. Mach. Learn. Res
, vol.11
, pp. 61-87
-
-
Guyon, I.1
Saffari, A.2
Dror, G.3
Cawley, G.4
-
19
-
-
34548453543
-
Modulation of flower colour by rationally designed dominant-negative chalcone synthase
-
Hanumappa, M., Choi, G., Ryu, S., and Choi, G. (2007). Modulation of flower colour by rationally designed dominant-negative chalcone synthase. J. Exp. Bot. 58: 2471-2478.
-
(2007)
J. Exp. Bot.
, vol.58
, pp. 2471-2478
-
-
Hanumappa, M.1
Choi, G.2
Ryu, S.3
Choi, G.4
-
20
-
-
37249090669
-
Zeaxanthin has enhanced antioxidant capacity with respect to all other xanthophylls in Arabidopsis leaves and functions independent of binding to PSII antennae
-
Havaux, M., Dall'osto, L., and Bassi, R. (2007). Zeaxanthin has enhanced antioxidant capacity with respect to all other xanthophylls in Arabidopsis leaves and functions independent of binding to PSII antennae. Plant Physiol. 145: 1506-1520.
-
(2007)
Plant Physiol
, vol.145
, pp. 1506-1520
-
-
Havaux, M.1
Dall'Osto, L.2
Bassi, R.3
-
21
-
-
66649130759
-
Arabidopsis CHLI2 can substitute for CHLI1
-
Huang, Y.S., and Li, H.M. (2009). Arabidopsis CHLI2 can substitute for CHLI1. Plant Physiol. 150: 636-645.
-
(2009)
Plant Physiol
, vol.150
, pp. 636-645
-
-
Huang, Y.S.1
Li, H.M.2
-
22
-
-
78650539578
-
Network-based function prediction and interactomics: The case for metabolic enzymes
-
Janga, S.C., Díaz-Mejía, J.J., and Moreno-Hagelsieb, G. (2011). Network-based function prediction and interactomics: The case for metabolic enzymes. Metab. Eng. 13: 1-10.
-
(2011)
Metab. Eng.
, vol.13
, pp. 1-10
-
-
Janga, S.C.1
Díaz-Mejía, J.J.2
Moreno-Hagelsieb, G.3
-
23
-
-
34547961560
-
Elevated zeaxanthin bound to oligomeric LHCII enhances the resistance of Arabidopsis to photooxidative stress by a lipid-protective, antioxidant mechanism
-
Johnson, M.P., Havaux, M., Triantaphylidès, C., Ksas, B., Pascal, A.A., Robert, B., Davison, P.A., Ruban, A.V., and Horton, P. (2007). Elevated zeaxanthin bound to oligomeric LHCII enhances the resistance of Arabidopsis to photooxidative stress by a lipid-protective, antioxidant mechanism. J. Biol. Chem. 282: 22605-22618.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 22605-22618
-
-
Johnson, M.P.1
Havaux, M.2
Triantaphylidès, C.3
Ksas, B.4
Pascal, A.A.5
Robert, B.6
Davison, P.A.7
Ruban, A.V.8
Horton, P.9
-
24
-
-
0033841024
-
A plastid terminal oxidase associated with carot-enoid desaturation during chromoplast differentiation
-
Josse, E.M., Simkin, A.J., Gaffé, J., Labouré, A.M., Kuntz, M., and Carol, P. (2000). A plastid terminal oxidase associated with carot-enoid desaturation during chromoplast differentiation. Plant Physi-ol. 123: 1427-1436.
-
(2000)
Plant Physi-ol
, vol.123
, pp. 1427-1436
-
-
Josse, E.M.1
Simkin, A.J.2
Gaffé, J.3
Labouré, A.M.4
Kuntz, M.5
Carol, P.6
-
25
-
-
12444251193
-
Identification and subcellular localization of two solanesyl diphosphate synthases from Arabidopsis thaliana
-
Jun, L., Saiki, R., Tatsumi, K., Nakagawa, T., and Kawamukai, M. (2004). Identification and subcellular localization of two solanesyl diphosphate synthases from Arabidopsis thaliana. Plant Cell Physiol. 45: 1882-1888.
-
(2004)
Plant Cell Physiol
, vol.45
, pp. 1882-1888
-
-
Jun, L.1
Saiki, R.2
Tatsumi, K.3
Nakagawa, T.4
Kawamukai, M.5
-
26
-
-
33646171940
-
Identifying metabolic enzymes with multiple types of association evidence
-
Kharchenko, P., Chen, L., Freund, Y., Vitkup, D., and Church, G.M. (2006). Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 7: 177.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 177
-
-
Kharchenko, P.1
Chen, L.2
Freund, Y.3
Vitkup, D.4
Church, G.M.5
-
27
-
-
33646200155
-
Expression dynamics of a cellular metabolic network
-
Kharchenko, P., Church, G.M., and Vitkup, D. (2005). Expression dynamics of a cellular metabolic network. Mol. Syst. Biol. 1: 2005.0016.
-
(2005)
Mol. Syst. Biol.
, vol.1
, Issue.2005
, pp. 0016
-
-
Kharchenko, P.1
Church, G.M.2
Vitkup, D.3
-
28
-
-
24744467372
-
Filling gaps in a metabolic network using expression information
-
Kharchenko, P., Vitkup, D., and Church, G.M. (2004). Filling gaps in a metabolic network using expression information. Bioinformatics 20(suppl. 1): i178-i185.
-
(2004)
Bioinformatics
, vol.20
, Issue.1 SUPPL.
-
-
Kharchenko, P.1
Vitkup, D.2
Church, G.M.3
-
29
-
-
24044489621
-
A previously found thylakoid membrane protein of 14kDa (TMP14) is a novel subunit of plant photosystem I and is designated PSI-P
-
Khrouchtchova, A., Hansson, M., Paakkarinen, V., Vainonen, J.P., Zhang, S., Jensen, P.E., Scheller, H.V., Vener, A.V., Aro, E.M., and Haldrup, A. (2005). A previously found thylakoid membrane protein of 14kDa (TMP14) is a novel subunit of plant photosystem I and is designated PSI-P. FEBS Lett. 579: 4808-4812.
-
(2005)
FEBS Lett
, vol.579
, pp. 4808-4812
-
-
Khrouchtchova, A.1
Hansson, M.2
Paakkarinen, V.3
Vainonen, J.P.4
Zhang, S.5
Jensen, P.E.6
Scheller, H.V.7
Vener, A.V.8
Aro, E.M.9
Haldrup, A.10
-
30
-
-
79952309382
-
Transgenic poplar expressing Arabidopsis NDPK2 enhances growth as well as oxidative stress tolerance
-
Kim, Y.H., Kim, M.D., Choi, Y.I., Park, S.C., Yun, D.J., Noh, E.W., Lee, H.S., and Kwak, S.S. (2011). Transgenic poplar expressing Arabidopsis NDPK2 enhances growth as well as oxidative stress tolerance. Plant Biotechnol. J. 9: 334-347.
-
(2011)
Plant Biotechnol. J
, vol.9
, pp. 334-347
-
-
Kim, Y.H.1
Kim, M.D.2
Choi, Y.I.3
Park, S.C.4
Yun, D.J.5
Noh, E.W.6
Lee, H.S.7
Kwak, S.S.8
-
32
-
-
77949748403
-
Bayesian Markov Random Field analysis for protein function prediction based on network data
-
Kourmpetis, Y.A.I., van Dijk, A.D.J., Bink, M.C.A.M., van Ham, R.C. H.J., and ter Braak, C.J.F. (2010). Bayesian Markov Random Field analysis for protein function prediction based on network data. PLoS ONE 5: e9293.
-
(2010)
PLoS ONE
, vol.5
-
-
Kourmpetis, Y.A.I.1
van Dijk, A.D.J.2
Bink, M.C.A.M.3
van Ham, R.C.H.J.4
Ter, B.C.J.F.5
-
33
-
-
34248157134
-
Signals from chloroplasts converge to regulate nuclear gene expression
-
Koussevitzky, S., Nott, A., Mockler, T.C., Hong, F., Sachetto-Martins, G., Surpin, M., Lim, J., Mittler, R., and Chory, J. (2007). Signals from chloroplasts converge to regulate nuclear gene expression. Science 316: 715-719.
-
(2007)
Science
, vol.316
, pp. 715-719
-
-
Koussevitzky, S.1
Nott, A.2
Mockler, T.C.3
Hong, F.4
Sachetto-Martins, G.5
Surpin, M.6
Lim, J.7
Mittler, R.8
Chory, J.9
-
34
-
-
33746227788
-
Gene classification using expression profiles: A feasibility study
-
Kuramochi, M., and Karypis, G. (2005). Gene classification using expression profiles: A feasibility study. Int. J. Artif. Intell. Tools 14: 641-660.
-
(2005)
Int. J. Artif. Intell. Tools
, vol.14
, pp. 641-660
-
-
Kuramochi, M.1
Karypis, G.2
-
35
-
-
77952382638
-
Global analysis of gene activity during Arabi-dopsis seed development and identification of seed-specific transcription factors
-
Le, B.H., et al. (2010). Global analysis of gene activity during Arabi-dopsis seed development and identification of seed-specific transcription factors. Proc. Natl. Acad. Sci. USA 107: 8063-8070.
-
(2010)
Proc. Natl. Acad. Sci.
, vol.107
, pp. 8063-8070
-
-
Le, B.H.1
-
36
-
-
84859516508
-
Combined tran-scriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation
-
Lee, J.M., Joung, J.-G., McQuinn, R., Chung, M.-Y., Fei, Z., Tieman, D., Klee, H., and Giovannoni, J. (2012). Combined tran-scriptome, genetic diversity and metabolite profiling in tomato fruit reveals that the ethylene response factor SlERF6 plays an important role in ripening and carotenoid accumulation. Plant J. 70: 191-204.
-
(2012)
Plant J
, vol.70
, pp. 191-204
-
-
Lee, J.M.1
Joung, J.G.2
McQuinn, R.3
Chung, M.Y.4
Fei, Z.5
Tieman, D.6
Klee, H.7
Giovannoni, J.8
-
37
-
-
0038104857
-
Genomic gene clustering analysis of pathways in eukaryotes
-
Lee, J.M., and Sonnhammer, E.L. (2003). Genomic gene clustering analysis of pathways in eukaryotes. Genome Res. 13: 875-882.
-
(2003)
Genome Res.
, vol.13
, pp. 875-882
-
-
Lee, J.M.1
Sonnhammer, E.L.2
-
38
-
-
1542271409
-
Predicting protein function from protein/protein interaction data: A probabilistic approach
-
Letovsky, S., and Kasif, S. (2003). Predicting protein function from protein/protein interaction data: A probabilistic approach. Bio-informatics 19(suppl. 1): i197-i204.
-
(2003)
Bio-informatics
, vol.19
, Issue.1
-
-
Letovsky, S.1
Kasif, S.2
-
39
-
-
51549106579
-
The maize phytoene synthase gene family: Overlapping roles for carotenogenesis in endosperm, photomorphogenesis, and thermal stress tolerance
-
Li, F., Vallabhaneni, R., Yu, J., Rocheford, T., and Wurtzel, E.T. (2008). The maize phytoene synthase gene family: Overlapping roles for carotenogenesis in endosperm, photomorphogenesis, and thermal stress tolerance. Plant Physiol. 147: 1334-1346.
-
(2008)
Plant Physiol
, vol.147
, pp. 1334-1346
-
-
Li, F.1
Vallabhaneni, R.2
Yu, J.3
Rocheford, T.4
Wurtzel, E.T.5
-
40
-
-
84855291545
-
Overlapping photo-protective function of vitamin E and carotenoids in Chlamydomo-nas
-
Li, Z., Keasling, J.D., and Niyogi, K.K. (2012). Overlapping photo-protective function of vitamin E and carotenoids in Chlamydomo-nas. Plant Physiol. 158: 313-323.
-
(2012)
Plant Physiol
, vol.158
, pp. 313-323
-
-
Li, Z.1
Keasling, J.D.2
Niyogi, K.K.3
-
41
-
-
12344328280
-
Resolution of (+)-abscisic acid using an Ara-bidopsis glycosyltransferase
-
Lim, E.K., Doucet, C.J., Hou, B., Jackson, R.G., Abrams, S.R., and Bowles, D.J. (2005). Resolution of (+)-abscisic acid using an Ara-bidopsis glycosyltransferase. Tetrahedron Asymmetry 16: 143-147.
-
(2005)
Tetrahedron Asymmetry
, vol.16
, pp. 143-147
-
-
Lim, E.K.1
Doucet, C.J.2
Hou, B.3
Jackson, R.G.4
Abrams, S.R.5
Bowles, D.J.6
-
42
-
-
78651323089
-
PAIR: The predicted Arabidopsis interactome resource
-
Lin, M, Shen, X, and Chen, X. (2011). PAIR: the predicted Arabidopsis interactome resource. Nucl. Acids Res. 39 (suppl 1): D1134-D1140.
-
(2011)
Nucl. Acids Res.
, vol.39
, Issue.1 SUPPL.
-
-
Lin, M.1
Shen, X.2
Chen, X.3
-
43
-
-
33747814803
-
Arabidopsis Co-expression Tool (ACT): Web server tools for microarray-based gene expression analysis
-
(Web Server issue)
-
Manfield, I.W., Jen, C.H., Pinney, J.W., Michalopoulos, I., Bradford, J.R., Gilmartin, P.M., and Westhead, D.R. (2006). Arabidopsis Co-expression Tool (ACT): Web server tools for microarray-based gene expression analysis. Nucleic Acids Res. 34(Web Server issue): W504-W509.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Manfield, I.W.1
Jen, C.H.2
Pinney, J.W.3
Michalopoulos, I.4
Bradford, J.R.5
Gilmartin, P.M.6
Westhead, D.R.7
-
44
-
-
0141907262
-
Maize phytoene desaturase and zeta-carotene desaturase catalyse a poly-Z desa-turation pathway: Implications for genetic engineering of carotenoid content among cereal crops
-
Matthews, P.D., Luo, R., and Wurtzel, E.T. (2003). Maize phytoene desaturase and zeta-carotene desaturase catalyse a poly-Z desa-turation pathway: Implications for genetic engineering of carotenoid content among cereal crops. J. Exp. Bot. 54: 2215-2230.
-
(2003)
J. Exp. Bot.
, vol.54
, pp. 2215-2230
-
-
Matthews, P.D.1
Luo, R.2
Wurtzel, E.T.3
-
45
-
-
0025325851
-
Quinone compounds are able to replace molecular oxygen as terminal electron acceptor in phytoene desaturation in chromoplasts of Narcissus pseudo-narcissus L
-
Mayer, M.P., Beyer, P., and Kleinig, H. (1990). Quinone compounds are able to replace molecular oxygen as terminal electron acceptor in phytoene desaturation in chromoplasts of Narcissus pseudo-narcissus L. Eur. J. Biochem. 191: 359-363.
-
(1990)
Eur. J. Biochem
, vol.191
, pp. 359-363
-
-
Mayer, M.P.1
Beyer, P.2
Kleinig, H.3
-
46
-
-
79956042387
-
A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana
-
Meier, S., Tzfadia, O., Vallabhaneni, R., Gehring, C., and Wurtzel, E.T. (2011). A transcriptional analysis of carotenoid, chlorophyll and plastidial isoprenoid biosynthesis genes during development and osmotic stress responses in Arabidopsis thaliana. BMC Syst. Biol. 5: 77.
-
(2011)
BMC Syst. Biol
, vol.5
, pp. 77
-
-
Meier, S.1
Tzfadia, O.2
Vallabhaneni, R.3
Gehring, C.4
Wurtzel, E.T.5
-
47
-
-
78049261567
-
Plas-tochromanol-8 and tocopherols are essential lipid-soluble anti-oxidants during seed desiccation and quiescence in Arabidopsis
-
Mène-Saffrané, L., Jones, A.D., and DellaPenna, D. (2010). Plas-tochromanol-8 and tocopherols are essential lipid-soluble anti-oxidants during seed desiccation and quiescence in Arabidopsis. Proc. Natl. Acad. Sci. USA 107: 17815-17820.
-
(2010)
Proc. Natl. Acad. Sci.
, vol.107
, pp. 17815-17820
-
-
Mène-Saffrané, L.1
Jones, A.D.2
Dellapenna, D.3
-
48
-
-
48549105883
-
Gene expression and metabolism in tomato fruit surface tissues
-
Mintz-Oron, S., Mandel, T., Rogachev, I., Feldberg, L., Lotan, O., Yativ, M., Wang, Z., Jetter, R., Venger, I., Adato, A., and Aharoni, A. (2008). Gene expression and metabolism in tomato fruit surface tissues. Plant Physiol. 147: 823-851.
-
(2008)
Plant Physiol
, vol.147
, pp. 823-851
-
-
Mintz-Oron, S.1
Mandel, T.2
Rogachev, I.3
Feldberg, L.4
Lotan, O.5
Yativ, M.6
Wang, Z.7
Jetter, R.8
Venger, I.9
Adato, A.10
Aharoni, A.11
-
49
-
-
0035852789
-
Arabidopsis genomes uncoupled 5 (GUN5) mutant reveals the involvement of Mg-chelatase H subunit in plastid-to-nucleus signal transduction
-
Mochizuki, N., Brusslan, J.A., Larkin, R., Nagatani, A., and Chory, J. (2001). Arabidopsis genomes uncoupled 5 (GUN5) mutant reveals the involvement of Mg-chelatase H subunit in plastid-to-nucleus signal transduction. Proc. Natl. Acad. Sci. USA 98: 2053-2058.
-
(2001)
Proc. Natl. Acad. Sci.
, vol.98
, pp. 2053-2058
-
-
Mochizuki, N.1
Brusslan, J.A.2
Larkin, R.3
Nagatani, A.4
Chory, J.5
-
50
-
-
0037422543
-
NDP kinase 2 interacts with two oxidative stress-activated MAPKs to regulate cellular redox state and enhances multiple stress tolerance in transgenic plants
-
Moon, H., et al. (2003). NDP kinase 2 interacts with two oxidative stress-activated MAPKs to regulate cellular redox state and enhances multiple stress tolerance in transgenic plants. Proc. Natl. Acad. Sci. USA 100: 358-363.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 358-363
-
-
Moon, H.1
-
51
-
-
70349099266
-
Defect in non-yellow coloring 3, an a/b hydrolase-fold family protein, causes a stay-green phenotype during leaf senescence in rice
-
Morita, R., Sato, Y., Masuda, Y., Nishimura, M., and Kusaba, M. (2009). Defect in non-yellow coloring 3, an a/b hydrolase-fold family protein, causes a stay-green phenotype during leaf senescence in rice. Plant J. 59: 940-952.
-
(2009)
Plant J
, vol.59
, pp. 940-952
-
-
Morita, R.1
Sato, Y.2
Masuda, Y.3
Nishimura, M.4
Kusaba, M.5
-
52
-
-
79955581503
-
PlaNet: Combined sequence and expression comparisons across plant networks derived from seven species
-
Mutwil, M., Klie, S., Tohge, T., Giorgi, F.M., Wilkins, O., Campbell, M.M., Fernie, A.R., Usadel, B., Nikoloski, Z., and Persson, S. (2011). PlaNet: Combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell 23: 895-910.
-
(2011)
Plant Cell
, vol.23
, pp. 895-910
-
-
Mutwil, M.1
Klie, S.2
Tohge, T.3
Giorgi, F.M.4
Wilkins, O.5
Campbell, M.M.6
Fernie, A.R.7
Usadel, B.8
Nikoloski, Z.9
Persson, S.10
-
53
-
-
48449091196
-
Gene-CAT-Novel webtools that combine BLAST and co-expression analyses
-
Mutwil, M., Obro, J., Willats, W.G., and Persson, S. (2008). Gene-CAT-Novel webtools that combine BLAST and co-expression analyses. Nucleic Acids Res. 36: W320-W326.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Mutwil, M.1
Obro, J.2
Willats, W.G.3
Persson, S.4
-
54
-
-
29144442904
-
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
-
Nabieva, E., Jim, K., Agarwal, A., Chazelle, B., and Singh, M. (2005). Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics 21(suppl. 1): i302-i310.
-
(2005)
Bioinformatics
, vol.21
, Issue.1
-
-
Nabieva, E.1
Jim, K.2
Agarwal, A.3
Chazelle, B.4
Singh, M.5
-
55
-
-
0029556712
-
Genetic dissection of carotenoid synthesis in Arabidopsis defines plasto-quinone as an essential component of phytoene desaturation
-
Norris, S.R., Barrette, T.R., and DellaPenna, D. (1995). Genetic dissection of carotenoid synthesis in Arabidopsis defines plasto-quinone as an essential component of phytoene desaturation. Plant Cell 7: 2139-2149.
-
(1995)
Plant Cell
, vol.7
, pp. 2139-2149
-
-
Norris, S.R.1
Barrette, T.R.2
Dellapenna, D.3
-
56
-
-
58149197587
-
ATTED-II provides coexpressed gene networks for Arabi-dopsis
-
(Database issue)
-
Obayashi, T., Hayashi, S., Saeki, M., Ohta, H., and Kinoshita, K. (2009). ATTED-II provides coexpressed gene networks for Arabi-dopsis. Nucleic Acids Res. 37(Database issue): D987-D991.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Obayashi, T.1
Hayashi, S.2
Saeki, M.3
Ohta, H.4
Kinoshita, K.5
-
57
-
-
78651335279
-
Systematizing the generation of missing metabolic knowledge
-
Orth, J.D., and Palsson, B.O. (2010). Systematizing the generation of missing metabolic knowledge. Biotechnol. Bioeng. 107: 403-412.
-
(2010)
Biotechnol. Bioeng
, vol.107
, pp. 403-412
-
-
Orth, J.D.1
Palsson, B.O.2
-
58
-
-
67650898284
-
Incorporating functional inter-relationships into protein function prediction algorithms
-
Pandey, G., Myers, C.L., and Kumar, V. (2009). Incorporating functional inter-relationships into protein function prediction algorithms. BMC Bioinformatics 10: 142.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 142
-
-
Pandey, G.1
Myers, C.L.2
Kumar, V.3
-
59
-
-
0033551248
-
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
-
Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D., and Yeates, T.O. (1999). Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96: 4285-4288.
-
(1999)
Proc. Natl. Acad. Sci.
, vol.96
, pp. 4285-4288
-
-
Pellegrini, M.1
Marcotte, E.M.2
Thompson, M.J.3
Eisenberg, D.4
Yeates, T.O.5
-
60
-
-
33646126286
-
Biosynthetic diversity in plant triterpene cyclization
-
Phillips, D.R., Rasbery, J.M., Bartel, B., and Matsuda, S.P. (2006). Biosynthetic diversity in plant triterpene cyclization. Curr. Opin. Plant Biol. 9: 305-314.
-
(2006)
Curr. Opin. Plant Biol.
, vol.9
, pp. 305-314
-
-
Phillips, D.R.1
Rasbery, J.M.2
Bartel, B.3
Matsuda, S.P.4
-
61
-
-
76749127527
-
Genotype-phenotype mapping and the end of the'genes as blueprint' metaphor
-
Pigliucci, M. (2009). Genotype-phenotype mapping and the end of the'genes as blueprint' metaphor. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365: 557-566.
-
(2009)
Philos. Trans. R. Soc. Lond. B Biol. Sci
, vol.365
, pp. 557-566
-
-
Pigliucci, M.1
-
62
-
-
84857658973
-
Computational approaches to disease-gene prediction: Rationale, classification and successes
-
Piro, R.M., and Di Cunto, F. (2012). Computational approaches to disease-gene prediction: Rationale, classification and successes. FEBS J. 279: 678-696.
-
(2012)
FEBS J
, vol.279
, pp. 678-696
-
-
Piro, R.M.1
Di, C.F.2
-
63
-
-
54549083103
-
Plastid signalling to the nucleus and beyond
-
Pogson, B.J., Woo, N.S., Förster, B., and Small, I.D. (2008). Plastid signalling to the nucleus and beyond. Trends Plant Sci. 13: 602-609.
-
(2008)
Trends Plant Sci.
, vol.13
, pp. 602-609
-
-
Pogson, B.J.1
Woo, N.S.2
Förster, B.3
Small, I.D.4
-
64
-
-
25444533305
-
Automation of gene assignments to metabolic pathways using high-throughput expression data
-
Popescu, L., and Yona, G. (2005). Automation of gene assignments to metabolic pathways using high-throughput expression data. BMC Bioinformatics 6: 217.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 217
-
-
Popescu, L.1
Yona, G.2
-
65
-
-
84862976010
-
Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development
-
Powell, A.L.T., et al. (2012). Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development. Science 336: 1711-1715.
-
(2012)
Science
, vol.336
, pp. 1711-1715
-
-
Powell, A.L.T.1
-
66
-
-
35848934561
-
2-induced cell death
-
Queval, G., Issakidis-Bourguet, E., Hoeberichts, F.A., Vandorpe, M., Gakière, B., Vanacker, H., Miginiac-Maslow, M., Van Breusegem, F., and Noctor, G. (2007). Conditional oxidative stress responses in the Arabidopsis photorespiratory mutant cat2 demonstrate that redox state is a key modulator of daylength-dependent gene expression, and define photoperiod as a crucial factor in the regulation of H2O2-induced cell death. Plant J. 52: 640-657.
-
(2007)
Plant J
, vol.52
, pp. 640-657
-
-
Queval, G.1
Issakidis-Bourguet, E.2
Hoeberichts, F.A.3
Vandorpe, M.4
Gakière, B.5
Vanacker, H.6
Miginiac-Maslow, M.7
van Breusegem, F.8
Noctor, G.9
-
67
-
-
37849020436
-
Decoding genes with coexpression networks and metabolomics -'Majority report by precogs'
-
Saito, K., Hirai, M.Y., and Yonekura-Sakakibara, K. (2008). Decoding genes with coexpression networks and metabolomics -'Majority report by precogs'. Trends Plant Sci. 13: 36-43.
-
(2008)
Trends Plant Sci.
, vol.13
, pp. 36-43
-
-
Saito, K.1
Hirai, M.Y.2
Yonekura-Sakakibara, K.3
-
68
-
-
84864479585
-
Identification of a photosystem II phosphatase involved in light acclimation in Arabidopsis
-
Samol, I., Shapiguzov, A., Ingelsson, B., Fucile, G., Crèvecoeur, M., Vener, A.V., Rochaix, J.D., and Goldschmidt-Clermont, M. (2012). Identification of a photosystem II phosphatase involved in light acclimation in Arabidopsis. Plant Cell 24: 2596-2609.
-
(2012)
Plant Cell
, vol.24
, pp. 2596-2609
-
-
Samol, I.1
Shapiguzov, A.2
Ingelsson, B.3
Fucile, G.4
Crèvecoeur, M.5
Vener, A.V.6
Rochaix, J.D.7
Goldschmidt-Clermont, M.8
-
69
-
-
33846465545
-
Molecular markers of early Parkinson's disease based on gene expression in blood
-
Scherzer, C.R., et al. (2007). Molecular markers of early Parkinson's disease based on gene expression in blood. Proc. Natl. Acad. Sci. USA 104: 955-960.
-
(2007)
Proc. Natl. Acad. Sci.
, vol.104
, pp. 955-960
-
-
Scherzer, C.R.1
-
70
-
-
6344235622
-
A novel NADPH thioredoxin reductase, localized in the chloroplast, which deficiency causes hypersensitivity to abiotic stress in Arabidopsis thaliana
-
Serrato, A.J., Pérez-Ruiz, J.M., Spínola, M.C., and Cejudo, F.J. (2004). A novel NADPH thioredoxin reductase, localized in the chloroplast, which deficiency causes hypersensitivity to abiotic stress in Arabidopsis thaliana. J. Biol. Chem. 279: 43821-43827.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 43821-43827
-
-
Serrato, A.J.1
Pérez-Ruiz, J.M.2
Spínola, M.C.3
Cejudo, F.J.4
-
71
-
-
0141506116
-
CLICK and EXPANDER: A system for clustering and visualizing gene expression data
-
Sharan, R., Maron-Katz, A., and Shamir, R. (2003). CLICK and EXPANDER: A system for clustering and visualizing gene expression data. Bio-informatics 19: 1787-1799.
-
(2003)
Bio-informatics
, vol.19
, pp. 1787-1799
-
-
Sharan, R.1
Maron-Katz, A.2
Shamir, R.3
-
72
-
-
33947252154
-
Network-based prediction of protein function
-
Sharan, R., Ulitsky, I., and Shamir, R. (2007). Network-based prediction of protein function. Mol. Syst. Biol. 3: 88.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 88
-
-
Sharan, R.1
Ulitsky, I.2
Shamir, R.3
-
73
-
-
51549093662
-
CressExpress: A tool for large-scale mining of expression data from Arabidopsis
-
Srinivasasainagendra, V., Page, G.P., Mehta, T., Coulibaly, I., and Loraine, A.E. (2008). CressExpress: A tool for large-scale mining of expression data from Arabidopsis. Plant Physiol. 147: 1004-1016.
-
(2008)
Plant Physiol
, vol.147
, pp. 1004-1016
-
-
Srinivasasainagendra, V.1
Page, G.P.2
Mehta, T.3
Coulibaly, I.4
Loraine, A.E.5
-
74
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart, J.M., Segal, E., Koller, D., and Kim, S.K. (2003). A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255.
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
76
-
-
1342287231
-
Lipoic acid-dependent oxidative catabolism of alpha-keto acids in mitochondria provides evidence for branched-chain amino acid catabolism in Arabidopsis
-
Taylor, N.L., Heazlewood, J.L., Day, D.A., and Millar, A.H. (2004). Lipoic acid-dependent oxidative catabolism of alpha-keto acids in mitochondria provides evidence for branched-chain amino acid catabolism in Arabidopsis. Plant Physiol. 134: 838-848.
-
(2004)
Plant Physiol
, vol.134
, pp. 838-848
-
-
Taylor, N.L.1
Heazlewood, J.L.2
Day, D.A.3
Millar, A.H.4
-
77
-
-
12144291195
-
MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
-
Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L.A., Rhee, S.Y., and Stitt, M. (2004). MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37: 914-939.
-
(2004)
Plant J
, vol.37
, pp. 914-939
-
-
Thimm, O.1
Blasing, O.2
Gibon, Y.3
Nagel, A.4
Meyer, S.5
Kruger, P.6
Selbig, J.7
Muller, L.A.8
Rhee, S.Y.9
Stitt, M.10
-
78
-
-
77954936165
-
Direct regulation of phytoene synthase gene expression and ca-rotenoid biosynthesis by phytochrome-interacting factors
-
Toledo-Ortiz, G., Huq, E., and Rodríguez-Concepción, M. (2010). Direct regulation of phytoene synthase gene expression and ca-rotenoid biosynthesis by phytochrome-interacting factors. Proc. Natl. Acad. Sci. USA 107: 11626-11631.
-
(2010)
Proc. Natl. Acad. Sci.
, vol.107
, pp. 11626-11631
-
-
Toledo-Ortiz, G.1
Huq, E.2
Rodríguez-Concepción, M.3
-
79
-
-
84863693752
-
The tomato genome sequence provides insights into fleshy fruit evolution
-
Tomato Genome Consortium
-
Tomato Genome Consortium (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641.
-
(2012)
Nature
, vol.485
, pp. 635-641
-
-
-
80
-
-
22044437388
-
The botany array resource: E-Northerns, expression angling, and promoter analyses
-
Toufighi, K., Brady, S.M., Austin, R., Ly, E., and Provart, N.J. (2005). The botany array resource: e-Northerns, expression angling, and promoter analyses. Plant J. 43: 153-163.
-
(2005)
Plant J
, vol.43
, pp. 153-163
-
-
Toufighi, K.1
Brady, S.M.2
Austin, R.3
Ly, E.4
Provart, N.J.5
-
81
-
-
76649122816
-
Expander: From expression microarrays to networks and functions
-
Ulitsky, I., Maron-Katz, A., Shavit, S., Sagir, D., Linhart, C, Elkon, R., Tanay, A., Sharan, R., Shiloh, Y., and Shamir, R. (2010). Expander: From expression microarrays to networks and functions. Nat. Protoc. 5: 303-322.
-
(2010)
Nat. Protoc
, vol.5
, pp. 303-322
-
-
Ulitsky, I.1
Maron-Katz, A.2
Shavit, S.3
Sagir, D.4
Linhart, C.5
Elkon, R.6
Tanay, A.7
Sharan, R.8
Shiloh, Y.9
Shamir, R.10
-
82
-
-
34548742517
-
Identification of functional modules using network topology and high-throughput data
-
Ulitsky, I., and Shamir, R. (2007). Identification of functional modules using network topology and high-throughput data. BMC Syst. Biol. 1: 8.
-
(2007)
BMC Syst. Biol.
, vol.1
, pp. 8
-
-
Ulitsky, I.1
Shamir, R.2
-
83
-
-
65449141657
-
Identifying functional modules using expression profiles and confidence-scored protein interactions
-
Ulitsky, I., and Shamir, R. (2009). Identifying functional modules using expression profiles and confidence-scored protein interactions. Bioinformatics 25: 1158-1164.
-
(2009)
Bioinformatics
, vol.25
, pp. 1158-1164
-
-
Ulitsky, I.1
Shamir, R.2
-
84
-
-
70449115789
-
Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats
-
Usadel, B., Obayashi, T., Mutwil, M., Giorgi, F.M., Bassel, G.W., Tanimoto, M., Chow, A., Steinhauser, D., Persson, S., and Provart, N.J. (2009). Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats. Plant Cell Environ. 32: 1633-1651.
-
(2009)
Plant Cell Environ.
, vol.32
, pp. 1633-1651
-
-
Usadel, B.1
Obayashi, T.2
Mutwil, M.3
Giorgi, F.M.4
Bassel, G.W.5
Tanimoto, M.6
Chow, A.7
Steinhauser, D.8
Persson, S.9
Provart, N.J.10
-
85
-
-
0005924596
-
-
PhD Dissertation (Utrecht The Netherlands: University of Utrecht)
-
Van Dongen, S. (2000). Graph Clustering by Flow Simulation. PhD dissertation (Utrecht, The Netherlands: University of Utrecht).
-
(2000)
Graph Clustering by Flow Simulation
-
-
van Dongen, S.1
-
86
-
-
65849100458
-
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs
-
Vlasblom, J., and Wodak, S.J. (2009). Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinformatics 10: 10.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 10
-
-
Vlasblom, J.1
Wodak, S.J.2
-
87
-
-
45149133700
-
The carotenoid cleavage dioxygenase 1 enzyme has broad substrate specificity, cleaving multiple carotenoids at two different bond positions
-
Vogel, J.T., Tan, B.C., McCarty, D.R., and Klee, H.J. (2008). The carotenoid cleavage dioxygenase 1 enzyme has broad substrate specificity, cleaving multiple carotenoids at two different bond positions. J. Biol. Chem. 283: 11364-11373.
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 11364-11373
-
-
Vogel, J.T.1
Tan, B.C.2
McCarty, D.R.3
Klee, H.J.4
-
89
-
-
63449102237
-
Molecular cloning and function analysis of an anthocyanidin synthase gene from Ginkgo biloba, and its expression in abiotic stress responses
-
Xu, F., Cheng, H., Cai, R., Li, L.L., Chang, J., Zhu, J., Zhang, F.X., Chen, L.J., Wang, Y., Cheng, S.H., and Cheng, S.Y. (2008). Molecular cloning and function analysis of an anthocyanidin synthase gene from Ginkgo biloba, and its expression in abiotic stress responses. Mol. Cells 26: 536-547.
-
(2008)
Mol. Cells
, vol.26
, pp. 536-547
-
-
Xu, F.1
Cheng, H.2
Cai, R.3
Li, L.L.4
Chang, J.5
Zhu, J.6
Zhang, F.X.7
Chen, L.J.8
Wang, Y.9
Cheng, S.H.10
Cheng, S.Y.11
-
90
-
-
19544389868
-
Protein network inference from multiple genomic data: A supervised approach
-
Yamanishi, Y., Vert, J.P., and Kanehisa, M. (2004). Protein network inference from multiple genomic data: A supervised approach. Bio-informatics 20(suppl. 1): i363-i370.
-
(2004)
Bio-informatics
, vol.20
, Issue.1 SUPPL.
-
-
Yamanishi, Y.1
Vert, J.P.2
Kanehisa, M.3
-
91
-
-
33947313355
-
A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data
-
Yao, Z.Z., and Ruzzo, W.L. (2006). A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data. BMC Bioinformatics 7: 7.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 7
-
-
Yao, Z.Z.1
Ruzzo, W.L.2
-
92
-
-
77957914336
-
Roles of xanthophyll carotenoids in protection against photoinhibition and oxidative stress in the cyano-bacterium Synechococcus sp strain PCC 7002. Arch. Biochem
-
Zhu, Y., Graham, J.E., Ludwig, M., Xiong, W., Alvey, R.M., Shen, G., and Bryant, D.A. (2010). Roles of xanthophyll carotenoids in protection against photoinhibition and oxidative stress in the cyano-bacterium Synechococcus sp strain PCC 7002. Arch. Biochem. Biophys. 504: 86-99.
-
(2010)
Biophys
, vol.504
, pp. 86-99
-
-
Zhu, Y.1
Graham, J.E.2
Ludwig, M.3
Xiong, W.4
Alvey, R.M.5
Shen, G.6
Bryant, D.A.7
|