-
1
-
-
84903649429
-
Temporal dynamics of growth and photosynthesis suppression in response to jasmonate signaling
-
Attaran E, Major IT, Cruz JA, Rosa BA, Koo AJ, Chen J, Kramer DM, He SY, Howe GA. 2014. Temporal dynamics of growth and photosynthesis suppression in response to jasmonate signaling. Plant Physiol 165: 1302-1314.
-
(2014)
Plant Physiol
, vol.165
, pp. 1302-1314
-
-
Attaran, E.1
Major, I.T.2
Cruz, J.A.3
Rosa, B.A.4
Koo, A.J.5
Chen, J.6
Kramer, D.M.7
He, S.Y.8
Howe, G.A.9
-
2
-
-
0028385745
-
The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression
-
Baker SS, Wilhelm KS, Thomashow MF. 1994. The 5′-region of Arabidopsis thaliana cor15a has cis-acting elements that confer cold-, drought- and ABA-regulated gene expression. Plant Mol Biol 24: 701-713.
-
(1994)
Plant Mol Biol
, vol.24
, pp. 701-713
-
-
Baker, S.S.1
Wilhelm, K.S.2
Thomashow, M.F.3
-
3
-
-
84872269321
-
Nucleosomedriven transcription factor binding and gene regulation
-
Ballare C, Castellano G, Gaveglia L, Althammer S, González-Vallinas J, Eyras E, Le Dily F, Zaurin R, Soronellas D, Vicent GP, et al. 2013. Nucleosomedriven transcription factor binding and gene regulation. Mol Cell 49: 67-79.
-
(2013)
Mol Cell
, vol.49
, pp. 67-79
-
-
Ballare, C.1
Castellano, G.2
Gaveglia, L.3
Althammer, S.4
González-Vallinas, J.5
Eyras, E.6
Le Dily, F.7
Zaurin, R.8
Soronellas, D.9
Vicent, G.P.10
-
4
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc 57: 289-300.
-
(1995)
J R Stat Soc
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
5
-
-
84924863892
-
A key general stress response motif is regulated non-uniformly by CAMTA transcription factors
-
Benn G, Wang CQ, Hicks DR, Stein J, Guthrie C, Dehesh K. 2014. A key general stress response motif is regulated non-uniformly by CAMTA transcription factors. Plant J 80: 82-92.
-
(2014)
Plant J
, vol.80
, pp. 82-92
-
-
Benn, G.1
Wang, C.Q.2
Hicks, D.R.3
Stein, J.4
Guthrie, C.5
Dehesh, K.6
-
6
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
7
-
-
3042741883
-
Conserved MYC transcription factors play a key role in jasmonate signaling both in tomato and Arabidopsis
-
Boter M, Ruíz-Rivero O, Abdeen A, Prat S. 2004. Conserved MYC transcription factors play a key role in jasmonate signaling both in tomato and Arabidopsis. Genes Dev 18: 1577-1591.
-
(2004)
Genes Dev
, vol.18
, pp. 1577-1591
-
-
Boter, M.1
Ruíz-Rivero, O.2
Abdeen, A.3
Prat, S.4
-
8
-
-
54949147307
-
F-Seq: A feature density estimator for high-throughput sequence tags
-
Boyle AP, Guinney J, Crawford GE, Furey TS. 2008. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24: 2537-2538.
-
(2008)
Bioinformatics
, vol.24
, pp. 2537-2538
-
-
Boyle, A.P.1
Guinney, J.2
Crawford, G.E.3
Furey, T.S.4
-
9
-
-
84891703149
-
Activator control of nucleosome occupancy in activation and repression of transcription
-
Bryant GO, Prabhu V, Floer M, Wang X, Spagna D, Schreiber D, Ptashne M. 2008. Activator control of nucleosome occupancy in activation and repression of transcription. PLoS Biol 6: 2928-2939.
-
(2008)
PLoS Biol
, vol.6
, pp. 2928-2939
-
-
Bryant, G.O.1
Prabhu, V.2
Floer, M.3
Wang, X.4
Spagna, D.5
Schreiber, D.6
Ptashne, M.7
-
11
-
-
77954659099
-
Relationship between nucleosome positioning and DNA methylation
-
Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, et al. 2010. Relationship between nucleosome positioning and DNA methylation. Nature 466: 388-392.
-
(2010)
Nature
, vol.466
, pp. 388-392
-
-
Chodavarapu, R.K.1
Feng, S.2
Bernatavichute, Y.V.3
Chen, P.Y.4
Stroud, H.5
Yu, Y.6
Hetzel, J.A.7
Kuo, F.8
Kim, J.9
Cokus, S.J.10
-
12
-
-
78650839429
-
The effect of micrococcal nuclease digestion on nucleosome positioning data
-
Chung HR, Dunkel I, Heise F, Linke C, Krobitsch S, Ehrenhofer-Murray AE, Sperling SR, Vingron M. 2010. The effect of micrococcal nuclease digestion on nucleosome positioning data. PLoS One 5: e15754.
-
(2010)
PLoS One
, vol.5
, pp. e15754
-
-
Chung, H.R.1
Dunkel, I.2
Heise, F.3
Linke, C.4
Krobitsch, S.5
Ehrenhofer-Murray, A.E.6
Sperling, S.R.7
Vingron, M.8
-
14
-
-
0028121490
-
Arabidopsis mutants selected for resistance to the phytotoxin coronatine are male sterile, insensitive to methyl jasmonate, and resistant to a bacterial pathogen
-
Feys B, Benedetti CE, Penfold CN, Turner JG. 1994. Arabidopsis mutants selected for resistance to the phytotoxin coronatine are male sterile, insensitive to methyl jasmonate, and resistant to a bacterial pathogen. Plant Cell 6: 751-759.
-
(1994)
Plant Cell
, vol.6
, pp. 751-759
-
-
Feys, B.1
Benedetti, C.E.2
Penfold, C.N.3
Turner, J.G.4
-
15
-
-
84878440106
-
Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales
-
Fincher JA, Vera DL, Hughes DD, McGinnis KM, Dennis JH, Bass HW. 2013. Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales. Plant Physiol 162: 1127-1141.
-
(2013)
Plant Physiol
, vol.162
, pp. 1127-1141
-
-
Fincher, J.A.1
Vera, D.L.2
Hughes, D.D.3
McGinnis, K.M.4
Dennis, J.H.5
Bass, H.W.6
-
16
-
-
77951915031
-
A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding
-
Floer M, Wang X, Prabhu V, Berrozpe G, Narayan S, Spagna D, Alvarez D, Kendall J, Krasnitz A, Stepansky A, et al. 2010. A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding. Cell 141: 407-418.
-
(2010)
Cell
, vol.141
, pp. 407-418
-
-
Floer, M.1
Wang, X.2
Prabhu, V.3
Berrozpe, G.4
Narayan, S.5
Spagna, D.6
Alvarez, D.7
Kendall, J.8
Krasnitz, A.9
Stepansky, A.10
-
17
-
-
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 111: 2367-2372.
-
(2014)
Proc Natl Acad Sci
, 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
-
18
-
-
79953126490
-
Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors
-
Godoy M, Franco-Zorrilla JM, Pérez-Pérez J, Oliveros JC, Lorenzo O, Solano R. 2011. Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors. Plant J 66: 700-711.
-
(2011)
Plant J
, vol.66
, pp. 700-711
-
-
Godoy, M.1
Franco-Zorrilla, J.M.2
Pérez-Pérez, J.3
Oliveros, J.C.4
Lorenzo, O.5
Solano, R.6
-
19
-
-
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
-
20
-
-
84864059329
-
In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae
-
Gossett AJ, Lieb JD. 2012. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 8: e1002771.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002771
-
-
Gossett, A.J.1
Lieb, J.D.2
-
21
-
-
0023899769
-
Nuclease hypersensitive sites in chromatin
-
Gross DS, Garrard WT. 1988. Nuclease hypersensitive sites in chromatin. Annu Rev Biochem 57: 159-197.
-
(1988)
Annu Rev Biochem
, vol.57
, pp. 159-197
-
-
Gross, D.S.1
Garrard, W.T.2
-
22
-
-
78049440475
-
Chromatin landscape dictates HSF binding to target DNA elements
-
Guertin MJ, Lis JT. 2010. Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet 6: e1001114.
-
(2010)
PLoS Genet
, vol.6
, pp. e1001114
-
-
Guertin, M.J.1
Lis, J.T.2
-
23
-
-
76749092270
-
The WEKA data mining software: An update
-
Hall M, Frank E, Holmes G, Pfahringer B, Reutemann P, Witten I. 2009. The WEKA data mining software: an update. SIGKDD Explor Newslett 11: 10-18.
-
(2009)
SIGKDD Explor Newslett
, vol.11
, pp. 10-18
-
-
Hall, M.1
Frank, E.2
Holmes, G.3
Pfahringer, B.4
Reutemann, P.5
Witten, I.6
-
24
-
-
81055141350
-
Epigenome characterization at single base-pair resolution
-
Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. 2011. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci 108: 18318-18323.
-
(2011)
Proc Natl Acad Sci
, vol.108
, pp. 18318-18323
-
-
Henikoff, J.G.1
Belsky, J.A.2
Krassovsky, K.3
MacAlpine, D.M.4
Henikoff, S.5
-
25
-
-
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
-
26
-
-
84879213336
-
A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves
-
Hickman R, Hill C, Penfold CA, Breeze E, Bowden L, Moore JD, Zhang P, Jackson A, Cooke E, Bewicke-Copley F, et al. 2013. A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. Plant J 75: 26-39.
-
(2013)
Plant J
, vol.75
, pp. 26-39
-
-
Hickman, R.1
Hill, C.2
Penfold, C.A.3
Breeze, E.4
Bowden, L.5
Moore, J.D.6
Zhang, P.7
Jackson, A.8
Cooke, E.9
Bewicke-Copley, F.10
-
27
-
-
77957725616
-
Ubiquitin ligase-coupled receptors extend their reach to jasmonate
-
Howe GA. 2010. Ubiquitin ligase-coupled receptors extend their reach to jasmonate. Plant Physiol 154: 471-474.
-
(2010)
Plant Physiol
, vol.154
, pp. 471-474
-
-
Howe, G.A.1
-
28
-
-
84901980324
-
Mechanisms underlying nucleosome positioning in vivo
-
Hughes AL, Rando OJ. 2014. Mechanisms underlying nucleosome positioning in vivo. Annu Rev Biophys 43: 41-63.
-
(2014)
Annu Rev Biophys
, vol.43
, pp. 41-63
-
-
Hughes, A.L.1
Rando, O.J.2
-
29
-
-
84867371116
-
A functional evolutionary approach to identify determinants of nucleosome positioning: A unifying model for establishing the genome-wide pattern
-
Hughes AL, Jin Y, Rando OJ, Struhl K. 2012. A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol Cell 48: 5-15.
-
(2012)
Mol Cell
, vol.48
, pp. 5-15
-
-
Hughes, A.L.1
Jin, Y.2
Rando, O.J.3
Struhl, K.4
-
30
-
-
34447092534
-
Expression of the ASYMMETRIC LEAVES2 gene in the adaxial domain of Arabidopsis leaves represses cell proliferation in this domain and is critical for the development of properly expanded leaves
-
Iwakawa H, Iwasaki M, Kojima S, Ueno Y, Soma T, Tanaka H, Semiarti E, Machida Y, Machida C. 2007. Expression of the ASYMMETRIC LEAVES2 gene in the adaxial domain of Arabidopsis leaves represses cell proliferation in this domain and is critical for the development of properly expanded leaves. Plant J 51: 173-184.
-
(2007)
Plant J
, vol.51
, pp. 173-184
-
-
Iwakawa, H.1
Iwasaki, M.2
Kojima, S.3
Ueno, Y.4
Soma, T.5
Tanaka, H.6
Semiarti, E.7
Machida, Y.8
Machida, C.9
-
31
-
-
0036516002
-
BZIP transcription factors in Arabidopsis
-
Jakoby M, Weisshaar B, Dröge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F, bZIPRG. 2002. bZIP transcription factors in Arabidopsis. Trends Plant Sci 7: 106-111.
-
(2002)
Trends Plant Sci
, vol.7
, pp. 106-111
-
-
Jakoby, M.1
Weisshaar, B.2
Dröge-Laser, W.3
Vicente-Carbajosa, J.4
Tiedemann, J.5
Kroj, T.6
Parcy, F.7
-
32
-
-
79952184341
-
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
-
John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, Johnson TA, Hager GL, Stamatoyannopoulos JA. 2011. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet 43: 264-268.
-
(2011)
Nat Genet
, vol.43
, pp. 264-268
-
-
John, S.1
Sabo, P.J.2
Thurman, R.E.3
Sung, M.H.4
Biddie, S.C.5
Johnson, T.A.6
Hager, G.L.7
Stamatoyannopoulos, J.A.8
-
33
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, et al. 2009. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
-
(2009)
Nature
, vol.458
, pp. 362-366
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
Field, Y.6
LeProust, E.M.7
Hughes, T.R.8
Lieb, J.D.9
Widom, J.10
-
35
-
-
65949090511
-
Target genes of the MADS transcription factor SEPALLATA3: Integration of developmental and hormonal pathways in the Arabidopsis flower
-
Kaufmann K, Muiño JM, Jauregui R, Airoldi CA, Smaczniak C, Krajewski P, Angenent GC. 2009. Target genes of the MADS transcription factor SEPALLATA3: integration of developmental and hormonal pathways in the Arabidopsis flower. PLoS Biol 7: e1000090.
-
(2009)
PLoS Biol
, vol.7
, pp. e1000090
-
-
Kaufmann, K.1
Muiño, J.M.2
Jauregui, R.3
Airoldi, C.A.4
Smaczniak, C.5
Krajewski, P.6
Angenent, G.C.7
-
36
-
-
70350516781
-
The wound hormone jasmonate
-
Koo AJ, Howe GA. 2009. The wound hormone jasmonate. Phytochemistry 70: 1571-1580.
-
(2009)
Phytochemistry
, vol.70
, pp. 1571-1580
-
-
Koo, A.J.1
Howe, G.A.2
-
37
-
-
62349130698
-
Ultrafast and memoryefficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.
-
(2009)
Genome Biol
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
38
-
-
34748826166
-
A high-resolution atlas of nucleosome occupancy in yeast
-
Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. 2007. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244.
-
(2007)
Nat Genet
, vol.39
, pp. 1235-1244
-
-
Lee, W.1
Tillo, D.2
Bray, N.3
Morse, R.H.4
Davis, R.W.5
Hughes, T.R.6
Nislow, C.7
-
39
-
-
84900474003
-
ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis
-
Li G, Liu S, Wang J, He J, Huang H, Zhang Y, Xu L. 2014. ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis. Plant J 78: 706-714.
-
(2014)
Plant J
, vol.78
, pp. 706-714
-
-
Li, G.1
Liu, S.2
Wang, J.3
He, J.4
Huang, H.5
Zhang, Y.6
Xu, L.7
-
40
-
-
77955944154
-
Overexpression of AHL20 negatively regulates defenses in Arabidopsis
-
Lu H, Zou Y, Feng N. 2010. Overexpression of AHL20 negatively regulates defenses in Arabidopsis. J Integr Plant Biol 52: 801-808.
-
(2010)
J Integr Plant Biol
, vol.52
, pp. 801-808
-
-
Lu, H.1
Zou, Y.2
Feng, N.3
-
41
-
-
79953044960
-
Genome-wide transcription factor binding: Beyond direct target regulation
-
MacQuarrie KL, Fong AP, Morse RH, Tapscott SJ. 2011. Genome-wide transcription factor binding: beyond direct target regulation. Trends Genet 27: 141-148.
-
(2011)
Trends Genet
, vol.27
, pp. 141-148
-
-
MacQuarrie, K.L.1
Fong, A.P.2
Morse, R.H.3
Tapscott, S.J.4
-
42
-
-
0024740034
-
Abscisic acid-responsive sequences from the em gene of wheat
-
Marcotte WR Jr, Russell SH, Quatrano RS. 1989. Abscisic acid-responsive sequences from the Em gene of wheat. Plant Cell 1: 969-976.
-
(1989)
Plant Cell
, vol.1
, pp. 969-976
-
-
Marcotte, W.R.1
Russell, S.H.2
Quatrano, R.S.3
-
43
-
-
73449098946
-
TCP genes: A family snapshot ten years later
-
Martín-Trillo M, Cubas P. 2010. TCP genes: a family snapshot ten years later. Trends Plant Sci 15: 31-39.
-
(2010)
Trends Plant Sci
, vol.15
, pp. 31-39
-
-
Martín-Trillo, M.1
Cubas, P.2
-
44
-
-
46449112319
-
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
-
Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. 2008. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18: 1073-1083.
-
(2008)
Genome Res
, vol.18
, pp. 1073-1083
-
-
Mavrich, T.N.1
Ioshikhes, I.P.2
Venters, B.J.3
Jiang, C.4
Tomsho, L.P.5
Qi, J.6
Schuster, S.C.7
Albert, I.8
Pugh, B.F.9
-
45
-
-
84908420287
-
Identification of target genes of the bZIP transcription factor OsTGAP1, whose overexpression causes elicitor-induced hyperaccumulation of diterpenoid phytoalexins in rice cells
-
Miyamoto K, Matsumoto T, Okada A, Komiyama K, Chujo T, Yoshikawa H, Nojiri H, Yamane H, Okada K. 2014. Identification of target genes of the bZIP transcription factor OsTGAP1, whose overexpression causes elicitor-induced hyperaccumulation of diterpenoid phytoalexins in rice cells. PLoS One 9: e105823.
-
(2014)
PLoS One
, vol.9
, pp. e105823
-
-
Miyamoto, K.1
Matsumoto, T.2
Okada, A.3
Komiyama, K.4
Chujo, T.5
Yoshikawa, H.6
Nojiri, H.7
Yamane, H.8
Okada, K.9
-
46
-
-
0025098288
-
Nuclear proteins bind conserved elements in the abscisic acid-responsive promoter of a rice rab gene
-
Mundy J, Yamaguchi-Shinozaki K, Chua NH. 1990. Nuclear proteins bind conserved elements in the abscisic acid-responsive promoter of a rice rab gene. Proc Natl Acad Sci 87: 1406-1410.
-
(1990)
Proc Natl Acad Sci
, vol.87
, pp. 1406-1410
-
-
Mundy, J.1
Yamaguchi-Shinozaki, K.2
Chua, N.H.3
-
47
-
-
84899047963
-
Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development
-
Pajoro A, Madrigal P, Muiño JM, Matus JT, Jin J, Mecchia MA, Debernardi JM, Palatnik JF, Balazadeh S, Arif M, et al. 2014. Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol 15: R41.
-
(2014)
Genome Biol
, vol.15
, pp. R41
-
-
Pajoro, A.1
Madrigal, P.2
Muiño, J.M.3
Matus, J.T.4
Jin, J.5
Mecchia, M.A.6
Debernardi, J.M.7
Palatnik, J.F.8
Balazadeh, S.9
Arif, M.10
-
48
-
-
84904303291
-
Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis
-
Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, et al. 2014. Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Proc Natl Acad Sci 111: 10371-10376.
-
(2014)
Proc Natl Acad Sci
, vol.111
, pp. 10371-10376
-
-
Para, A.1
Li, Y.2
Marshall-Colón, A.3
Varala, K.4
Francoeur, N.J.5
Moran, T.M.6
Edwards, M.B.7
Hackley, C.8
Bargmann, B.O.9
Birnbaum, K.D.10
-
49
-
-
84863304598
-
-
R Foundation for Statistical Computing, Vienna, Austria
-
R Core Team. 2014. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.Rproject.org/.
-
(2014)
R: A Language and Environment for Statistical Computing
-
-
-
50
-
-
84862984796
-
Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast
-
Raveh-Sadka T, Levo M, Shabi U, Shany B, Keren L, Lotan-Pompan M, Zeevi D, Sharon E, Weinberger A, Segal E. 2012. Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet 44: 743-750.
-
(2012)
Nat Genet
, vol.44
, pp. 743-750
-
-
Raveh-Sadka, T.1
Levo, M.2
Shabi, U.3
Shany, B.4
Keren, L.5
Lotan-Pompan, M.6
Zeevi, D.7
Sharon, E.8
Weinberger, A.9
Segal, E.10
-
51
-
-
0037992395
-
The structure of DNA in the nucleosome core
-
Richmond TJ, Davey CA. 2003. The structure of DNA in the nucleosome core. Nature 423: 145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
52
-
-
77956858986
-
The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from della proteins and phytochrome-interacting factors
-
Richter R, Behringer C, Müller IK, Schwechheimer C. 2010. The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS. Genes Dev 24: 2093-2104.
-
(2010)
Genes Dev
, vol.24
, pp. 2093-2104
-
-
Richter, R.1
Behringer, C.2
Müller, I.K.3
Schwechheimer, C.4
-
53
-
-
75249087100
-
EdgeR: A bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
54
-
-
84884679689
-
Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior
-
Schweizer F, Fernández-Calvo P, Zander M, Diez-Diaz M, Fonseca S, Glauser G, Lewsey MG, Ecker JR, Solano R, Reymond P. 2013. Arabidopsis basic helix-loop-helix transcription factors MYC2, MYC3, and MYC4 regulate glucosinolate biosynthesis, insect performance, and feeding behavior. Plant Cell 25: 3117-3132.
-
(2013)
Plant Cell
, vol.25
, pp. 3117-3132
-
-
Schweizer, F.1
Fernández-Calvo, P.2
Zander, M.3
Diez-Diaz, M.4
Fonseca, S.5
Glauser, G.6
Lewsey, M.G.7
Ecker, J.R.8
Solano, R.9
Reymond, P.10
-
55
-
-
84880126285
-
Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNASeq
-
Shamimuzzaman M, Vodkin L. 2013. Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNASeq. BMC Genomics 14: 477.
-
(2013)
BMC Genomics
, vol.14
, pp. 477
-
-
Shamimuzzaman, M.1
Vodkin, L.2
-
57
-
-
84890072854
-
Exonic transcription factor binding directs codon choice and affects protein evolution
-
Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, et al. 2013. Exonic transcription factor binding directs codon choice and affects protein evolution. Science 342: 1367-1372.
-
(2013)
Science
, vol.342
, pp. 1367-1372
-
-
Stergachis, A.B.1
Haugen, E.2
Shafer, A.3
Fu, W.4
Vernot, B.5
Reynolds, A.6
Raubitschek, A.7
Ziegler, S.8
LeProust, E.M.9
Akey, J.M.10
-
58
-
-
84875196326
-
Determinants of nucleosome positioning
-
Struhl K, Segal E. 2013. Determinants of nucleosome positioning. Nat Struct Mol Biol 20: 267-273.
-
(2013)
Nat Struct Mol Biol
, vol.20
, pp. 267-273
-
-
Struhl, K.1
Segal, E.2
-
59
-
-
84907381991
-
Mapping and dynamics of regulatory DNA and transcription factor networks in A. Thaliana
-
Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, et al. 2014. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Rep 8: 2015-2030.
-
(2014)
Cell Rep
, 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
-
60
-
-
84922589001
-
DNase footprint signatures are dictated by factor dynamics and DNA sequence
-
Sung MH, Guertin MJ, Baek S, Hager GL. 2014. DNase footprint signatures are dictated by factor dynamics and DNA sequence. Mol Cell 56: 275-285.
-
(2014)
Mol Cell
, vol.56
, pp. 275-285
-
-
Sung, M.H.1
Guertin, M.J.2
Baek, S.3
Hager, G.L.4
-
61
-
-
84869089058
-
Genome-wide nucleosome positioning during embryonic stem cell development
-
Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Höfer T, Rippe K. 2012. Genome-wide nucleosome positioning during embryonic stem cell development. Nat Struct Mol Biol 19: 1185-1192.
-
(2012)
Nat Struct Mol Biol
, vol.19
, pp. 1185-1192
-
-
Teif, V.B.1
Vainshtein, Y.2
Caudron-Herger, M.3
Mallm, J.P.4
Marth, C.5
Höfer, T.6
Rippe, K.7
-
62
-
-
0042421751
-
The Arabidopsis basic/helix-loop-helix transcription factor family
-
Toledo-Ortiz G, Huq E, Quail PH. 2003. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15: 1749-1770.
-
(2003)
Plant Cell
, vol.15
, pp. 1749-1770
-
-
Toledo-Ortiz, G.1
Huq, E.2
Quail, P.H.3
-
63
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
64
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
65
-
-
17844378494
-
The phytotoxin coronatine and methyl jasmonate impact multiple phytohormone pathways in tomato
-
Uppalapati SR, Ayoubi P, Weng H, Palmer DA, Mitchell RE, Jones W, Bender CL. 2005. The phytotoxin coronatine and methyl jasmonate impact multiple phytohormone pathways in tomato. Plant J 42: 201-217.
-
(2005)
Plant J
, vol.42
, pp. 201-217
-
-
Uppalapati, S.R.1
Ayoubi, P.2
Weng, H.3
Palmer, D.A.4
Mitchell, R.E.5
Jones, W.6
Bender, C.L.7
-
66
-
-
79959557189
-
Determinants of nucleosome organization in primary human cells
-
Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. 2011. Determinants of nucleosome organization in primary human cells. Nature 474: 516-520.
-
(2011)
Nature
, vol.474
, pp. 516-520
-
-
Valouev, A.1
Johnson, S.M.2
Boyd, S.D.3
Smith, C.L.4
Fire, A.Z.5
Sidow, A.6
-
67
-
-
84912133362
-
Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize
-
Vera DL, Madzima TF, Labonne JD, Alam MP, Hoffman GG, Girimurugan SB, Zhang J, McGinnis KM, Dennis JH, Bass HW. 2014. Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. Plant Cell 26: 3883-3893.
-
(2014)
Plant Cell
, vol.26
, pp. 3883-3893
-
-
Vera, D.L.1
Madzima, T.F.2
Labonne, J.D.3
Alam, M.P.4
Hoffman, G.G.5
Girimurugan, S.B.6
Zhang, J.7
McGinnis, K.M.8
Dennis, J.H.9
Bass, H.W.10
-
68
-
-
84894651254
-
Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH
-
Vierstra J, Wang H, John S, Sandstrom R, Stamatoyannopoulos JA. 2014. Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH. Nat Methods 11: 66-72.
-
(2014)
Nat Methods
, vol.11
, pp. 66-72
-
-
Vierstra, J.1
Wang, H.2
John, S.3
Sandstrom, R.4
Stamatoyannopoulos, J.A.5
-
69
-
-
34447129612
-
Identification of a bipartite jasmonate-responsive promoter element in the Catharanthus roseus ORCA3 transcription factor gene that interacts specifically with AT-Hook DNA-binding proteins
-
Vom Endt D, Soares e Silva M, Kijne JW, Pasquali G, Memelink J. 2007. Identification of a bipartite jasmonate-responsive promoter element in the Catharanthus roseus ORCA3 transcription factor gene that interacts specifically with AT-Hook DNA-binding proteins. Plant Physiol 144: 1680-1689.
-
(2007)
Plant Physiol
, vol.144
, pp. 1680-1689
-
-
Vom Endt, D.1
Soares-E-Silva, M.2
Kijne, J.W.3
Pasquali, G.4
Memelink, J.5
-
70
-
-
84865852567
-
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
-
Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, et al. 2012. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 22: 1798-1812.
-
(2012)
Genome Res
, vol.22
, pp. 1798-1812
-
-
Wang, J.1
Zhuang, J.2
Iyer, S.3
Lin, X.4
Whitfield, T.W.5
Greven, M.C.6
Pierce, B.G.7
Dong, X.8
Kundaje, A.9
Cheng, Y.10
-
71
-
-
84907413210
-
Determination and inference of eukaryotic transcription factor sequence specificity
-
Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, et al. 2014. Determination and inference of eukaryotic transcription factor sequence specificity. Cell 158: 1431-1443.
-
(2014)
Cell
, vol.158
, pp. 1431-1443
-
-
Weirauch, M.T.1
Yang, A.2
Albu, M.3
Cote, A.G.4
Montenegro-Montero, A.5
Drewe, P.6
Najafabadi, H.S.7
Lambert, S.A.8
Mann, I.9
Cook, K.10
-
72
-
-
0024712231
-
Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data
-
Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH. 1989. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci 86: 6201-6205.
-
(1989)
Proc Natl Acad Sci
, vol.86
, pp. 6201-6205
-
-
Wolfe, K.H.1
Gouy, M.2
Yang, Y.W.3
Sharp, P.M.4
Li, W.H.5
-
73
-
-
84901611019
-
Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice
-
Wu Y, Zhang W, Jiang J. 2014. Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. PLoS Genet 10: e1004378.
-
(2014)
PLoS Genet
, vol.10
, pp. e1004378
-
-
Wu, Y.1
Zhang, W.2
Jiang, J.3
-
74
-
-
22744432660
-
Genome-scale identification of nucleosome positions in S. Cerevisiae
-
Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630.
-
(2005)
Science
, vol.309
, pp. 626-630
-
-
Yuan, G.C.1
Liu, Y.J.2
Dion, M.F.3
Slack, M.D.4
Wu, L.F.5
Altschuler, S.J.6
Rando, O.J.7
-
75
-
-
79956316470
-
A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome
-
Zhang Z, Wippo CJ, Wal M, Ward E, Korber P, Pugh BF. 2011. A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome. Science 332: 977-980.
-
(2011)
Science
, vol.332
, pp. 977-980
-
-
Zhang, Z.1
Wippo, C.J.2
Wal, M.3
Ward, E.4
Korber, P.5
Pugh, B.F.6
-
76
-
-
84865331447
-
Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis
-
Zhang W, Zhang T, Wu Y, Jiang J. 2012. Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 24: 2719-2731.
-
(2012)
Plant Cell
, vol.24
, pp. 2719-2731
-
-
Zhang, W.1
Zhang, T.2
Wu, Y.3
Jiang, J.4
-
77
-
-
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 108: 14992-14997.
-
(2011)
Proc Natl Acad Sci
, 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
|