-
1
-
-
0035800467
-
Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock
-
Alabadí D, Oyama T, Yanovsky MJ, Harmon FG, Más P, Kay SA (2001) Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science 293: 880-883
-
(2001)
Science
, vol.293
, pp. 880-883
-
-
Alabadí, D.1
Oyama, T.2
Yanovsky, M.J.3
Harmon, F.G.4
Más, P.5
Kay, S.A.6
-
4
-
-
21344470923
-
Circadian rhythms from multiple oscillators: Lessons from diverse organisms
-
Bell-Pedersen D, Cassone VM, Earnest DJ, Golden SS, Hardin PE, Thomas TL, Zoran MJ (2005) Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat Rev Genet 6: 544-556
-
(2005)
Nat Rev Genet
, vol.6
, pp. 544-556
-
-
Bell-Pedersen, D.1
Cassone, V.M.2
Earnest, D.J.3
Golden, S.S.4
Hardin, P.E.5
Thomas, T.L.6
Zoran, M.J.7
-
5
-
-
84863645983
-
Screening for in planta protein-protein interactions combining bimolecular fluorescence complementation with flow cytometry
-
Berendzen KW, Böhmer M, Wallmeroth N, Peter S, Vesič M, Zhou Y, Tiesler FK, Schleifenbaum F, Harter K (2012) Screening for in planta protein-protein interactions combining bimolecular fluorescence complementation with flow cytometry. Plant Methods 8: 25
-
(2012)
Plant Methods
, vol.8
, pp. 25
-
-
Berendzen, K.W.1
Böhmer, M.2
Wallmeroth, N.3
Peter, S.4
Vesič, M.5
Zhou, Y.6
Tiesler, F.K.7
Schleifenbaum, F.8
Harter, K.9
-
6
-
-
33644816031
-
Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis
-
Bläsing OE, Gibon Y, Günther M, Höhne M, Morcuende R, Osuna D, Thimm O, Usadel B, Scheible WR, Stitt M (2005) Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis. Plant Cell 17: 3257-3281
-
(2005)
Plant Cell
, vol.17
, pp. 3257-3281
-
-
Bläsing, O.E.1
Gibon, Y.2
Günther, M.3
Höhne, M.4
Morcuende, R.5
Osuna, D.6
Thimm, O.7
Usadel, B.8
Scheible, W.R.9
Stitt, M.10
-
7
-
-
84857822152
-
An effective statistical evaluation of ChIPseq dataset similarity
-
Chikina MD, Troyanskaya OG (2012) An effective statistical evaluation of ChIPseq dataset similarity. Bioinformatics 28: 607-613
-
(2012)
Bioinformatics
, vol.28
, pp. 607-613
-
-
Chikina, M.D.1
Troyanskaya, O.G.2
-
8
-
-
0032447801
-
Floral dip: A simplified method for Agrobacteriummediated transformation of Arabidopsis thaliana
-
Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacteriummediated transformation of Arabidopsis thaliana. Plant J 16: 735-743
-
(1998)
Plant J
, vol.16
, pp. 735-743
-
-
Clough, S.J.1
Bent, A.F.2
-
9
-
-
73249122674
-
Clocks in the green lineage: Comparative functional analysis of the circadian architecture of the picoeukaryote ostreococcus
-
Corellou F, Schwartz C, Motta JP, Djouani-Tahri B, Sanchez F, Bouget FY (2009) Clocks in the green lineage: comparative functional analysis of the circadian architecture of the picoeukaryote ostreococcus. Plant Cell 21: 3436-3449
-
(2009)
Plant Cell
, vol.21
, pp. 3436-3449
-
-
Corellou, F.1
Schwartz, C.2
Motta, J.P.3
Djouani-Tahri, B.4
Sanchez, F.5
Bouget, F.Y.6
-
10
-
-
0142245636
-
A gateway cloning vector set for highthroughput functional analysis of genes in planta
-
Curtis MD, Grossniklaus U (2003) A gateway cloning vector set for highthroughput functional analysis of genes in planta. Plant Physiol 133: 462-469
-
(2003)
Plant Physiol
, vol.133
, pp. 462-469
-
-
Curtis, M.D.1
Grossniklaus, U.2
-
11
-
-
79151483729
-
Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis
-
Dixon LE, Knox K, Kozma-Bognar L, Southern MM, Pokhilko A, Millar AJ (2011) Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis. Curr Biol 21: 120-125
-
(2011)
Curr Biol
, vol.21
, pp. 120-125
-
-
Dixon, L.E.1
Knox, K.2
Kozma-Bognar, L.3
Southern, M.M.4
Pokhilko, A.5
Millar, A.J.6
-
12
-
-
22744451756
-
Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage
-
Dodd AN, Salathia N, Hall A, Kévei E, Tóth R, Nagy F, Hibberd JM, Millar AJ, Webb AAR (2005) Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309: 630-633
-
(2005)
Science
, vol.309
, pp. 630-633
-
-
Dodd, A.N.1
Salathia, N.2
Hall, A.3
Kévei, E.4
Tóth, R.5
Nagy, F.6
Hibberd, J.M.7
Millar, A.J.8
Webb, A.A.R.9
-
13
-
-
33646510841
-
FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock
-
Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JC, Lynn JR, Straume M, Smith JQ, Millar AJ (2006) FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell 18: 639-650
-
(2006)
Plant Cell
, vol.18
, pp. 639-650
-
-
Edwards, K.D.1
Anderson, P.E.2
Hall, A.3
Salathia, N.S.4
Locke, J.C.5
Lynn, J.R.6
Straume, M.7
Smith, J.Q.8
Millar, A.J.9
-
14
-
-
84911478558
-
Tissuespecific clocks in Arabidopsis show asymmetric coupling
-
Endo M, Shimizu H, Nohales MA, Araki T, Kay SA (2014) Tissuespecific clocks in Arabidopsis show asymmetric coupling. Nature 515: 419-422
-
(2014)
Nature
, vol.515
, pp. 419-422
-
-
Endo, M.1
Shimizu, H.2
Nohales, M.A.3
Araki, T.4
Kay, S.A.5
-
15
-
-
79955007772
-
Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation
-
Farinas B, Mas P (2011) Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation. Plant J 66: 318-329
-
(2011)
Plant J
, vol.66
, pp. 318-329
-
-
Farinas, B.1
Mas, P.2
-
16
-
-
11844289579
-
Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock
-
Farré EM, Harmer SL, Harmon FG, Yanovsky MJ, Kay SA (2005) Overlapping and distinct roles of PRR7 and PRR9 in the Arabidopsis circadian clock. Curr Biol 15: 47-54
-
(2005)
Curr Biol
, vol.15
, pp. 47-54
-
-
Farré, E.M.1
Harmer, S.L.2
Harmon, F.G.3
Yanovsky, M.J.4
Kay, S.A.5
-
17
-
-
35448992952
-
PRR7 protein levels are regulated by light and the circadian clock in Arabidopsis
-
Farré EM, Kay SA (2007) PRR7 protein levels are regulated by light and the circadian clock in Arabidopsis. Plant J 52: 548-560
-
(2007)
Plant J
, vol.52
, pp. 548-560
-
-
Farré, E.M.1
Kay, S.A.2
-
18
-
-
84885387188
-
The PRR family of transcriptional regulators reflects the complexity and evolution of plant circadian clocks
-
Farré EM, Liu T (2013) The PRR family of transcriptional regulators reflects the complexity and evolution of plant circadian clocks. Curr Opin Plant Biol 16: 621-629
-
(2013)
Curr Opin Plant Biol
, vol.16
, pp. 621-629
-
-
Farré, E.M.1
Liu, T.2
-
19
-
-
79958268862
-
Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules
-
Filichkin SA, Breton G, Priest HD, Dharmawardhana P, Jaiswal P, Fox SE, Michael TP, Chory J, Kay SA, Mockler TC (2011) Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules. PLoS One 6: e16907
-
(2011)
PLoS One
, vol.6
-
-
Filichkin, S.A.1
Breton, G.2
Priest, H.D.3
Dharmawardhana, P.4
Jaiswal, P.5
Fox, S.E.6
Michael, T.P.7
Chory, J.8
Kay, S.A.9
Mockler, T.C.10
-
20
-
-
67650473072
-
Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response
-
Fornara F, Panigrahi KCS, Gissot L, Sauerbrunn N, Rühl M, Jarillo JA, Coupland G (2009) Arabidopsis DOF transcription factors act redundantly to reduce CONSTANS expression and are essential for a photoperiodic flowering response. Dev Cell 17: 75-86
-
(2009)
Dev Cell
, vol.17
, pp. 75-86
-
-
Fornara, F.1
Panigrahi, K.C.S.2
Gissot, L.3
Sauerbrunn, N.4
Rühl, M.5
Jarillo, J.A.6
Coupland, G.7
-
21
-
-
0023957762
-
Mutational analysis of upstream activation sequence 2 of the CYC1 gene of Saccharomyces cerevisiae: A HAP2- HAP3-responsive site
-
Forsburg SL, Guarente L (1988) Mutational analysis of upstream activation sequence 2 of the CYC1 gene of Saccharomyces cerevisiae: a HAP2- HAP3-responsive site. Mol Cell Biol 8: 647-654
-
(1988)
Mol Cell Biol
, vol.8
, pp. 647-654
-
-
Forsburg, S.L.1
Guarente, L.2
-
22
-
-
84893861206
-
DNA-binding specificities of plant transcription factors and their potential to define target genes
-
Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R (2014) DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci USA 111: 2367-2372
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. 2367-2372
-
-
Franco-Zorrilla, J.M.1
López-Vidriero, I.2
Carrasco, J.L.3
Godoy, M.4
Vera, P.5
Solano, R.6
-
23
-
-
53149108244
-
Post-translational regulation of the Arabidopsis circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins
-
Fujiwara S, Wang L, Han L, Suh SS, Salomé PA, McClung CR, Somers DE (2008) Post-translational regulation of the Arabidopsis circadian clock through selective proteolysis and phosphorylation of pseudo-response regulator proteins. J Biol Chem 283: 23073- 23083
-
(2008)
J Biol Chem
, vol.283
, pp. 23073-23083
-
-
Fujiwara, S.1
Wang, L.2
Han, L.3
Suh, S.S.4
Salomé, P.A.5
McClung, C.R.6
Somers, D.E.7
-
24
-
-
84857383458
-
Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor
-
Gendron JM, Pruneda-Paz JL, Doherty CJ, Gross AM, Kang SE, Kay SA (2012) Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. Proc Natl Acad Sci USA 109: 3167-3172
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 3167-3172
-
-
Gendron, J.M.1
Pruneda-Paz, J.L.2
Doherty, C.J.3
Gross, A.M.4
Kang, S.E.5
Kay, S.A.6
-
25
-
-
25144442704
-
TAMO: A flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs
-
Gordon DB, Nekludova L, McCallum S, Fraenkel E (2005) TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs. Bioinformatics 21: 3164-3165
-
(2005)
Bioinformatics
, vol.21
, pp. 3164-3165
-
-
Gordon, D.B.1
Nekludova, L.2
McCallum, S.3
Fraenkel, E.4
-
26
-
-
79953300078
-
FIMO: Scanning for occurrences of a given motif
-
Grant CE, Bailey TL, Noble WS (2011) FIMO: scanning for occurrences of a given motif. Bioinformatics 27: 1017-1018
-
(2011)
Bioinformatics
, vol.27
, pp. 1017-1018
-
-
Grant, C.E.1
Bailey, T.L.2
Noble, W.S.3
-
28
-
-
0037143757
-
Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes
-
Gutierrez RA, Ewing RM, Cherry JM, Green PJ (2002) Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc Natl Acad Sci USA 99: 11513-11518
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 11513-11518
-
-
Gutierrez, R.A.1
Ewing, R.M.2
Cherry, J.M.3
Green, P.J.4
-
29
-
-
0035193638
-
Dissection of the light signal transduction pathways regulating the two early light-induced protein genes in Arabidopsis
-
Harari-Steinberg O, Ohad I, Chamovitz DA (2001) Dissection of the light signal transduction pathways regulating the two early light-induced protein genes in Arabidopsis. Plant Physiol 127: 986-997
-
(2001)
Plant Physiol
, vol.127
, pp. 986-997
-
-
Harari-Steinberg, O.1
Ohad, I.2
Chamovitz, D.A.3
-
30
-
-
79952255290
-
Genome-wide profiling of the core clock protein BMAL1 targets reveals a strict relationship with metabolism
-
Hatanaka F, Matsubara C, Myung J, Yoritaka T, Kamimura N, Tsutsumi S, Kanai A, Suzuki Y, Sassone-Corsi P, Aburatani H, Sugano S, Takumi T (2010) Genome-wide profiling of the core clock protein BMAL1 targets reveals a strict relationship with metabolism. Mol Cell Biol 30: 5636- 5648
-
(2010)
Mol Cell Biol
, vol.30
, pp. 5636-5648
-
-
Hatanaka, F.1
Matsubara, C.2
Myung, J.3
Yoritaka, T.4
Kamimura, N.5
Tsutsumi, S.6
Kanai, A.7
Suzuki, Y.8
Sassone-Corsi, P.9
Aburatani, H.10
Sugano, S.11
Takumi, T.12
-
31
-
-
84881028642
-
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions
-
Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, et al (2013) An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet 45: 891-898
-
(2013)
Nat Genet
, vol.45
, pp. 891-898
-
-
Haudry, A.1
Platts, A.E.2
Vello, E.3
Hoen, D.R.4
Leclercq, M.5
Williamson, R.J.6
Forczek, E.7
Joly-Lopez, Z.8
Steffen, J.G.9
Hazzouri, K.M.10
Dewar, K.11
Stinchcombe, J.R.12
-
32
-
-
79151483227
-
LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock
-
Helfer A, Nusinow DA, Chow BY, Gehrke AR, Bulyk ML, Kay SA (2011) LUX ARRHYTHMO encodes a nighttime repressor of circadian gene expression in the Arabidopsis core clock. Curr Biol 21: 126-133
-
(2011)
Curr Biol
, vol.21
, pp. 126-133
-
-
Helfer, A.1
Nusinow, D.A.2
Chow, B.Y.3
Gehrke, A.R.4
Bulyk, M.L.5
Kay, S.A.6
-
33
-
-
84859043500
-
EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock
-
Herrero E, Kolmos E, Bujdoso N, Yuan Y, Wang M, Berns MC, Uhlworm H, Coupland G, Saini R, Jaskolski M, Webb A, Gonçalves J, et al (2012) EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock. Plant Cell 24: 428- 443
-
(2012)
Plant Cell
, vol.24
, pp. 428-443
-
-
Herrero, E.1
Kolmos, E.2
Bujdoso, N.3
Yuan, Y.4
Wang, M.5
Berns, M.C.6
Uhlworm, H.7
Coupland, G.8
Saini, R.9
Jaskolski, M.10
Webb, A.11
Gonçalves, J.12
-
34
-
-
84912124204
-
A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana
-
Heyndrickx KS, Van de Velde J, Wang C, Weigel D, Vandepoele K (2014) A functional and evolutionary perspective on transcription factor binding in Arabidopsis thaliana. Plant Cell 26: 3894-3910
-
(2014)
Plant Cell
, vol.26
, pp. 3894-3910
-
-
Heyndrickx, K.S.1
Van de Velde, J.2
Wang, C.3
Weigel, D.4
Vandepoele, K.5
-
35
-
-
84879065464
-
Accurate timekeeping is controlled by a cycling activator in Arabidopsis
-
Hsu PY, Devisetty UK, Harmer SL (2013) Accurate timekeeping is controlled by a cycling activator in Arabidopsis. eLife 2: e00473
-
(2013)
eLife
, vol.2
-
-
Hsu, P.Y.1
Devisetty, U.K.2
Harmer, S.L.3
-
36
-
-
84897418780
-
Wheels within wheels: The plant circadian system
-
Hsu PY, Harmer SL (2014) Wheels within wheels: the plant circadian system. Trends Plant Sci 19: 240-249
-
(2014)
Trends Plant Sci
, vol.19
, pp. 240-249
-
-
Hsu, P.Y.1
Harmer, S.L.2
-
37
-
-
84859508042
-
Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator
-
Huang W, Pérez-García P, Pokhilko A, Millar AJ, Antoshechkin I, Riechmann JL, Mas P (2012) Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science 336: 75-79
-
(2012)
Science
, vol.336
, pp. 75-79
-
-
Huang, W.1
Pérez-García, P.2
Pokhilko, A.3
Millar, A.J.4
Antoshechkin, I.5
Riechmann, J.L.6
Mas, P.7
-
38
-
-
84921441090
-
The 'dark matter' in the plant genomes: Non-coding and unannotated DNA sequences associated with open chromatin
-
Jiang J (2015) The 'dark matter' in the plant genomes: non-coding and unannotated DNA sequences associated with open chromatin. Curr Opin Plant Biol 24: 17-23
-
(2015)
Curr Opin Plant Biol
, vol.24
, pp. 17-23
-
-
Jiang, J.1
-
39
-
-
71049138076
-
The phytochrome-interacting factor PIF7 negatively regulates DREB1 expression under circadian control in Arabidopsis
-
Kidokoro S, Maruyama K, Nakashima K, Imura Y, Narusaka Y, Shinwari ZK, Osakabe Y, Fujita Y, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2009) The phytochrome-interacting factor PIF7 negatively regulates DREB1 expression under circadian control in Arabidopsis. Plant Physiol 151: 2046-2057
-
(2009)
Plant Physiol
, vol.151
, pp. 2046-2057
-
-
Kidokoro, S.1
Maruyama, K.2
Nakashima, K.3
Imura, Y.4
Narusaka, Y.5
Shinwari, Z.K.6
Osakabe, Y.7
Fujita, Y.8
Mizoi, J.9
Shinozaki, K.10
Yamaguchi-Shinozaki, K.11
-
40
-
-
33749031807
-
Molecular components of the mammalian circadian clock
-
Ko CH, Takahashi JS (2006) Molecular components of the mammalian circadian clock. Hum Mol Genet 15: R271-R277
-
(2006)
Hum Mol Genet
, vol.15
, pp. R271-R277
-
-
Ko, C.H.1
Takahashi, J.S.2
-
41
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
42
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
43
-
-
84938826120
-
Determinants of nucleosome positioning and their influence on plant gene expression
-
Liu MJ, Seddon AE, Tsai ZT, Major IT, Floer M, Howe GA, Shiu SH (2015) Determinants of nucleosome positioning and their influence on plant gene expression. Genome Res 25: 1182-1195
-
(2015)
Genome Res
, vol.25
, pp. 1182-1195
-
-
Liu, M.J.1
Seddon, A.E.2
Tsai, Z.T.3
Major, I.T.4
Floer, M.5
Howe, G.A.6
Shiu, S.H.7
-
44
-
-
84884909996
-
Direct regulation of abiotic responses by the Arabidopsis circadian clock component PRR7
-
Liu T, Carlsson J, Takeuchi T, Newton L, Farré EM (2013) Direct regulation of abiotic responses by the Arabidopsis circadian clock component PRR7. Plant J 76: 101-114
-
(2013)
Plant J
, vol.76
, pp. 101-114
-
-
Liu, T.1
Carlsson, J.2
Takeuchi, T.3
Newton, L.4
Farré, E.M.5
-
45
-
-
79958117256
-
MEME-ChIP: Motif analysis of large DNA datasets
-
Machanick P, Bailey TL (2011) MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27: 1696-1697
-
(2011)
Bioinformatics
, vol.27
, pp. 1696-1697
-
-
Machanick, P.1
Bailey, T.L.2
-
46
-
-
0036008343
-
The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. Characterization with APRR1-overexpressing plants
-
Makino S, Matsushika A, Kojima M, Yamashino T, Mizuno T (2002) The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. Characterization with APRR1-overexpressing plants. Plant Cell Physiol 43: 58-69
-
(2002)
Plant Cell Physiol
, vol.43
, pp. 58-69
-
-
Makino, S.1
Matsushika, A.2
Kojima, M.3
Yamashino, T.4
Mizuno, T.5
-
47
-
-
84891808382
-
JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles
-
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H, Lim J, Shyr C, et al (2014) JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res 42: D142-D147
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D142-D147
-
-
Mathelier, A.1
Zhao, X.2
Zhang, A.W.3
Parcy, F.4
Worsley-Hunt, R.5
Arenillas, D.J.6
Buchman, S.7
Chen, C.Y.8
Chou, A.9
Ienasescu, H.10
Lim, J.11
Shyr, C.12
-
48
-
-
40149105297
-
Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules
-
Michael TP, Mockler TC, Breton G, McEntee C, Byer A, Trout JD, Hazen SP, Shen R, Priest HD, Sullivan CM, Givan SA, Yanovsky M, et al (2008) Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 4: e14
-
(2008)
PLoS Genet
, vol.4
-
-
Michael, T.P.1
Mockler, T.C.2
Breton, G.3
McEntee, C.4
Byer, A.5
Trout, J.D.6
Hazen, S.P.7
Shen, R.8
Priest, H.D.9
Sullivan, C.M.10
Givan, S.A.11
Yanovsky, M.12
-
49
-
-
84899139852
-
Ambient temperature signal feeds into the circadian clock transcriptional circuitry through the EC nighttime repressor in Arabidopsis thaliana
-
Mizuno T, Nomoto Y, Oka H, Kitayama M, Takeuchi A, Tsubouchi M, Yamashino T (2014) Ambient temperature signal feeds into the circadian clock transcriptional circuitry through the EC nighttime repressor in Arabidopsis thaliana. Plant Cell Physiol 55: 958- 976
-
(2014)
Plant Cell Physiol
, vol.55
, pp. 958-976
-
-
Mizuno, T.1
Nomoto, Y.2
Oka, H.3
Kitayama, M.4
Takeuchi, A.5
Tsubouchi, M.6
Yamashino, T.7
-
50
-
-
40149093631
-
The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis
-
Mockler TC, Michael TP, Priest HD, Shen R, Sullivan CM, Givan SA, McEntee C, Kay SA, Chory J (2007) The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis. Cold Spring Harb Symp Quant Biol 72: 353- 363
-
(2007)
Cold Spring Harb Symp Quant Biol
, vol.72
, pp. 353-363
-
-
Mockler, T.C.1
Michael, T.P.2
Priest, H.D.3
Shen, R.4
Sullivan, C.M.5
Givan, S.A.6
McEntee, C.7
Kay, S.A.8
Chory, J.9
-
51
-
-
84940552331
-
Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis
-
Nagel DH, Doherty CJ, Pruneda-Paz JL, Schmitz RJ, Ecker JR, Kay SA (2015) Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci USA 112: E4802-E4810
-
(2015)
Proc Natl Acad Sci USA
, vol.112
, pp. E4802-E4810
-
-
Nagel, D.H.1
Doherty, C.J.2
Pruneda-Paz, J.L.3
Schmitz, R.J.4
Ecker, J.R.5
Kay, S.A.6
-
52
-
-
34547702730
-
Arabidopsis clock-associated pseudo-response regulators PRR9, PRR7 and PRR5 coordinately and positively regulate flowering time through the canonical CONSTANS-dependent photoperiodic pathway
-
Nakamichi N, Kita M, Niinuma K, Ito S, Yamashino T, Mizoguchi T, Mizuno T (2007) Arabidopsis clock-associated pseudo-response regulators PRR9, PRR7 and PRR5 coordinately and positively regulate flowering time through the canonical CONSTANS-dependent photoperiodic pathway. Plant Cell Physiol 48: 822-832
-
(2007)
Plant Cell Physiol
, vol.48
, pp. 822-832
-
-
Nakamichi, N.1
Kita, M.2
Niinuma, K.3
Ito, S.4
Yamashino, T.5
Mizoguchi, T.6
Mizuno, T.7
-
53
-
-
63049122216
-
Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response
-
Nakamichi N, Kusano M, Fukushima A, Kita M, Ito S, Yamashino T, Saito K, Sakakibara H, Mizuno T (2009) Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response. Plant Cell Physiol 50: 447-462
-
(2009)
Plant Cell Physiol
, vol.50
, pp. 447-462
-
-
Nakamichi, N.1
Kusano, M.2
Fukushima, A.3
Kita, M.4
Ito, S.5
Yamashino, T.6
Saito, K.7
Sakakibara, H.8
Mizuno, T.9
-
54
-
-
77952919484
-
PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock
-
Nakamichi N, Kiba T, Henriques R, Mizuno T, Chua NH, Sakakibara H (2010) PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock. Plant Cell 22: 594- 605
-
(2010)
Plant Cell
, vol.22
, pp. 594-605
-
-
Nakamichi, N.1
Kiba, T.2
Henriques, R.3
Mizuno, T.4
Chua, N.H.5
Sakakibara, H.6
-
55
-
-
84867656050
-
Transcriptional repressor PRR5 directly regulates clock-output pathways
-
Nakamichi N, Kiba T, Kamioka M, Suzuki T, Yamashino T, Higashiyama T, Sakakibara H, Mizuno T (2012) Transcriptional repressor PRR5 directly regulates clock-output pathways. Proc Natl Acad Sci USA 109: 17123- 17128
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 17123-17128
-
-
Nakamichi, N.1
Kiba, T.2
Kamioka, M.3
Suzuki, T.4
Yamashino, T.5
Higashiyama, T.6
Sakakibara, H.7
Mizuno, T.8
-
56
-
-
65249184988
-
The circadian clock regulates the photoperiodic response of hypocotyl elongation through a coincidence mechanism in Arabidopsis thaliana
-
Niwa Y, Yamashino T, Mizuno T (2009) The circadian clock regulates the photoperiodic response of hypocotyl elongation through a coincidence mechanism in Arabidopsis thaliana. Plant Cell Physiol 50: 838-854
-
(2009)
Plant Cell Physiol
, vol.50
, pp. 838-854
-
-
Niwa, Y.1
Yamashino, T.2
Mizuno, T.3
-
57
-
-
0023663882
-
Yeast HAP2 and HAP3 activators both bind to the CYC1 upstream activation site, UAS2, in an interdependent manner
-
Olesen J, Hahn S, Guarente L (1987) Yeast HAP2 and HAP3 activators both bind to the CYC1 upstream activation site, UAS2, in an interdependent manner. Cell 51: 953-961
-
(1987)
Cell
, vol.51
, pp. 953-961
-
-
Olesen, J.1
Hahn, S.2
Guarente, L.3
-
58
-
-
84964312519
-
Prevalence, evolution, and cis-regulation of diel transcription in Chlamydomonas reinhardtii
-
Panchy N, Wu GX, Newton L, Tsai CH, Chen J, Benning C, Farre EM, Shiu SH (2014) Prevalence, evolution, and cis-regulation of diel transcription in Chlamydomonas reinhardtii. G3 4: 2461-2471
-
(2014)
G3
, vol.4
, pp. 2461-2471
-
-
Panchy, N.1
Wu, G.X.2
Newton, L.3
Tsai, C.H.4
Chen, J.5
Benning, C.6
Farre, E.M.7
Shiu, S.H.8
-
59
-
-
37849047792
-
PRR3 is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock
-
Para A, Farré EM, Imaizumi T, Pruneda-Paz JL, Harmon FG, Kay SA (2007) PRR3 is a vascular regulator of TOC1 stability in the Arabidopsis circadian clock. Plant Cell 19: 3462-3473
-
(2007)
Plant Cell
, vol.19
, pp. 3462-3473
-
-
Para, A.1
Farré, E.M.2
Imaizumi, T.3
Pruneda-Paz, J.L.4
Harmon, F.G.5
Kay, S.A.6
-
60
-
-
0031159538
-
Quantitative analysis of Drosophila period gene transcription in living animals
-
Plautz JD, Straume M, Stanewsky R, Jamison CF, Brandes C, Dowse HB, Hall JC, Kay SA (1997) Quantitative analysis of Drosophila period gene transcription in living animals. J Biol Rhythms 12: 204-217
-
(1997)
J Biol Rhythms
, vol.12
, pp. 204-217
-
-
Plautz, J.D.1
Straume, M.2
Stanewsky, R.3
Jamison, C.F.4
Brandes, C.5
Dowse, H.B.6
Hall, J.C.7
Kay, S.A.8
-
61
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
62
-
-
79953730633
-
REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock
-
Rawat R, Takahashi N, Hsu PY, Jones MA, Schwartz J, Salemi MR, Phinney BS, Harmer SL (2011) REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock. PLoS Genet 7: e1001350
-
(2011)
PLoS Genet
, vol.7
-
-
Rawat, R.1
Takahashi, N.2
Hsu, P.Y.3
Jones, M.A.4
Schwartz, J.5
Salemi, M.R.6
Phinney, B.S.7
Harmer, S.L.8
-
63
-
-
78651271733
-
Integrative genomics viewer
-
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29: 24-26
-
(2011)
Nat Biotechnol
, vol.29
, pp. 24-26
-
-
Robinson, J.T.1
Thorvaldsdóttir, H.2
Winckler, W.3
Guttman, M.4
Lander, E.S.5
Getz, G.6
Mesirov, J.P.7
-
64
-
-
84880391363
-
LNK genes integrate light and clock signaling networks at the core of the Arabidopsis oscillator
-
Rugnone ML, Faigón Soverna A, Sanchez SE, Schlaen RG, Hernando CE, Seymour DK, Mancini E, Chernomoretz A,Weigel D,Más P, Yanovsky MJ (2013) LNK genes integrate light and clock signaling networks at the core of the Arabidopsis oscillator. Proc Natl Acad Sci USA 110: 12120- 12125
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 12120-12125
-
-
Rugnone, M.L.1
Faigón Soverna, A.2
Sanchez, S.E.3
Schlaen, R.G.4
Hernando, C.E.5
Seymour, D.K.6
Mancini, E.7
Chernomoretz, A.8
Weigel, D.9
Más, P.10
Yanovsky, M.J.11
-
65
-
-
0036857414
-
Aberrant expression of the Arabidopsis circadian-regulated APRR5 gene belonging to the APRR1/TOC1 quintet results in early flowering and hypersensitiveness to light in early photomorphogenesis
-
Sato E, Nakamichi N, Yamashino T, Mizuno T (2002) Aberrant expression of the Arabidopsis circadian-regulated APRR5 gene belonging to the APRR1/TOC1 quintet results in early flowering and hypersensitiveness to light in early photomorphogenesis. Plant Cell Physiol 43: 1374-1385
-
(2002)
Plant Cell Physiol
, vol.43
, pp. 1374-1385
-
-
Sato, E.1
Nakamichi, N.2
Yamashino, T.3
Mizuno, T.4
-
66
-
-
0034604423
-
Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog
-
Strayer C, Oyama T, Schultz TF, Raman R, Somers DE, Más P, Panda S, Kreps JA, Kay SA (2000) Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289: 768-771
-
(2000)
Science
, vol.289
, pp. 768-771
-
-
Strayer, C.1
Oyama, T.2
Schultz, T.F.3
Raman, R.4
Somers, D.E.5
Más, P.6
Panda, S.7
Kreps, J.A.8
Kay, S.A.9
-
67
-
-
84907381991
-
Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana
-
Sullivan AM, Arsovski AA, Lempe J, Bubb KL,WeirauchMT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, et al (2014) Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Reports 8: 2015- 2030
-
(2014)
Cell Reports
, vol.8
, pp. 2015-2030
-
-
Sullivan, A.M.1
Arsovski, A.A.2
Lempe, J.3
Bubb, K.L.4
Weirauch, M.T.5
Sabo, P.J.6
Sandstrom, R.7
Thurman, R.E.8
Neph, S.9
Reynolds, A.P.10
Stergachis, A.B.11
Vernot, B.12
-
68
-
-
59849108361
-
Molecular phylogeny and expression of poplar circadian clock genes, LHY1 and LHY2
-
Takata N, Saito S, Saito CT, Nanjo T, Shinohara K, Uemura M (2009) Molecular phylogeny and expression of poplar circadian clock genes, LHY1 and LHY2. New Phytol 181: 808-819
-
(2009)
New Phytol
, vol.181
, pp. 808-819
-
-
Takata, N.1
Saito, S.2
Saito, C.T.3
Nanjo, T.4
Shinohara, K.5
Uemura, M.6
-
69
-
-
77951589569
-
Phylogenetic footprint of the plant clock system in angiosperms: Evolutionary processes of pseudo-response regulators
-
Takata N, Saito S, Saito CT, Uemura M (2010) Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of pseudo-response regulators. BMC Evol Biol 10: 126
-
(2010)
BMC Evol Biol
, vol.10
, pp. 126
-
-
Takata, N.1
Saito, S.2
Saito, C.T.3
Uemura, M.4
-
70
-
-
84913533826
-
Light and the circadian clock mediate time-specific changes in sensitivity to UV-B stress under light/dark cycles
-
Takeuchi T, Newton L, Burkhardt A, Mason S, Farré EM (2014) Light and the circadian clock mediate time-specific changes in sensitivity to UV-B stress under light/dark cycles. J Exp Bot 65: 6003-6012
-
(2014)
J Exp Bot
, vol.65
, pp. 6003-6012
-
-
Takeuchi, T.1
Newton, L.2
Burkhardt, A.3
Mason, S.4
Farré, E.M.5
-
71
-
-
33845780071
-
CONSTANS and the CCAAT box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis
-
Wenkel S, Turck F, Singer K, Gissot L, Le Gourrierec J, Samach A, Coupland G (2006) CONSTANS and the CCAAT box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis. Plant Cell 18: 2971-2984
-
(2006)
Plant Cell
, vol.18
, pp. 2971-2984
-
-
Wenkel, S.1
Turck, F.2
Singer, K.3
Gissot, L.4
Le Gourrierec, J.5
Samach, A.6
Coupland, G.7
-
72
-
-
4344699146
-
The adaptive value of circadian clocks: An experimental assessment in cyanobacteria
-
Woelfle MA, Ouyang Y, Phanvijhitsiri K, Johnson CH (2004) The adaptive value of circadian clocks: an experimental assessment in cyanobacteria. Curr Biol 14: 1481-1486
-
(2004)
Curr Biol
, vol.14
, pp. 1481-1486
-
-
Woelfle, M.A.1
Ouyang, Y.2
Phanvijhitsiri, K.3
Johnson, C.H.4
-
73
-
-
84907351550
-
LNK1 and LNK2 are transcriptional coactivators in the Arabidopsis circadian oscillator
-
Xie Q, Wang P, Liu X, Yuan L, Wang L, Zhang C, Li Y, Xing H, Zhi L, Yue Z, Zhao C, McClung CR, et al (2014) LNK1 and LNK2 are transcriptional coactivators in the Arabidopsis circadian oscillator. Plant Cell 26: 2843- 2857
-
(2014)
Plant Cell
, vol.26
, pp. 2843-2857
-
-
Xie, Q.1
Wang, P.2
Liu, X.3
Yuan, L.4
Wang, L.5
Zhang, C.6
Li, Y.7
Xing, H.8
Zhi, L.9
Yue, Z.10
Zhao, C.11
McClung, C.R.12
-
74
-
-
68849098242
-
Evidence for the adaptive significance of circadian rhythms
-
Yerushalmi S, Green RM (2009) Evidence for the adaptive significance of circadian rhythms. Ecol Lett 12: 970-981
-
(2009)
Ecol Lett
, vol.12
, pp. 970-981
-
-
Yerushalmi, S.1
Green, R.M.2
-
75
-
-
79952404897
-
Circadian clocks and adaptation in Arabidopsis
-
Yerushalmi S, Yakir E, Green RM (2011) Circadian clocks and adaptation in Arabidopsis. Mol Ecol 20: 1155-1165
-
(2011)
Mol Ecol
, vol.20
, pp. 1155-1165
-
-
Yerushalmi, S.1
Yakir, E.2
Green, R.M.3
-
76
-
-
84899144072
-
CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes
-
Yoshitane H, Ozaki H, Terajima H, Du NH, Suzuki Y, Fujimori T, Kosaka N, Shimba S, Sugano S, Takagi T, Iwasaki W, Fukada Y (2014) CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes. Mol Cell Biol 34: 1776- 1787
-
(2014)
Mol Cell Biol
, vol.34
, pp. 1776-1787
-
-
Yoshitane, H.1
Ozaki, H.2
Terajima, H.3
Du, N.H.4
Suzuki, Y.5
Fujimori, T.6
Kosaka, N.7
Shimba, S.8
Sugano, S.9
Takagi, T.10
Iwasaki, W.11
Fukada, Y.12
-
77
-
-
70349534866
-
Conserved daily transcriptional programs in Carica papaya
-
Zdepski A, Wang W, Priest HD, Ali F, Alam M, Mockler TC, Michael TP (2008) Conserved daily transcriptional programs in Carica papaya. Trop Plant Biol 1: 236-245
-
(2008)
Trop Plant Biol
, vol.1
, pp. 236-245
-
-
Zdepski, A.1
Wang, W.2
Priest, H.D.3
Ali, F.4
Alam, M.5
Mockler, T.C.6
Michael, T.P.7
-
78
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
Liu, X.S.11
-
79
-
-
77951947707
-
ChIPpeakAnno: A Bioconductor package to annotate ChIP-seq and ChIP-chip data
-
Zhu LJ, Gazin C, Lawson ND, Pagès H, Lin SM, Lapointe DS, Green MR (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 11: 237
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 237
-
-
Zhu, L.J.1
Gazin, C.2
Lawson, N.D.3
Pagès, H.4
Lin, S.M.5
Lapointe, D.S.6
Green, M.R.7
-
80
-
-
80052576152
-
Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana
-
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. Proc Natl Acad Sci USA 108: 14992- 14997
-
(2011)
Proc Natl Acad Sci USA
, 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
|