-
1
-
-
77954272855
-
Translator X: Multiple alignment of nucleotide sequences guided by amino acid translations
-
PMID: 20435676
-
Abascal F, Zardoya R, Telford MJ. 2010. Translator X: multiple alignment of nucleotide sequences guided by amino acid translations. Nucleic Acids Research 38:W7–W13. doi: 10.1093/nar/gkq291, PMID: 20435676
-
(2010)
Nucleic Acids Research
, vol.38
, pp. WW7-W13
-
-
Abascal, F.1
Zardoya, R.2
Telford, M.J.3
-
2
-
-
84928987900
-
HTSeq–a Python framework to work with high-throughput sequencing data
-
PMID: 25260700
-
Anders S, Pyl Pt, Huber W. 2015. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169. doi: 10.1093/bioinformatics/btu638, PMID: 25260700
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pt, P.2
Huber, W.3
-
3
-
-
84857780876
-
Evidence for network evolution in an Arabidopsis interactome map
-
PMID: 21798944
-
Arabidopsis Interactome Mapping Consortium. 2011. Evidence for network evolution in an Arabidopsis interactome map. Science 333:601–607. doi: 10.1126/science.1203877, PMID: 21798944
-
(2011)
Science
, vol.333
, pp. 601-607
-
-
-
4
-
-
84929001104
-
Human genomics. The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans
-
PMID: 25954001
-
Ardlie KG, DeLuca DS, Segre AV, GTEx Consortium. 2015. Human genomics. The genotype-tissue expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348:648–660. doi: 10.1126/science. 1262110, PMID: 25954001
-
(2015)
Science
, vol.348
, pp. 648-660
-
-
Ardlie, K.G.1
Deluca, D.S.2
Segre, A.V.3
-
5
-
-
0034096525
-
Jasmonate-induced responses of Nicotiana sylvestris results in fitness costs due to impaired competitive ability for nitrogen
-
Baldwin IT, Hamilton W. 2000. Jasmonate-induced responses of Nicotiana sylvestris results in fitness costs due to impaired competitive ability for nitrogen. Journal of Chemical Ecology 26:915–952. doi: 10.1023/A: 1005408208826
-
(2000)
Journal of Chemical Ecology
, vol.26
, pp. 915-952
-
-
Baldwin, I.T.1
Hamilton, W.2
-
6
-
-
0032493349
-
Jasmonate-induced responses are costly but benefit plants under attack in native populations
-
PMID: 9653149
-
Baldwin IT. 1998. Jasmonate-induced responses are costly but benefit plants under attack in native populations. PNAS 95:8113–8118. doi: 10.1073/pnas.95.14.8113, PMID: 9653149
-
(1998)
PNAS
, vol.95
, pp. 8113-8118
-
-
Baldwin, I.T.1
-
7
-
-
64549104807
-
ClueGo: A Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
-
PMID: 19237447
-
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagés F, Trajanoski Z, Galon J. 2009. ClueGo: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25:1091–1093. doi: 10.1093/bioinformatics/btp101, PMID: 19237447
-
(2009)
Bioinformatics
, vol.25
, pp. 1091-1093
-
-
Bindea, G.1
Mlecnik, B.2
Hackl, H.3
Charoentong, P.4
Tosolini, M.5
Kirilovsky, A.6
Fridman, W.H.7
Pagés, F.8
Trajanoski, Z.9
Galon, J.10
-
8
-
-
34250632677
-
The gene balance hypothesis: From classical genetics to modern genomics
-
PMID: 17293565
-
Birchler JA, Veitia RA. 2007. The gene balance hypothesis: from classical genetics to modern genomics. The Plant Cell 19:395–402. doi: 10.1105/tpc.106.049338, PMID: 17293565
-
(2007)
The Plant Cell
, vol.19
, pp. 395-402
-
-
Birchler, J.A.1
Veitia, R.A.2
-
9
-
-
3142732892
-
Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution
-
PMID: 15208398
-
Blanc G, Wolfe KH. 2004. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. The Plant Cell 16:1679–1691. doi: 10.1105/tpc.021410, PMID: 15208398
-
(2004)
The Plant Cell
, vol.16
, pp. 1679-1691
-
-
Blanc, G.1
Wolfe, K.H.2
-
10
-
-
79958054864
-
Herbivore-associated elicitors: Fac signaling and metabolism
-
PMID: 21354852
-
Bonaventure G, VanDoorn A, Baldwin IT. 2011. Herbivore-associated elicitors: Fac signaling and metabolism. Trends in Plant Science 16:294–299. doi: 10.1016/j.tplants.2011.01.006, PMID: 21354852
-
(2011)
Trends in Plant Science
, vol.16
, pp. 294-299
-
-
Bonaventure, G.1
Vandoorn, A.2
Baldwin, I.T.3
-
11
-
-
67650757433
-
TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
-
PMID: 1 9505945
-
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973. doi: 10.1093/bioinformatics/btp348, PMID: 1 9505945
-
(2009)
Bioinformatics
, vol.25
, pp. 1972-1973
-
-
Capella-Gutiérrez, S.1
Silla-Martínez, J.M.2
Gabaldón, T.3
-
12
-
-
33646859550
-
Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana
-
PMID: 16507168
-
Casneuf T, De Bodt S, Raes J, Maere S, Van de Peer Y. 2006. Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biology 7:R13. doi: 10.1186/gb-2006-7-2-r13, PMID: 16507168
-
(2006)
Genome Biology
, vol.7
-
-
Casneuf, T.1
De Bodt, S.2
Raes, J.3
Maere, S.4
Van De Peer, Y.5
-
13
-
-
84856598466
-
The role of Wrky transcription factors in plant abiotic stresses
-
Chen L, Song Y, Li S, Zhang L, Zou C, Yu D, Song YLSJ. 2012. The role of Wrky transcription factors in plant abiotic stresses. Biochimica Et Biophysica Acta (Bba) - Gene Regulatory Mechanisms 1819:120–128. doi: 10. 1016/j.bbagrm.2011.09.002
-
(2012)
Biochimica Et Biophysica Acta (Bba) - Gene Regulatory Mechanisms
, vol.1819
, pp. 120-128
-
-
Chen, L.1
Song, Y.2
Li, S.3
Zhang, L.4
Zou, C.5
Yu, D.6
Song, Y.7
-
14
-
-
84864453108
-
JModelTest 2: More models, new heuristics and parallel computing
-
PMID: 22847109
-
Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9:772. doi: 10.1038/nmeth.2109, PMID: 22847109
-
(2012)
Nature Methods
, vol.9
, pp. 772
-
-
Darriba, D.1
Taboada, G.L.2
Doallo, R.3
Posada, D.4
-
15
-
-
84859890901
-
Redundancy and rewiring of genetic networks following genome-wide duplication events
-
PMID: 22305522
-
De Smet R, Van de Peer Y. 2012. Redundancy and rewiring of genetic networks following genome-wide duplication events. Current Opinion in Plant Biology 15:168–176. doi: 10.1016/j.pbi.2012.01.003, PMID: 22305522
-
(2012)
Current Opinion in Plant Biology
, vol.15
, pp. 168-176
-
-
De Smet, R.1
Van De Peer, Y.2
-
16
-
-
77956812192
-
Natural variation of transcriptional auxin response networks in Arabidopsis thaliana
-
PMID: 20622145
-
Delker C, Pöschl Y, Raschke A, Ullrich K, Ettingshausen S, Hauptmann V, Grosse I, Quint M. 2010. Natural variation of transcriptional auxin response networks in Arabidopsis thaliana. Plant Cell 22:2184–2200. doi: 10. 1105/tpc.110.073957, PMID: 20622145
-
(2010)
Plant Cell
, vol.22
, pp. 2184-2200
-
-
Delker, C.1
Pöschl, Y.2
Raschke, A.3
Ullrich, K.4
Ettingshausen, S.5
Hauptmann, V.6
Grosse, I.7
Quint, M.8
-
17
-
-
84881004186
-
The Herbivore Elicitor-REGULATED1 gene enhances abscisic acid levels and defenses against herbivores in Nicotiana attenuata plants
-
PMID: 23784463
-
Dinh ST, Baldwin IT, Galis I. 2013. The Herbivore Elicitor-REGULATED1 gene enhances abscisic acid levels and defenses against herbivores in Nicotiana attenuata plants. Plant Physiology 162:2106–2124. doi: 10.1104/pp.113.221150, PMID: 23784463
-
(2013)
Plant Physiology
, vol.162
, pp. 2106-2124
-
-
Dinh, S.T.1
Baldwin, I.T.2
Galis, I.3
-
18
-
-
16544376193
-
Downstream divergence of the ethylene signaling pathway for harpin-stimulated Arabidopsis growth and insect defense
-
PMID: 15516507
-
Dong HP, Peng J, Bao Z, Meng X, Bonasera JM, Chen G, Beer SV, Dong H. 2004. Downstream divergence of the ethylene signaling pathway for harpin-stimulated Arabidopsis growth and insect defense. Plant Physiology 136: 3628–3638. doi: 10.1104/pp.104.048900, PMID: 15516507
-
(2004)
Plant Physiology
, vol.136
, pp. 3628-3638
-
-
Dong, H.P.1
Peng, J.2
Bao, Z.3
Meng, X.4
Bonasera, J.M.5
Chen, G.6
Beer, S.V.7
Dong, H.8
-
19
-
-
30744464824
-
Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis
-
PMID: 16280546
-
Duarte JM, Cui L, Wall PK, Zhang Q, Zhang X, Leebens-Mack J, Ma H, Altman N, dePamphilis CW. 2006. Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis. Molecular Biology and Evolution 23:469–478. doi: 10.1093/molbev/msj051, PMID: 16280546
-
(2006)
Molecular Biology and Evolution
, vol.23
, pp. 469-478
-
-
Duarte, J.M.1
Cui, L.2
Wall, P.K.3
Zhang, Q.4
Zhang, X.5
Leebens-Mack, J.6
Ma, H.7
Altman, N.8
Depamphilis, C.W.9
-
20
-
-
33644872218
-
Gateway-compatible vectors for plant functional genomics and proteomics
-
PMID: 16441352
-
Earley KW, Haag JR, Pontes O, Opper K, Juehne T, Song K, Pikaard CS. 2006. Gateway-compatible vectors for plant functional genomics and proteomics. The Plant Journal 45:616–629. doi: 10.1111/j.1365-313X.2005.02617.x, PMID: 16441352
-
(2006)
The Plant Journal
, vol.45
, pp. 616-629
-
-
Earley, K.W.1
Haag, J.R.2
Pontes, O.3
Opper, K.4
Juehne, T.5
Song, K.6
Pikaard, C.S.7
-
21
-
-
3042666256
-
Muscle: Multiple sequence alignment with high accuracy and high throughput
-
PMID: 15034147
-
Edgar RC. 2004. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792–1797. doi: 10.1093/nar/gkh340, PMID: 15034147
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
22
-
-
70349682921
-
Gene and genome duplications: The impact of dosage-sensitivity on the fate of nuclear genes
-
Edger PP, Pires JC. 2009. Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Research 17:699–717. doi: 10.1007/s10577-009-9055-9
-
(2009)
Chromosome Research
, vol.17
, pp. 699-717
-
-
Edger, P.P.1
Pires, J.C.2
-
23
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
PMID: 11917018
-
Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 30:1575–1584. doi: 10.1093/nar/30.7.1575, PMID: 11917018
-
(2002)
Nucleic Acids Research
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
24
-
-
84860686181
-
Role of phytohormones in insect-specific plant reactions
-
PMID: 22305233
-
Erb M, Meldau S, Howe GA. 2012. Role of phytohormones in insect-specific plant reactions. Trends in Plant Science 17:250–259. doi: 10.1016/j.tplants.2012.01.003, PMID: 22305233
-
(2012)
Trends in Plant Science
, vol.17
, pp. 250-259
-
-
Erb, M.1
Meldau, S.2
Howe, G.A.3
-
25
-
-
11944260974
-
Octadecanoid precursors of jasmonic acid activate the synthesis of wound-inducible proteinase-inhibitors
-
PMID: 12297644
-
Farmer EE, Ryan CA. 1992. Octadecanoid precursors of jasmonic acid activate the synthesis of wound-inducible proteinase-inhibitors. Plant Cell 4:129–134. doi: 10.1105/tpc.4.2.129, PMID: 12297644
-
(1992)
Plant Cell
, vol.4
, pp. 129-134
-
-
Farmer, E.E.1
Ryan, C.A.2
-
26
-
-
67651039811
-
Bias in plant gene content following different sorts of duplication: Tandem, whole-genome, segmental, or by transposition
-
PMID: 19575588
-
Freeling M. 2009. Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. Annual Review of Plant Biology 60:433–453. doi: 10.1146/annurev.arplant.043008.092122, PMID: 19575588
-
(2009)
Annual Review of Plant Biology
, vol.60
, pp. 433-453
-
-
Freeling, M.1
-
27
-
-
23644461190
-
Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: Functional and evolutionary implications
-
PMID: 16027976
-
Gachon CM, Langlois-Meurinne M, Henry Y, Saindrenan P. 2005. Transcriptional co-regulation of secondary metabolism enzymes in Arabidopsis: functional and evolutionary implications. Plant Molecular Biology 58:229–245. doi: 10.1007/s11103-005-5346-5, PMID: 16027976
-
(2005)
Plant Molecular Biology
, vol.58
, pp. 229-245
-
-
Gachon, C.M.1
Langlois-Meurinne, M.2
Henry, Y.3
Saindrenan, P.4
-
28
-
-
84880154856
-
The use of Vigs technology to study plant-herbivore interactions
-
Galis I, Schuman MC, Gase K. 2013. The use of Vigs technology to study plant-herbivore interactions. Methods in Molecular 975:109–137. doi: 10.1007/978-1-62703-278-0_9
-
(2013)
Methods in Molecular
, vol.975
, pp. 109-137
-
-
Galis, I.1
Schuman, M.C.2
Gase, K.3
-
29
-
-
84973367318
-
Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana
-
Gao R, Liu P, Yong Y, Wong S-M. 2016. Genome-wide transcriptomic analysis reveals correlation between higher WRKY61 expression and reduced symptom severity in Turnip crinkle virus infected Arabidopsis thaliana. Scientific Reports 6:24604. doi: 10.1038/srep24604
-
(2016)
Scientific Reports
, vol.6
, pp. 24604
-
-
Gao, R.1
Liu, P.2
Yong, Y.3
Wong, S.-M.4
-
30
-
-
80055000869
-
Nicotiana attenuata Lectin Receptor KINASE1 suppresses the insect-mediated inhibition of induced defense responses during Manduca sexta herbivory
-
PMID: 21926334
-
Gilardoni PA, Hettenhausen C, Baldwin IT, Bonaventure G. 2011. Nicotiana attenuata Lectin Receptor KINASE1 suppresses the insect-mediated inhibition of induced defense responses during Manduca sexta herbivory. The Plant Cell 23:3512–3532. doi: 10.1105/tpc.111.088229, PMID: 21926334
-
(2011)
The Plant Cell
, vol.23
, pp. 3512-3532
-
-
Gilardoni, P.A.1
Hettenhausen, C.2
Baldwin, I.T.3
Bonaventure, G.4
-
31
-
-
0013158671
-
Ecological costs and benefits correlated with trypsin protease inhibitor production in Nicotiana attenuata
-
Glawe GA, Zavala JA, Kessler A. 2003. Ecological costs and benefits correlated with trypsin protease inhibitor production in Nicotiana attenuata. Ecology 84:79–90. doi: 10.1890/0012-9658(2003)084[0079:ecabcw]2.0.co;2
-
(2003)
Ecology
, vol.84
, pp. 79-90
-
-
Glawe, G.A.1
Zavala, J.A.2
Kessler, A.3
-
32
-
-
45549089420
-
High-throughput functional annotation and data mining with the Blast2Go suite
-
PMID: 18445632
-
Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A. 2008. High-throughput functional annotation and data mining with the Blast2Go suite. Nucleic Acids Research 36:3420–3435. doi: 10.1093/nar/gkn176, PMID: 18445632
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 3420-3435
-
-
Götz, S.1
García-Gómez, J.M.2
Terol, J.3
Williams, T.D.4
Nagaraj, S.H.5
Nueda, M.J.6
Robles, M.7
Talón, M.8
Dopazo, J.9
Conesa, A.10
-
33
-
-
84866505605
-
In planta transient expression analysis of monoterpene synthases
-
David A. H (Ed), Academic Press
-
Green SA, Chen XY, Matich AJ. 2012. In planta transient expression analysis of monoterpene synthases. In: David A. H (Ed). Methods in Enzymology. Academic Press.
-
(2012)
Methods in Enzymology
-
-
Green, S.A.1
Chen, X.Y.2
Matich, A.J.3
-
34
-
-
0347033256
-
Role of duplicate genes in genetic robustness against null mutations
-
PMID: 12511954
-
Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, Li WH. 2003. Role of duplicate genes in genetic robustness against null mutations. Nature 421:63–66. doi: 10.1038/nature01198, PMID: 12511954
-
(2003)
Nature
, vol.421
, pp. 63-66
-
-
Gu, Z.1
Steinmetz, L.M.2
Gu, X.3
Scharfe, C.4
Davis, R.W.5
Li, W.H.6
-
36
-
-
84895922172
-
The roots of plant defenses: Integrative multivariate analyses uncover dynamic behaviors of gene and metabolic networks of roots elicited by leaf herbivory
-
PMID: 24456376
-
Gulati J, Baldwin IT, Gaquerel E. 2014. The roots of plant defenses: integrative multivariate analyses uncover dynamic behaviors of gene and metabolic networks of roots elicited by leaf herbivory. The Plant Journal 77: 880–892. doi: 10.1111/tpj.12439, PMID: 24456376
-
(2014)
The Plant Journal
, vol.77
, pp. 880-892
-
-
Gulati, J.1
Baldwin, I.T.2
Gaquerel, E.3
-
37
-
-
84878435254
-
Deciphering herbivory-induced gene-to-metabolite dynamics in Nicotiana attenuata tissues using a multifactorial approach
-
PMID: 23656894
-
Gulati J, Kim SG, Baldwin IT, Gaquerel E. 2013. Deciphering herbivory-induced gene-to-metabolite dynamics in Nicotiana attenuata tissues using a multifactorial approach. Plant Physiology 162:1042–1059. doi: 10.1104/pp.113.217588, PMID: 23656894
-
(2013)
Plant Physiology
, vol.162
, pp. 1042-1059
-
-
Gulati, J.1
Kim, S.G.2
Baldwin, I.T.3
Gaquerel, E.4
-
38
-
-
34047134940
-
External factors accelerate expression divergence between duplicate genes
-
PMID: 17320239
-
Ha M, Li WH, Chen ZJ. 2007. External factors accelerate expression divergence between duplicate genes. Trends in Genetics 23:162–166. doi: 10.1016/j.tig.2007.02.005, PMID: 17320239
-
(2007)
Trends in Genetics
, vol.23
, pp. 162-166
-
-
Ha, M.1
Li, W.H.2
Chen, Z.J.3
-
39
-
-
38049133600
-
All duplicates are not equal: The difference between small-scale and genome duplication
-
PMID: 17916239
-
Hakes L, Pinney JW, Lovell SC, Oliver SG, Robertson DL. 2007. All duplicates are not equal: the difference between small-scale and genome duplication. Genome Biology 8:R209. doi: 10.1186/gb-2007-8-10-r209, PMID: 17916239
-
(2007)
Genome Biology
, vol.8
-
-
Hakes, L.1
Pinney, J.W.2
Lovell, S.C.3
Oliver, S.G.4
Robertson, D.L.5
-
40
-
-
0035112479
-
Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. Iii. Fatty acid- amino acid conjugates in herbivore oral secretions are necessary and sufficient for herbivore-specific plant responses
-
PMID: 11161028
-
Halitschke R, Schittko U, Pohnert G, Boland W, Baldwin IT. 2001. Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. Iii. Fatty acid- amino acid conjugates in herbivore oral secretions are necessary and sufficient for herbivore-specific plant responses. Plant Physiology 125:711–717. doi: 10.1104/pp.125.2.711, PMID: 11161028
-
(2001)
Plant Physiology
, vol.125
, pp. 711-717
-
-
Halitschke, R.1
Schittko, U.2
Pohnert, G.3
Boland, W.4
Baldwin, I.T.5
-
41
-
-
57749085421
-
Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli
-
PMID: 18715958
-
Hanada K, Zou C, Lehti-Shiu MD, Shinozaki K, Shiu SH. 2008. Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli. Plant Physiology 148:993–1003. doi: 10.1104/pp.108.122457, PMID: 18715958
-
(2008)
Plant Physiology
, vol.148
, pp. 993-1003
-
-
Hanada, K.1
Zou, C.2
Lehti-Shiu, M.D.3
Shinozaki, K.4
Shiu, S.H.5
-
42
-
-
0036482416
-
Fitness costs of induced resistance: Emerging experimental support for a slippery concept
-
PMID: 11832276
-
Heil M, Baldwin IT. 2002. Fitness costs of induced resistance: emerging experimental support for a slippery concept. Trends in Plant Science 7:61–67. doi: 10.1016/S1360-1385(01)02186-0, PMID: 11832276
-
(2002)
Trends in Plant Science
, vol.7
, pp. 61-67
-
-
Heil, M.1
Baldwin, I.T.2
-
43
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
PMID: 20513432
-
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Molecular Cell 38:576–589. doi: 10.1016/j.molcel.2010.05.004, PMID: 20513432
-
(2010)
Molecular Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
Benner, C.2
Spann, N.3
Bertolino, E.4
Lin, Y.C.5
Laslo, P.6
Cheng, J.X.7
Murre, C.8
Singh, H.9
Glass, C.K.10
-
44
-
-
84880316494
-
Nicotiana attenuata MPK4 suppresses a novel jasmonic acid (Ja) signaling-independent defense pathway against the specialist insect Manduca sexta, but is not required for the resistance to the generalist Spodoptera littoralis
-
PMID: 23672856
-
Hettenhausen C, Baldwin IT, Wu J. 2013. Nicotiana attenuata MPK4 suppresses a novel jasmonic acid (Ja) signaling-independent defense pathway against the specialist insect Manduca sexta, but is not required for the resistance to the generalist Spodoptera littoralis. New Phytologist 199:787–799. doi: 10.1111/nph.12312, PMID: 23672856
-
(2013)
New Phytologist
, vol.199
, pp. 787-799
-
-
Hettenhausen, C.1
Baldwin, I.T.2
Wu, J.3
-
45
-
-
84892641918
-
Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family
-
PMID: 24171911
-
Hofberger JA, Lyons E, Edger PP, Chris Pires J, Eric Schranz M. 2013. Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family. Genome Biology and Evolution 5:2155–2173. doi: 10.1093/gbe/evt162, PMID: 24171911
-
(2013)
Genome Biology and Evolution
, vol.5
, pp. 2155-2173
-
-
Hofberger, J.A.1
Lyons, E.2
Edger, P.P.3
Chris Pires, J.4
Eric Schranz, M.5
-
46
-
-
44449179468
-
Plant immunity to insect herbivores
-
PMID: 18031220
-
Howe GA, Jander G. 2008. Plant immunity to insect herbivores. Annual Review of Plant Biology 59:41–66. doi: 10.1146/annurev.arplant.59.032607.092825, PMID: 18031220
-
(2008)
Annual Review of Plant Biology
, vol.59
, pp. 41-66
-
-
Howe, G.A.1
Jander, G.2
-
47
-
-
33845432928
-
Adjusting batch effects in microarray expression data using empirical Bayes methods
-
PMID: 16632515
-
Johnson WE, Li C, Rabinovic A. 2007. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8:118–127. doi: 10.1093/biostatistics/kxj037, PMID: 16632515
-
(2007)
Biostatistics
, vol.8
, pp. 118-127
-
-
Johnson, W.E.1
Li, C.2
Rabinovic, A.3
-
48
-
-
33947422242
-
Microarray-based screening of jasmonate-responsive genes in Arabidopsis thaliana
-
PMID: 17297615
-
Jung C, Lyou SH, Yeu S, Kim MA, Rhee S, Kim M, Lee JS, Choi YD, Cheong JJ. 2007. Microarray-based screening of jasmonate-responsive genes in Arabidopsis thaliana. Plant Cell Reports 26:1053–1063. doi: 10.1007/s00299-007-0311-1, PMID: 17297615
-
(2007)
Plant Cell Reports
, vol.26
, pp. 1053-1063
-
-
Jung, C.1
Lyou, S.H.2
Yeu, S.3
Kim, M.A.4
Rhee, S.5
Kim, M.6
Lee, J.S.7
Choi, Y.D.8
Cheong, J.J.9
-
49
-
-
0033985359
-
Herbivore-induced ethylene suppresses a direct defense but not a putative indirect defense against an adapted herbivore
-
PMID: 10664141
-
Kahl J, Siemens DH, Aerts RJ, Gäbler R, Kühnemann F, Preston CA, Baldwin IT. 2000. Herbivore-induced ethylene suppresses a direct defense but not a putative indirect defense against an adapted herbivore. Planta 210:336–342. doi: 10.1007/PL00008142, PMID: 10664141
-
(2000)
Planta
, vol.210
, pp. 336-342
-
-
Kahl, J.1
Siemens, D.H.2
Aerts, R.J.3
Gäbler, R.4
Kühnemann, F.5
Preston, C.A.6
Baldwin, I.T.7
-
50
-
-
84862173649
-
Empoasca leafhoppers attack wild tobacco plants in a jasmonate-dependent manner and identify jasmonate mutants in natural populations
-
PMID: 22615404
-
Kallenbach M, Bonaventure G, Gilardoni PA, Wissgott A, Baldwin IT. 2012. Empoasca leafhoppers attack wild tobacco plants in a jasmonate-dependent manner and identify jasmonate mutants in natural populations. Pnas 109:E1548–E1557. doi: 10.1073/pnas.1200363109, PMID: 22615404
-
(2012)
Pnas
, vol.109
, pp. E1548-E1557
-
-
Kallenbach, M.1
Bonaventure, G.2
Gilardoni, P.A.3
Wissgott, A.4
Baldwin, I.T.5
-
51
-
-
80051599180
-
C12 derivatives of the hydroperoxide lyase pathway are produced by product recycling through lipoxygenase-2 in Nicotiana attenuata leaves
-
PMID: 21615741
-
Kallenbach M, Gilardoni PA, Allmann S, Baldwin IT, Bonaventure G. 2011. C12 derivatives of the hydroperoxide lyase pathway are produced by product recycling through lipoxygenase-2 in Nicotiana attenuata leaves. New Phytologist 191:1054–1068. doi: 10.1111/j.1469-8137.2011.03767.x, PMID: 21615741
-
(2011)
New Phytologist
, vol.191
, pp. 1054-1068
-
-
Kallenbach, M.1
Gilardoni, P.A.2
Allmann, S.3
Baldwin, I.T.4
Bonaventure, G.5
-
52
-
-
33845803150
-
Silencing threonine deaminase and JAR4 in Nicotiana attenuata impairs jasmonic acid-isoleucine-mediated defenses against Manduca sexta
-
PMID: 17085687
-
Kang JH, Wang L, Giri A, Baldwin IT. 2006. Silencing threonine deaminase and JAR4 in Nicotiana attenuata impairs jasmonic acid-isoleucine-mediated defenses against Manduca sexta. The Plant Cell 18:3303–3320. doi: 10.1105/tpc.106.041103, PMID: 17085687
-
(2006)
The Plant Cell
, vol.18
, pp. 3303-3320
-
-
Kang, J.H.1
Wang, L.2
Giri, A.3
Baldwin, I.T.4
-
53
-
-
77949509407
-
R2R3-NaMYB8 regulates the accumulation of phenylpropanoid-polyamine conjugates, which are essential for local and systemic defense against insect herbivores in Nicotiana attenuata
-
PMID: 200 89770
-
Kaur H, Heinzel N, Schöttner M, Baldwin IT, Gális I. 2010. R2R3-NaMYB8 regulates the accumulation of phenylpropanoid-polyamine conjugates, which are essential for local and systemic defense against insect herbivores in Nicotiana attenuata. Plant Physiology 152:1731–1747. doi: 10.1104/pp.109.151738, PMID: 200 89770
-
(2010)
Plant Physiology
, vol.152
, pp. 1731-1747
-
-
Kaur, H.1
Heinzel, N.2
Schöttner, M.3
Baldwin, I.T.4
Gális, I.5
-
54
-
-
3442892984
-
Silencing the jasmonate cascade: Induced plant defenses and insect populations
-
PMID: 15232071
-
Kessler A, Halitschke R, Baldwin IT. 2004. Silencing the jasmonate cascade: induced plant defenses and insect populations. Science 305:665–668. doi: 10.1126/science.1096931, PMID: 15232071
-
(2004)
Science
, vol.305
, pp. 665-668
-
-
Kessler, A.1
Halitschke, R.2
Baldwin, I.T.3
-
55
-
-
80054755079
-
Tissue specific diurnal rhythms of metabolites and their regulation during herbivore attack in a native tobacco, Nicotiana attenuata
-
PMID: 22028833
-
Kim SG, Yon F, Gaquerel E, Gulati J, Baldwin IT. 2011. Tissue specific diurnal rhythms of metabolites and their regulation during herbivore attack in a native tobacco, Nicotiana attenuata. PLoS One 6:e26214. doi: 10.1371/journal.pone.0026214, PMID: 22028833
-
(2011)
Plos One
, vol.6
-
-
Kim, S.G.1
Yon, F.2
Gaquerel, E.3
Gulati, J.4
Baldwin, I.T.5
-
56
-
-
84901975336
-
Biological cluster evaluation for gene function prediction
-
PMID: 20059365
-
Klie S, Nikoloski Z, Selbig J. 2014. Biological cluster evaluation for gene function prediction. Journal of Computational Biology 21:428–445. doi: 10.1089/cmb.2009.0129, PMID: 20059365
-
(2014)
Journal of Computational Biology
, vol.21
, pp. 428-445
-
-
Klie, S.1
Nikoloski, Z.2
Selbig, J.3
-
57
-
-
0036931955
-
Agrobacterium-mediated transformation of Nicotiana attenuata, a model ecological expression system
-
Krügel T, Lim M, Gase K, Halitschke R, Baldwin IT. 2002. Agrobacterium-mediated transformation of Nicotiana attenuata, a model ecological expression system. Chemoecology 12:177–183. doi: 10.1007/PL00012666
-
(2002)
Chemoecology
, vol.12
, pp. 177-183
-
-
Krügel, T.1
Lim, M.2
Gase, K.3
Halitschke, R.4
Baldwin, I.T.5
-
58
-
-
60549111634
-
Wgcna: An R package for weighted correlation network analysis
-
PMID: 19114008
-
Langfelder P, Horvath S. 2008. Wgcna: an R package for weighted correlation network analysis. Bmc Bioinformatics 9:559. doi: 10.1186/1471-2105-9-559, PMID: 19114008
-
(2008)
Bmc Bioinformatics
, vol.9
, pp. 559
-
-
Langfelder, P.1
Horvath, S.2
-
59
-
-
84961291810
-
Virulence factors of geminivirus interact with MYC2 to subvert plant resistance and promote vector performance
-
PMID: 25490915
-
Li R, Weldegergis BT, Li J, Jung C, Qu J, Sun Y, Qian H, Tee C, van Loon JJ, Dicke M, Chua NH, Liu SS, Ye J. 2014. Virulence factors of geminivirus interact with MYC2 to subvert plant resistance and promote vector performance. The Plant Cell 26:4991–5008. doi: 10.1105/tpc.114.133181, PMID: 25490915
-
(2014)
The Plant Cell
, vol.26
, pp. 4991-5008
-
-
Li, R.1
Weldegergis, B.T.2
Li, J.3
Jung, C.4
Qu, J.5
Sun, Y.6
Qian, H.7
Tee, C.8
Van Loon, J.J.9
Dicke, M.10
Chua, N.H.11
Liu, S.S.12
Ye, J.13
-
60
-
-
84863101693
-
AdapterRemoval: Easy cleaning of next-generation sequencing reads
-
PMID: 22748135
-
Lindgreen S. 2012. AdapterRemoval: easy cleaning of next-generation sequencing reads. Bmc Research Notes 5: 337. doi: 10.1186/1756-0500-5-337, PMID: 22748135
-
(2012)
Bmc Research Notes
, vol.5
, pp. 337
-
-
Lindgreen, S.1
-
61
-
-
1642564016
-
Cdpk-mediated signalling pathways: Specificity and cross-talk
-
PMID: 14623901
-
Ludwig AA, Romeis T, Jones JD. 2004. Cdpk-mediated signalling pathways: specificity and cross-talk. Journal of Experimental Botany 55:181–188. doi: 10.1093/jxb/erh008, PMID: 14623901
-
(2004)
Journal of Experimental Botany
, vol.55
, pp. 181-188
-
-
Ludwig, A.A.1
Romeis, T.2
Jones, J.D.3
-
62
-
-
84964664237
-
COI1-Regulated hydroxylation of jasmonoyl-l-isoleucine impairs Nicotiana attenuata’s resistance to the generalist herbivore Spodoptera litura
-
PMID: 26985773
-
Luo J, Wei K, Wang S, Zhao W, Ma C, Hettenhausen C, Wu J, Cao G, Sun G, Baldwin IT, Wu J, Wang L. 2016. COI1-Regulated hydroxylation of jasmonoyl-l-isoleucine impairs Nicotiana attenuata’s resistance to the generalist herbivore Spodoptera litura. Journal of Agricultural and Food Chemistry 64:2822–2831. doi: 10.1021/acs.jafc.5b06056, PMID: 26985773
-
(2016)
Journal of Agricultural and Food Chemistry
, vol.64
, pp. 2822-2831
-
-
Luo, J.1
Wei, K.2
Wang, S.3
Zhao, W.4
Ma, C.5
Hettenhausen, C.6
Wu, J.7
Cao, G.8
Sun, G.9
Baldwin, I.T.10
Wu, J.11
Wang, L.12
-
63
-
-
84887044931
-
Leaf-herbivore attack reduces carbon reserves and regrowth from the roots via jasmonate and auxin signaling
-
Machado RAR, Ferrieri AP, Robert CAM, Glauser G, Kallenbach M, Baldwin IT, Erb M. 2013b. Leaf-herbivore attack reduces carbon reserves and regrowth from the roots via jasmonate and auxin signaling. New Phytologist 200:1234–1246. doi: 10.1111/nph.12438
-
(2013)
New Phytologist
, vol.200
, pp. 1234-1246
-
-
Machado, R.1
Ferrieri, A.P.2
Robert, C.3
Glauser, G.4
Kallenbach, M.5
Baldwin, I.T.6
Erb, M.7
-
64
-
-
84887044931
-
Leaf-herbivore attack reduces carbon reserves and regrowth from the roots via jasmonate and auxin signaling
-
Machado RAR, Ferrieri AP, Robert CAM, Glauser G, Kallenbach M, Baldwin IT, Erb M. 2013a. Leaf-herbivore attack reduces carbon reserves and regrowth from the roots via jasmonate and auxin signaling. New Phytologist 200: 1234–1246. doi: 10.1111/nph.12438
-
(2013)
New Phytologist
, vol.200
, pp. 1234-1246
-
-
Machado, R.1
Ferrieri, A.P.2
Robert, C.3
Glauser, G.4
Kallenbach, M.5
Baldwin, I.T.6
Erb, M.7
-
65
-
-
84929959395
-
Jasmonate-dependent depletion of soluble sugars compromises plant resistance to Manduca sexta
-
PMID: 25704234
-
Machado RA, Arce CC, Ferrieri AP, Baldwin IT, Erb M. 2015. Jasmonate-dependent depletion of soluble sugars compromises plant resistance to Manduca sexta. New Phytologist 207:91–105. doi: 10.1111/nph.13337, PMID: 25704234
-
(2015)
New Phytologist
, vol.207
, pp. 91-105
-
-
Machado, R.A.1
Arce, C.C.2
Ferrieri, A.P.3
Baldwin, I.T.4
Erb, M.5
-
66
-
-
17244368487
-
Modeling gene and genome duplications in eukaryotes
-
PMID: 15800040
-
Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y. 2005. Modeling gene and genome duplications in eukaryotes. Pnas 102:5454–5459. doi: 10.1073/pnas.0501102102, PMID: 15800040
-
(2005)
Pnas
, vol.102
, pp. 5454-5459
-
-
Maere, S.1
De Bodt, S.2
Raes, J.3
Casneuf, T.4
Van Montagu, M.5
Kuiper, M.6
Van De Peer, Y.7
-
67
-
-
57449083112
-
Silencing two herbivory-activated Map kinases, Sipk and Wipk, does not increase Nicotiana attenuata’s susceptibility to herbivores in the glasshouse and in nature
-
PMID: 19076722
-
Meldau S, Wu J, Baldwin IT. 2009. Silencing two herbivory-activated Map kinases, Sipk and Wipk, does not increase Nicotiana attenuata’s susceptibility to herbivores in the glasshouse and in nature. New Phytologist 181:161–173. doi: 10.1111/j.1469-8137.2008.02645.x, PMID: 19076722
-
(2009)
New Phytologist
, vol.181
, pp. 161-173
-
-
Meldau, S.1
Wu, J.2
Baldwin, I.T.3
-
68
-
-
26944435924
-
Major signaling pathways modulate Arabidopsis glucosinolate accumulation and response to both phloem-feeding and chewing insects
-
PMID: 15923339
-
Mewis I, Appel HM, Hom A, Raina R, Schultz JC. 2005. Major signaling pathways modulate Arabidopsis glucosinolate accumulation and response to both phloem-feeding and chewing insects. Plant Physiology 138: 1149–1162. doi: 10.1104/pp.104.053389, PMID: 15923339
-
(2005)
Plant Physiology
, vol.138
, pp. 1149-1162
-
-
Mewis, I.1
Appel, H.M.2
Hom, A.3
Raina, R.4
Schultz, J.C.5
-
69
-
-
70350515004
-
Unexpected consequences of a sudden and massive transposon amplification on rice gene expression
-
PMID: 19847266
-
Naito K, Zhang F, Tsukiyama T, Saito H, Hancock CN, Richardson AO, Okumoto Y, Tanisaka T, Wessler SR. 2009. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461:U1130–U1232. doi: 10.1038/nature08479, PMID: 19847266
-
(2009)
Nature
, vol.461
, pp. U1130-U1232
-
-
Naito, K.1
Zhang, F.2
Tsukiyama, T.3
Saito, H.4
Hancock, C.N.5
Richardson, A.O.6
Okumoto, Y.7
Tanisaka, T.8
Wessler, S.R.9
-
70
-
-
77953180099
-
Jasmonic acid and ethylene modulate local responses to wounding and simulated herbivory in Nicotiana attenuata leaves
-
PMID: 20382894
-
Onkokesung N, Gális I, von Dahl CC, Matsuoka K, Saluz HP, Baldwin IT. 2010. Jasmonic acid and ethylene modulate local responses to wounding and simulated herbivory in Nicotiana attenuata leaves. Plant Physiology 153:785–798. doi: 10.1104/pp.110.156232, PMID: 20382894
-
(2010)
Plant Physiology
, vol.153
, pp. 785-798
-
-
Onkokesung, N.1
Gális, I.2
Von Dahl, C.C.3
Matsuoka, K.4
Saluz, H.P.5
Baldwin, I.T.6
-
71
-
-
0031110886
-
From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem
-
PMID: 9126565
-
Page RD, Charleston MA. 1997. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Molecular Phylogenetics and Evolution 7:231–240. doi: 10.1006/mpev.1996.0390, PMID: 9126565
-
(1997)
Molecular Phylogenetics and Evolution
, vol.7
, pp. 231-240
-
-
Page, R.D.1
Charleston, M.A.2
-
72
-
-
49449088487
-
Jasmonate perception regulates jasmonate biosynthesis and Ja-Ile metabolism: The case of COI1 in Nicotiana attenuata
-
PMID: 18559356
-
Paschold A, Bonaventure G, Kant MR, Baldwin IT. 2008. Jasmonate perception regulates jasmonate biosynthesis and Ja-Ile metabolism: the case of COI1 in Nicotiana attenuata. Plant and Cell Physiology 49:1165–1175. doi: 10.1093/pcp/pcn091, PMID: 18559356
-
(2008)
Plant and Cell Physiology
, vol.49
, pp. 1165-1175
-
-
Paschold, A.1
Bonaventure, G.2
Kant, M.R.3
Baldwin, I.T.4
-
73
-
-
34250713585
-
Co(I)-ordinating defenses: NaCOI1 mediates herbivore- induced resistance in Nicotiana attenuata and reveals the role of herbivore movement in avoiding defenses
-
PMID: 17561925
-
Paschold A, Halitschke R, Baldwin IT. 2007. Co(i)-ordinating defenses: NaCOI1 mediates herbivore- induced resistance in Nicotiana attenuata and reveals the role of herbivore movement in avoiding defenses. The Plant Journal 51:79–91. doi: 10.1111/j.1365-313X.2007.03119.x, PMID: 17561925
-
(2007)
The Plant Journal
, vol.51
, pp. 79-91
-
-
Paschold, A.1
Halitschke, R.2
Baldwin, I.T.3
-
74
-
-
0037460091
-
Evolving protein interaction networks through gene duplication
-
PMID: 12727455
-
Pastor-Satorras R, Smith E, Solé RV. 2003. Evolving protein interaction networks through gene duplication. Journal of Theoretical Biology 222:199–210. doi: 10.1016/S0022-5193(03)00028-6, PMID: 12727455
-
(2003)
Journal of Theoretical Biology
, vol.222
, pp. 199-210
-
-
Pastor-Satorras, R.1
Smith, E.2
Solé, R.V.3
-
75
-
-
20844445318
-
Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets
-
PMID: 15932943
-
Persson S, Wei H, Milne J, Page GP, Somerville CR. 2005. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Pnas 102:8633–8638. doi: 10.1073/pnas.0503392102, PMID: 15932943
-
(2005)
Pnas
, vol.102
, pp. 8633-8638
-
-
Persson, S.1
Wei, H.2
Milne, J.3
Page, G.P.4
Somerville, C.R.5
-
76
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
PMID: 20110278
-
Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. doi: 10.1093/bioinformatics/btq033, PMID: 20110278
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
77
-
-
33847267229
-
PlnTfdb: An integrative plant transcription factor database
-
PMID: 17286856
-
Riaño-Pachón DM, Ruzicic S, Dreyer I, Mueller-Roeber B. 2007. PlnTfdb: an integrative plant transcription factor database. Bmc Bioinformatics 8:42. doi: 10.1186/1471-2105-8-42, PMID: 17286856
-
(2007)
Bmc Bioinformatics
, vol.8
, pp. 42
-
-
Riaño-Pachón, D.M.1
Ruzicic, S.2
Dreyer, I.3
Mueller-Roeber, B.4
-
78
-
-
33749357831
-
Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice
-
PMID: 16948529
-
Rizzon C, Ponger L, Gaut BS. 2006. Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice. PLoS Computational Biology 2:e115. doi: 10.1371/journal.pcbi.0020115, PMID: 16948529
-
(2006)
Plos Computational Biology
, vol.2
-
-
Rizzon, C.1
Ponger, L.2
Gaut, B.S.3
-
79
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
PMID: 1 9910308
-
Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140. doi: 10.1093/bioinformatics/btp616, PMID: 1 9910308
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
80
-
-
84897100061
-
From local to global: CDPKs in systemic defense signaling upon microbial and herbivore attack
-
PMID: 24681995
-
Romeis T, Herde M. 2014. From local to global: CDPKs in systemic defense signaling upon microbial and herbivore attack. Current Opinion in Plant Biology 20:1–10. doi: 10.1016/j.pbi.2014.03.002, PMID: 24681995
-
(2014)
Current Opinion in Plant Biology
, vol.20
, pp. 1-10
-
-
Romeis, T.1
Herde, M.2
-
81
-
-
84863693752
-
The tomato genome sequence provides insights into fleshy fruit evolution
-
PMID: 22660326
-
Sato S, Tabata S, Hirakawa H, Tomato Genome Consortium. 2012. The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641. doi: 10.1038/nature11119, PMID: 22660326
-
(2012)
Nature
, vol.485
, pp. 635-641
-
-
Sato, S.1
Tabata, S.2
Hirakawa, H.3
-
82
-
-
84973375264
-
High-throughput quantification of more than 100 primary- and secondary-metabolites, and phytohormones by a single solid-phase extraction based sample preparation with analysis by Uhplc-Hesi-Ms/Ms
-
PMID: 27239220
-
Schäfer M, Brütting C, Baldwin IT, Kallenbach M. 2016. High-throughput quantification of more than 100 primary- and secondary-metabolites, and phytohormones by a single solid-phase extraction based sample preparation with analysis by Uhplc-Hesi-Ms/Ms. Plant Methods 12:30. doi: 10.1186/s13007-016-0130-x, PMID: 27239220
-
(2016)
Plant Methods
, vol.12
, pp. 30
-
-
Schäfer, M.1
Brütting, C.2
Baldwin, I.T.3
Kallenbach, M.4
-
83
-
-
84973640841
-
The full-size Abcg transporters Nb-ABCG1 and Nb-ABCG2 function in pre-and post-invasion defense against phytophthora infestans in Nicotiana benthamiana
-
PMID: 27102667
-
Shibata Y, Ojika M, Sugiyama A, Yazaki K, Jones DA, Kawakita K, Takemoto D. 2016. The full-size Abcg transporters Nb-ABCG1 and Nb-ABCG2 function in pre-and post-invasion defense against phytophthora infestans in Nicotiana benthamiana. The Plant Cell 28:1163–1181. doi: 10.1105/tpc.15.00721, PMID: 27102667
-
(2016)
The Plant Cell
, vol.28
, pp. 1163-1181
-
-
Shibata, Y.1
Ojika, M.2
Sugiyama, A.3
Yazaki, K.4
Jones, D.A.5
Kawakita, K.6
Takemoto, D.7
-
84
-
-
0033771664
-
Ethylene suppresses jasmonate-induced gene expression in nicotine biosynthesis
-
PMID: 11100780
-
Shoji T, Nakajima K, Hashimoto T. 2000. Ethylene suppresses jasmonate-induced gene expression in nicotine biosynthesis. Plant and Cell Physiology 41:1072–1076. doi: 10.1093/pcp/pcd027, PMID: 11100780
-
(2000)
Plant and Cell Physiology
, vol.41
, pp. 1072-1076
-
-
Shoji, T.1
Nakajima, K.2
Hashimoto, T.3
-
85
-
-
57449104828
-
Induced plant defenses in the natural environment: Nicotiana attenuata WRKY3 and WRKY6 coordinate responses to herbivory
-
PMID: 18641266
-
Skibbe M, Qu N, Galis I, Baldwin IT. 2008. Induced plant defenses in the natural environment: Nicotiana attenuata WRKY3 and WRKY6 coordinate responses to herbivory. The Plant Cell 20:1984–2000. doi: 10.1105/ tpc.108.058594, PMID: 18641266
-
(2008)
The Plant Cell
, vol.20
, pp. 1984-2000
-
-
Skibbe, M.1
Qu, N.2
Galis, I.3
Baldwin, I.T.4
-
86
-
-
0035983852
-
Jasmonate response locus JAR1 and several related Arabidopsis genes encode enzymes of the firefly luciferase superfamily that show activity on jasmonic, salicylic, and indole-3-acetic acids in an assay for adenylation
-
PMID: 12084835
-
Staswick PE, Tiryaki I, Rowe ML. 2002. Jasmonate response locus JAR1 and several related Arabidopsis genes encode enzymes of the firefly luciferase superfamily that show activity on jasmonic, salicylic, and indole-3-acetic acids in an assay for adenylation. Plant Cell 14:1405–1415. doi: 10.1105/tpc.000885, PMID: 12084835
-
(2002)
Plant Cell
, vol.14
, pp. 1405-1415
-
-
Staswick, P.E.1
Tiryaki, I.2
Rowe, M.L.3
-
87
-
-
4043089251
-
The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in Arabidopsis
-
PMID: 15258265
-
Staswick PE, Tiryaki I. 2004. The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in Arabidopsis. The Plant Cell 16:2117–2127. doi: 10.1105/tpc.104.023549, PMID: 15258265
-
(2004)
The Plant Cell
, vol.16
, pp. 2117-2127
-
-
Staswick, P.E.1
Tiryaki, I.2
-
88
-
-
80052394993
-
Ectopic expression of AtJmt in Nicotiana attenuata: Creating a metabolic sink has tissue-specific consequences for the jasmonate metabolic network and silences downstream gene expression
-
PMID: 21753114
-
Stitz M, Gase K, Baldwin IT, Gaquerel E. 2011. Ectopic expression of AtJmt in Nicotiana attenuata: creating a metabolic sink has tissue-specific consequences for the jasmonate metabolic network and silences downstream gene expression. Plant Physiology 157:341–354. doi: 10.1104/pp.111.178582, PMID: 21753114
-
(2011)
Plant Physiology
, vol.157
, pp. 341-354
-
-
Stitz, M.1
Gase, K.2
Baldwin, I.T.3
Gaquerel, E.4
-
89
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
PMID: 12934013
-
Stuart JM, Segal E, Koller D, Kim SK. 2003. A gene-coexpression network for global discovery of conserved genetic modules. Science 302:249–255. doi: 10.1126/science.1087447, PMID: 12934013
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
90
-
-
2442537233
-
Gene regulatory network growth by duplication
-
PMID: 15107850
-
Teichmann SA, Babu MM. 2004. Gene regulatory network growth by duplication. Nature Genetics 36:492–496. doi: 10.1038/ng1340, PMID: 15107850
-
(2004)
Nature Genetics
, vol.36
, pp. 492-496
-
-
Teichmann, S.A.1
Babu, M.M.2
-
91
-
-
12144291195
-
Mapman: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
-
PMID: 14996223
-
Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M. 2004. Mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. The Plant Journal 37:914–939. doi: 10.1111/j.1365-313X.2004.02016.x, PMID: 14996223
-
(2004)
The Plant Journal
, vol.37
, pp. 914-939
-
-
Thimm, O.1
Bläsing, O.2
Gibon, Y.3
Nagel, A.4
Meyer, S.5
Krüger, P.6
Selbig, J.7
Müller, L.A.8
Rhee, S.Y.9
Stitt, M.10
-
92
-
-
65449136284
-
TopHat: Discovering splice junctions with Rna-Seq
-
PMID: 19289445
-
Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with Rna-Seq. Bioinformatics 25: 1105–1111. doi: 10.1093/bioinformatics/btp120, PMID: 19289445
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
93
-
-
70449115789
-
Co-expression tools for plant biology: Opportunities for hypothesis generation and caveats. Plant
-
PMID: 19712066
-
Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ. 2009. Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant, Cell & Environment 32:1633–1651. doi: 10.1111/j.1365-3040.2009.02040.x, PMID: 19712066
-
(2009)
Cell & Environment
, 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
-
94
-
-
0002438492
-
Costs of jasmonate-induced responses in plants competing for limited resources
-
van Dam NM, Baldwin IT. 1998. Costs of jasmonate-induced responses in plants competing for limited resources. Ecology Letters 1:30–33. doi: 10.1046/j.1461-0248.1998.00010.x
-
(1998)
Ecology Letters
, vol.1
, pp. 30-33
-
-
Van Dam, N.M.1
Baldwin, I.T.2
-
95
-
-
0034984603
-
Ontogeny constrains systemic protease inhibitor response in Nicotiana attenuata
-
PMID: 11441445
-
van Dam NM, Horn M, Mares M, Baldwin IT. 2001. Ontogeny constrains systemic protease inhibitor response in Nicotiana attenuata. Journal of Chemical Ecology 27:547–568. doi: 10.1023/A:1010341022761, PMID: 11441445
-
(2001)
Journal of Chemical Ecology
, vol.27
, pp. 547-568
-
-
Van Dam, N.M.1
Horn, M.2
Mares, M.3
Baldwin, I.T.4
-
96
-
-
33847634233
-
Evidence of interaction network evolution by whole-genome duplications: A case study in Mads-box proteins
-
PMID: 17175526
-
Veron AS, Kaufmann K, Bornberg-Bauer E. 2007. Evidence of interaction network evolution by whole-genome duplications: a case study in Mads-box proteins. Molecular Biology and Evolution 24:670–678. doi: 10.1093/molbev/msl197, PMID: 17175526
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 670-678
-
-
Veron, A.S.1
Kaufmann, K.2
Bornberg-Bauer, E.3
-
97
-
-
0035036713
-
Herbivore-induced ethylene burst reduces fitness costs of jasmonate- and oral secretion-induced defenses in Nicotiana attenuata
-
PMID: 24577660
-
Voelckel C, Schittko U, Baldwin IT. 2001. Herbivore-induced ethylene burst reduces fitness costs of jasmonate- and oral secretion-induced defenses in Nicotiana attenuata. Oecologia 127:274–280. doi: 10.1007/s004420000581, PMID: 24577660
-
(2001)
Oecologia
, vol.127
, pp. 274-280
-
-
Voelckel, C.1
Schittko, U.2
Baldwin, I.T.3
-
98
-
-
34250620899
-
Tuning the herbivore-induced ethylene burst: The role of transcript accumulation and ethylene perception in Nicotiana attenuata
-
von Dahl CC, Winz RA, Halitschke R, Kühnemann F, Gase K, Baldwin IT. 2007. Tuning the herbivore-induced ethylene burst: the role of transcript accumulation and ethylene perception in Nicotiana attenuata. The Plant Journal 51:293–307. doi: 10.1111/j.1365-313X.2007.03142.x
-
(2007)
The Plant Journal
, vol.51
, pp. 293-307
-
-
Von Dahl, C.C.1
Winz, R.A.2
Halitschke, R.3
Kühnemann, F.4
Gase, K.5
Baldwin, I.T.6
-
99
-
-
34248589740
-
Independently silencing two Jar family members impairs levels of trypsin proteinase inhibitors but not nicotine
-
PMID: 17273867
-
Wang L, Halitschke R, Kang Jh, Berg A, Harnisch F, Baldwin IT. 2007. Independently silencing two Jar family members impairs levels of trypsin proteinase inhibitors but not nicotine. Planta 226:159–167. doi: 10.1007/s00425-007-0477-3, PMID: 17273867
-
(2007)
Planta
, vol.226
, pp. 159-167
-
-
Wang, L.1
Halitschke, R.2
Kang, J.3
Berg, A.4
Harnisch, F.5
Baldwin, I.T.6
-
100
-
-
34548501747
-
Natural history and evolutionary principles of gene duplication in fungi
-
PMID: 17805289
-
Wapinski I, Pfeffer A, Friedman N, Regev A. 2007. Natural history and evolutionary principles of gene duplication in fungi. Nature 449:54–61. doi: 10.1038/nature06107, PMID: 17805289
-
(2007)
Nature
, vol.449
, pp. 54-61
-
-
Wapinski, I.1
Pfeffer, A.2
Friedman, N.3
Regev, A.4
-
101
-
-
83855162851
-
Exact and approximate area-proportional circular Venn and Euler diagrams
-
Wilkinson L. 2011. Exact and approximate area-proportional circular Venn and Euler diagrams. IEEE Transactions on Visualization and Computer Graphics 18:321–331. doi: 10.1109/TVCG.2011.56
-
(2011)
IEEE Transactions on Visualization and Computer Graphics
, vol.18
, pp. 321-331
-
-
Wilkinson, L.1
-
102
-
-
78149423236
-
New insights into plant responses to the attack from insect herbivores
-
PMID: 20649414
-
Wu J, Baldwin IT. 2010. New insights into plant responses to the attack from insect herbivores. Annual Review of Genetics 44:1–24. doi: 10.1146/annurev-genet-102209-163500, PMID: 20649414
-
(2010)
Annual Review of Genetics
, vol.44
, pp. 1-24
-
-
Wu, J.1
Baldwin, I.T.2
-
103
-
-
34250613463
-
Herbivory rapidly activates Mapk signaling in attacked and unattacked leaf regions but not between leaves of Nicotiana attenuata
-
PMID: 17400894
-
Wu J, Hettenhausen C, Meldau S, Baldwin IT. 2007. Herbivory rapidly activates Mapk signaling in attacked and unattacked leaf regions but not between leaves of Nicotiana attenuata. The Plant Cell 19:1096–1122. doi: 10.1105/tpc.106.049353, PMID: 17400894
-
(2007)
The Plant Cell
, vol.19
, pp. 1096-1122
-
-
Wu, J.1
Hettenhausen, C.2
Meldau, S.3
Baldwin, I.T.4
-
104
-
-
84932604774
-
Herbivore associated elicitor-induced defences are highly specific among closely related Nicotiana species
-
Xu S, Zhou W, Pottinger S, Baldwin IT. 2015. Herbivore associated elicitor-induced defences are highly specific among closely related Nicotiana species. Bmc Plant Biology 15:2. doi: 10.1186/s12870-014-0406-0
-
(2015)
Bmc Plant Biology
, vol.15
, pp. 2
-
-
Xu, S.1
Zhou, W.2
Pottinger, S.3
Baldwin, I.T.4
-
105
-
-
78650642605
-
BAK1 regulates the accumulation of jasmonic acid and the levels of trypsin proteinase inhibitors in Nicotiana attenuata’s responses to herbivory
-
PMID: 20937731
-
Yang Dh, Hettenhausen C, Baldwin IT, Wu J. 2011. BAK1 regulates the accumulation of jasmonic acid and the levels of trypsin proteinase inhibitors in Nicotiana attenuata’s responses to herbivory. Journal of Experimental Botany 62:641–652. doi: 10.1093/jxb/erq298, PMID: 20937731
-
(2011)
Journal of Experimental Botany
, vol.62
, pp. 641-652
-
-
Yang, D.1
Hettenhausen, C.2
Baldwin, I.T.3
Wu, J.4
-
106
-
-
84864677414
-
Silencing Nicotiana attenuata calcium-dependent protein kinases, CDPK4 and CDPK5, strongly up-regulates wound- and herbivory-induced jasmonic acid accumulations
-
PMID: 22715110
-
Yang Dh, Hettenhausen C, Baldwin IT, Wu J. 2012. Silencing Nicotiana attenuata calcium-dependent protein kinases, CDPK4 and CDPK5, strongly up-regulates wound- and herbivory-induced jasmonic acid accumulations. Plant Physiology 159:1591–1607. doi: 10.1104/pp.112.199018, PMID: 22715110
-
(2012)
Plant Physiology
, vol.159
, pp. 1591-1607
-
-
Yang, D.1
Hettenhausen, C.2
Baldwin, I.T.3
Wu, J.4
-
107
-
-
31344455118
-
A two-edged role for the transposable element Kiddo in the rice ubiquitin2 promoter
-
PMID: 15 805485
-
Yang G, Lee YH, Jiang Y, Shi X, Kertbundit S, Hall TC. 2005. A two-edged role for the transposable element Kiddo in the rice ubiquitin2 promoter. The Plant Cell 17:1559–1568. doi: 10.1105/tpc.104.030528, PMID: 15 805485
-
(2005)
The Plant Cell
, vol.17
, pp. 1559-1568
-
-
Yang, G.1
Lee, Y.H.2
Jiang, Y.3
Shi, X.4
Kertbundit, S.5
Hall, T.C.6
-
108
-
-
84884666640
-
Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice
-
PMID: 240787 85
-
Yasuda K, Ito M, Sugita T, Tsukiyama T, Saito H, Naito K, Teraishi M, Tanisaka T, Okumoto Y. 2013. Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice. Molecular Breeding: New Strategies in Plant Improvement 32:505–516. doi: 10.1007/s11032-013-9885-1, PMID: 240787 85
-
(2013)
Molecular Breeding: New Strategies in Plant Improvement
, vol.32
, pp. 505-516
-
-
Yasuda, K.1
Ito, M.2
Sugita, T.3
Tsukiyama, T.4
Saito, H.5
Naito, K.6
Teraishi, M.7
Tanisaka, T.8
Okumoto, Y.9
-
109
-
-
57749089675
-
Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis
-
PMID: 18757557
-
Yonekura-Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H, Niida R, Watanabe-Takahashi A, Inoue E, Saito K. 2008. Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. The Plant Cell 20:2160–2176. doi: 10.1105/tpc.108. 058040, PMID: 18757557
-
(2008)
The Plant Cell
, vol.20
, pp. 2160-2176
-
-
Yonekura-Sakakibara, K.1
Tohge, T.2
Matsuda, F.3
Nakabayashi, R.4
Takayama, H.5
Niida, R.6
Watanabe-Takahashi, A.7
Inoue, E.8
Saito, K.9
-
110
-
-
23944458138
-
A general framework for weighted gene co-expression network analysis
-
Article17, PMID: 16646834
-
Zhang B, Horvath S. 2005. A general framework for weighted gene co-expression network analysis. Statistical Applications in Genetics and Molecular Biology 4:Article17. doi: 10.2202/1544-6115.1128, PMID: 16646834
-
(2005)
Statistical Applications in Genetics and Molecular Biology
, vol.4
-
-
Zhang, B.1
Horvath, S.2
-
111
-
-
34248669040
-
KaKs Calculator: Calculating Ka and Ks through model selection and model averaging. Genomics
-
PMID: 17531802
-
Zhang Z, Li J, Zhao XQ, Wang J, Wong GK, Yu J. 2006. KaKs Calculator: calculating Ka and Ks through model selection and model averaging. Genomics, Proteomics & Bioinformatics 4:259–263. doi: 10.1016/S1672-0229(07)60007-2, PMID: 17531802
-
(2006)
Proteomics & Bioinformatics
, vol.4
, pp. 259-263
-
-
Zhang, Z.1
Li, J.2
Zhao, X.Q.3
Wang, J.4
Wong, G.K.5
Yu, J.6
-
112
-
-
80052576152
-
Cis-regulatory code of stress- responsive transcription in Arabidopsis thaliana
-
PMID: 21849619
-
Zou C, Sun K, Mackaluso JD, Seddon AE, Jin R, Thomashow MF, Shiu SH. 2011. Cis-regulatory code of stress- responsive transcription in Arabidopsis thaliana. PNAS 108:14992–14997. doi: 10.1073/pnas.1103202108, PMID: 21849619
-
(2011)
PNAS
, vol.108
, pp. 14992-14997
-
-
Zou, C.1
Sun, K.2
Mackaluso, J.D.3
Seddon, A.E.4
Jin, R.5
Thomashow, M.F.6
Shiu, S.H.7
|