-
1
-
-
54249124501
-
Learning biological networks: from modules to dynamics
-
Bonneau R: Learning biological networks: from modules to dynamics. Nat Chem Biol. 2008, 4: 658-664.
-
(2008)
Nat Chem Biol
, vol.4
, pp. 658-664
-
-
Bonneau, R.1
-
2
-
-
37349099750
-
A predictive model for transcriptional control of physiology in a free living cell
-
Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson V, Shannon P, Johnson MH, Bare JC, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, Diruggiero J, Johnson CH, Hood L, Baliga NS: A predictive model for transcriptional control of physiology in a free living cell. Cell. 2007, 131: 1354-1365.
-
(2007)
Cell
, vol.131
, pp. 1354-1365
-
-
Bonneau, R.1
Facciotti, M.T.2
Reiss, D.J.3
Schmid, A.K.4
Pan, M.5
Kaur, A.6
Thorsson, V.7
Shannon, P.8
Johnson, M.H.9
Bare, J.C.10
Longabaugh, W.11
Vuthoori, M.12
Whitehead, K.13
Madar, A.14
Suzuki, L.15
Mori, T.16
Chang, D.E.17
Diruggiero, J.18
Johnson, C.H.19
Hood, L.20
Baliga, N.S.21
more..
-
3
-
-
0032573426
-
A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome
-
Robison K, McGuire AM, Church GM: A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol. 1998, 284: 241-254.
-
(1998)
J Mol Biol
, vol.284
, pp. 241-254
-
-
Robison, K.1
McGuire, A.M.2
Church, G.M.3
-
4
-
-
9144270496
-
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
-
Salgado H, Gama-Castro S, Martinez-Antonio A, Diaz-Peredo E, Sanchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jimenez-Jacinto V, Santos-Zavaleta A, Bonavides-Martinez C, Collado-Vides J: RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res. 2004, 32: D303-306.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. D303-306
-
-
Salgado, H.1
Gama-Castro, S.2
Martinez-Antonio, A.3
Diaz-Peredo, E.4
Sanchez-Solano, F.5
Peralta-Gil, M.6
Garcia-Alonso, D.7
Jimenez-Jacinto, V.8
Santos-Zavaleta, A.9
Bonavides-Martinez, C.10
Collado-Vides, J.11
-
5
-
-
84870705693
-
Modeling regulatory networks to understand plant development: small is beautiful
-
Middleton AM, Farcot E, Owen MR, Vernoux T: Modeling regulatory networks to understand plant development: small is beautiful. Plant Cell. 2012, 24: 3876-3891.
-
(2012)
Plant Cell
, vol.24
, pp. 3876-3891
-
-
Middleton, A.M.1
Farcot, E.2
Owen, M.R.3
Vernoux, T.4
-
6
-
-
79960090553
-
The auxin signalling network translates dynamic input into robust patterning at the shoot apex
-
Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J: The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol Syst Biol. 2011, 7: 508-
-
(2011)
Mol Syst Biol
, vol.7
, pp. 508
-
-
Vernoux, T.1
Brunoud, G.2
Farcot, E.3
Morin, V.4
Van den Daele, H.5
Legrand, J.6
Oliva, M.7
Das, P.8
Larrieu, A.9
Wells, D.10
Guédon, Y.11
Armitage, L.12
Picard, F.13
Guyomarc'h, S.14
Cellier, C.15
Parry, G.16
Koumproglou, R.17
Doonan, J.H.18
Estelle, M.19
Godin, C.20
Kepinski, S.21
Bennett, M.22
De Veylder, L.23
Traas, J.24
more..
-
7
-
-
79955781219
-
A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk
-
Sankar M, Osmont KS, Rolcik J, Gujas B, Tarkowska D, Strnad M, Xenarios I, Hardtke CS: A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk. Bioinformatics. 2011, 27: 1404-1412.
-
(2011)
Bioinformatics
, vol.27
, pp. 1404-1412
-
-
Sankar, M.1
Osmont, K.S.2
Rolcik, J.3
Gujas, B.4
Tarkowska, D.5
Strnad, M.6
Xenarios, I.7
Hardtke, C.S.8
-
8
-
-
84865848723
-
A synthetic approach reveals extensive tunability of auxin signaling
-
Havens KA, Guseman JM, Jang SS, Pierre-Jerome E, Bolten N, Klavins E, Nemhauser JL: A synthetic approach reveals extensive tunability of auxin signaling. Plant Physiol. 2012, 160: 135-142.
-
(2012)
Plant Physiol
, vol.160
, pp. 135-142
-
-
Havens, K.A.1
Guseman, J.M.2
Jang, S.S.3
Pierre-Jerome, E.4
Bolten, N.5
Klavins, E.6
Nemhauser, J.L.7
-
9
-
-
84857952188
-
The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops
-
Pokhilko A, Fernandez AP, Edwards KD, Southern MM, Halliday KJ, Millar AJ: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol. 2012, 8: 574-
-
(2012)
Mol Syst Biol
, vol.8
, pp. 574
-
-
Pokhilko, A.1
Fernandez, A.P.2
Edwards, K.D.3
Southern, M.M.4
Halliday, K.J.5
Millar, A.J.6
-
10
-
-
84866181814
-
Digital clocks: simple Boolean models can quantitatively describe circadian systems
-
Akman OE, Watterson S, Parton A, Binns N, Millar AJ, Ghazal P: Digital clocks: simple Boolean models can quantitatively describe circadian systems. J R Soc Interface. 2012, 9: 2365-2382.
-
(2012)
J R Soc Interface
, vol.9
, pp. 2365-2382
-
-
Akman, O.E.1
Watterson, S.2
Parton, A.3
Binns, N.4
Millar, A.J.5
Ghazal, P.6
-
11
-
-
71449120958
-
Prediction of photoperiodic regulators from quantitative gene circuit models
-
Salazar JD, Saithong T, Brown PE, Foreman J, Locke JC, Halliday KJ, Carre IA, Rand DA, Millar AJ: Prediction of photoperiodic regulators from quantitative gene circuit models. Cell. 2009, 139: 1170-1179.
-
(2009)
Cell
, vol.139
, pp. 1170-1179
-
-
Salazar, J.D.1
Saithong, T.2
Brown, P.E.3
Foreman, J.4
Locke, J.C.5
Halliday, K.J.6
Carre, I.A.7
Rand, D.A.8
Millar, A.J.9
-
12
-
-
16644389406
-
A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles
-
Espinosa-Soto C, Padilla-Longoria P, Alvarez-Buylla ER: A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles. Plant Cell. 2004, 16: 2923-2939.
-
(2004)
Plant Cell
, vol.16
, pp. 2923-2939
-
-
Espinosa-Soto, C.1
Padilla-Longoria, P.2
Alvarez-Buylla, E.R.3
-
13
-
-
84856552374
-
A data-driven integrative model of sepal primordium polarity in Arabidopsis
-
La Rota C, Chopard J, Das P, Paindavoine S, Rozier F, Farcot E, Godin C, Traas J, Moneger F: A data-driven integrative model of sepal primordium polarity in Arabidopsis. Plant Cell. 2011, 23: 4318-4333.
-
(2011)
Plant Cell
, vol.23
, pp. 4318-4333
-
-
La Rota, C.1
Chopard, J.2
Das, P.3
Paindavoine, S.4
Rozier, F.5
Farcot, E.6
Godin, C.7
Traas, J.8
Moneger, F.9
-
14
-
-
84876746933
-
Interlocking feedback loops govern the dynamic behavior of the floral transition in Arabidopsis
-
Jaeger KE, Pullen N, Lamzin S, Morris RJ, Wigge PA: Interlocking feedback loops govern the dynamic behavior of the floral transition in Arabidopsis. Plant Cell. 2013, 25: 820-833.
-
(2013)
Plant Cell
, vol.25
, pp. 820-833
-
-
Jaeger, K.E.1
Pullen, N.2
Lamzin, S.3
Morris, R.J.4
Wigge, P.A.5
-
15
-
-
84878336478
-
Mathematical modeling of an oscillating gene circuit to unravel the circadian clock network of Arabidopsis thaliana
-
Bujdoso N, Davis SJ: Mathematical modeling of an oscillating gene circuit to unravel the circadian clock network of Arabidopsis thaliana. Front Plant Sci. 2013, 4: 3-
-
(2013)
Front Plant Sci
, vol.4
, pp. 3
-
-
Bujdoso, N.1
Davis, S.J.2
-
16
-
-
15244359622
-
Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana
-
Locke JC, Millar AJ, Turner MS: Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana. J Theor Biol. 2005, 234: 383-393.
-
(2005)
J Theor Biol
, vol.234
, pp. 383-393
-
-
Locke, J.C.1
Millar, A.J.2
Turner, M.S.3
-
17
-
-
77957260103
-
Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model
-
Pokhilko A, Hodge SK, Stratford K, Knox K, Edwards KD, Thomson AW, Mizuno T, Millar AJ: Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model. Mol Syst Biol. 2010, 6: 416-
-
(2010)
Mol Syst Biol
, vol.6
, pp. 416
-
-
Pokhilko, A.1
Hodge, S.K.2
Stratford, K.3
Knox, K.4
Edwards, K.D.5
Thomson, A.W.6
Mizuno, T.7
Millar, A.J.8
-
18
-
-
77953293491
-
An expanding universe of circadian networks in higher plants
-
Pruneda-Paz JL, Kay SA: An expanding universe of circadian networks in higher plants. Trends Plant Sci. 2010, 15: 259-265.
-
(2010)
Trends Plant Sci
, vol.15
, pp. 259-265
-
-
Pruneda-Paz, J.L.1
Kay, S.A.2
-
19
-
-
0026417225
-
The war of the whorls: genetic interactions controlling flower development
-
Coen ES, Meyerowitz EM: The war of the whorls: genetic interactions controlling flower development. Nature. 1991, 353: 31-37.
-
(1991)
Nature
, vol.353
, pp. 31-37
-
-
Coen, E.S.1
Meyerowitz, E.M.2
-
20
-
-
84870305264
-
Wisdom of crowds for robust gene network inference
-
Marbach D, Costello JC, Kuffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Consortium D, Kellis M, Collins JJ, Stolovitzky G: Wisdom of crowds for robust gene network inference. Nat Methods. 2012, 9: 796-804.
-
(2012)
Nat Methods
, vol.9
, pp. 796-804
-
-
Marbach, D.1
Costello, J.C.2
Kuffner, R.3
Vega, N.M.4
Prill, R.J.5
Camacho, D.M.6
Allison, K.R.7
Consortium, D.8
Kellis, M.9
Collins, J.J.10
Stolovitzky, G.11
-
21
-
-
37849020261
-
Network inference, analysis, and modeling in systems biology
-
Albert R: Network inference, analysis, and modeling in systems biology. Plant Cell. 2007, 19: 3327-3338.
-
(2007)
Plant Cell
, vol.19
, pp. 3327-3338
-
-
Albert, R.1
-
22
-
-
75949101552
-
A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling
-
Ruffel S, Krouk G, Coruzzi GM: A systems view of responses to nutritional cues in Arabidopsis: toward a paradigm shift for predictive network modeling. Plant Physiol. 2010, 152: 445-452.
-
(2010)
Plant Physiol
, vol.152
, pp. 445-452
-
-
Ruffel, S.1
Krouk, G.2
Coruzzi, G.M.3
-
23
-
-
71749094192
-
Arabidopsis gene co-expression network and its functional modules
-
Mao L, Van Hemert JL, Dash S, Dickerson JA: Arabidopsis gene co-expression network and its functional modules. BMC Bioinformatics. 2009, 10: 346-
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 346
-
-
Mao, L.1
Van Hemert, J.L.2
Dash, S.3
Dickerson, J.A.4
-
24
-
-
34147133691
-
Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis
-
Gutierrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM: Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol. 2007, 8: R7-
-
(2007)
Genome Biol
, vol.8
, pp. R7
-
-
Gutierrez, R.A.1
Lejay, L.V.2
Dean, A.3
Chiaromonte, F.4
Shasha, D.E.5
Coruzzi, G.M.6
-
25
-
-
75949087420
-
VirtualPlant: a software platform to support systems biology research
-
Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutiérrez RA: VirtualPlant: a software platform to support systems biology research. Plant Physiol. 2010, 152: 500-515.
-
(2010)
Plant Physiol
, vol.152
, pp. 500-515
-
-
Katari, M.S.1
Nowicki, S.D.2
Aceituno, F.F.3
Nero, D.4
Kelfer, J.5
Thompson, L.P.6
Cabello, J.M.7
Davidson, R.S.8
Goldberg, A.P.9
Shasha, D.E.10
Coruzzi, G.M.11
Gutiérrez, R.A.12
-
26
-
-
42449106989
-
Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1
-
Gutierrez RA, Stokes TL, Thum K, Xu X, Obertello M, Katari MS, Tanurdzic M, Dean A, Nero DC, McClung CR, Coruzzi GM: Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proc Natl Acad Sci USA. 2008, 105: 4939-4944.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 4939-4944
-
-
Gutierrez, R.A.1
Stokes, T.L.2
Thum, K.3
Xu, X.4
Obertello, M.5
Katari, M.S.6
Tanurdzic, M.7
Dean, A.8
Nero, D.C.9
McClung, C.R.10
Coruzzi, G.M.11
-
27
-
-
67649872569
-
Starch as a major integrator in the regulation of plant growth
-
Sulpice R, Pyl E-T, Ishihara H, Trenkamp S, Steinfath M, Witucka-Wall H, Gibon Y, Usadel B, Poree F, Piques MC, Von Korff M, Steinhauser MC, Keurentjes JJ, Guenther M, Hoehne M, Selbig J, Fernie AR, Altmann T, Stitt M: Starch as a major integrator in the regulation of plant growth. Proc Natl Acad Sci USA. 2009, 106: 10348-10353.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 10348-10353
-
-
Sulpice, R.1
Pyl, E.-T.2
Ishihara, H.3
Trenkamp, S.4
Steinfath, M.5
Witucka-Wall, H.6
Gibon, Y.7
Usadel, B.8
Poree, F.9
Piques, M.C.10
Von Korff, M.11
Steinhauser, M.C.12
Keurentjes, J.J.13
Guenther, M.14
Hoehne, M.15
Selbig, J.16
Fernie, A.R.17
Altmann, T.18
Stitt, M.19
-
29
-
-
84864931487
-
Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model
-
Ingkasuwan P, Netrphan S, Prasitwattanaseree S, Tanticharoen M, Bhumiratana S, Meechai A, Chaijaruwanich J, Takahashi H, Cheevadhanarak S: Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model. BMC Syst Biol. 2012, 6: 100-
-
(2012)
BMC Syst Biol
, vol.6
, pp. 100
-
-
Ingkasuwan, P.1
Netrphan, S.2
Prasitwattanaseree, S.3
Tanticharoen, M.4
Bhumiratana, S.5
Meechai, A.6
Chaijaruwanich, J.7
Takahashi, H.8
Cheevadhanarak, S.9
-
30
-
-
35948931439
-
An Arabidopsis gene network based on the graphical Gaussian model
-
Ma S, Gong Q, Bohnert HJ: An Arabidopsis gene network based on the graphical Gaussian model. Genome Res. 2007, 17: 1614-1625.
-
(2007)
Genome Res
, vol.17
, pp. 1614-1625
-
-
Ma, S.1
Gong, Q.2
Bohnert, H.J.3
-
31
-
-
79955626693
-
High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation
-
Breeze E, Harrison E, McHattie S, Hughes L, Hickman R, Hill C, Kiddle S, Kim YS, Penfold CA, Jenkins D, Zhang C, Morris K, Jenner C, Jackson S, Thomas B, Tabrett A, Legaie R, Moore JD, Wild DL, Ott S, Rand D, Beynon J, Denby K, Mead A, Buchanan-Wollaston V: High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. Plant Cell. 2011, 23: 873-894.
-
(2011)
Plant Cell
, vol.23
, pp. 873-894
-
-
Breeze, E.1
Harrison, E.2
McHattie, S.3
Hughes, L.4
Hickman, R.5
Hill, C.6
Kiddle, S.7
Kim, Y.S.8
Penfold, C.A.9
Jenkins, D.10
Zhang, C.11
Morris, K.12
Jenner, C.13
Jackson, S.14
Thomas, B.15
Tabrett, A.16
Legaie, R.17
Moore, J.D.18
Wild, D.L.19
Ott, S.20
Rand, D.21
Beynon, J.22
Denby, K.23
Mead, A.24
Buchanan-Wollaston, V.25
more..
-
32
-
-
78650335757
-
Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate
-
Krouk G, Mirowski P, LeCun Y, Shasha DE, Coruzzi GM: Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate. Genome Biol. 2010, 11: R123-
-
(2010)
Genome Biol
, vol.11
, pp. R123
-
-
Krouk, G.1
Mirowski, P.2
LeCun, Y.3
Shasha, D.E.4
Coruzzi, G.M.5
-
33
-
-
15944364151
-
An empirical Bayes approach to inferring large-scale gene association networks
-
Schäfer J, Strimmer K: An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics. 2005, 21: 754-764.
-
(2005)
Bioinformatics
, vol.21
, pp. 754-764
-
-
Schäfer, J.1
Strimmer, K.2
-
34
-
-
69249150110
-
Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli
-
Yuan J, Doucette CD, Fowler WU, Feng XJ, Piazza M, Rabitz HA, Wingreen NS, Rabinowitz JD: Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol Syst Biol. 2009, 5: 302-
-
(2009)
Mol Syst Biol
, vol.5
, pp. 302
-
-
Yuan, J.1
Doucette, C.D.2
Fowler, W.U.3
Feng, X.J.4
Piazza, M.5
Rabitz, H.A.6
Wingreen, N.S.7
Rabinowitz, J.D.8
-
35
-
-
77958570788
-
Inferring regulatory networks from expression data using tree-based methods
-
Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P: Inferring regulatory networks from expression data using tree-based methods. PLoS One. 2010, 5: e12776-
-
(2010)
PLoS One
, vol.5
-
-
Huynh-Thu, V.A.1
Irrthum, A.2
Wehenkel, L.3
Geurts, P.4
-
36
-
-
77949644952
-
Towards a rigorous assessment of systems biology models: the DREAM3 challenges
-
Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G: Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One. 2010, 5: e9202-
-
(2010)
PLoS One
, vol.5
-
-
Prill, R.J.1
Marbach, D.2
Saez-Rodriguez, J.3
Sorger, P.K.4
Alexopoulos, L.G.5
Xue, X.6
Clarke, N.D.7
Altan-Bonnet, G.8
Stolovitzky, G.9
-
37
-
-
80054088836
-
Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics
-
Mendoza-Parra MA, Walia M, Sankar M, Gronemeyer H: Dissecting the retinoid-induced differentiation of F9 embryonal stem cells by integrative genomics. Mol Syst Biol. 2011, 7: 538-
-
(2011)
Mol Syst Biol
, vol.7
, pp. 538
-
-
Mendoza-Parra, M.A.1
Walia, M.2
Sankar, M.3
Gronemeyer, H.4
-
38
-
-
84876207916
-
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks
-
Greenfield A, Hafemeister C, Bonneau R: Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks. Bioinformatics. 2013, 29: 1060-1067.
-
(2013)
Bioinformatics
, vol.29
, pp. 1060-1067
-
-
Greenfield, A.1
Hafemeister, C.2
Bonneau, R.3
-
39
-
-
84924906267
-
Network Inference in Molecular Biology: A Hands-on Framework
-
New York: Springer
-
Lingeman JM, Shasha D: Network Inference in Molecular Biology: A Hands-on Framework. 2012, New York: Springer
-
(2012)
-
-
Lingeman, J.M.1
Shasha, D.2
-
40
-
-
78751513159
-
A stele-enriched gene regulatory network in the Arabidopsis root
-
Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJ, Benfey PN: A stele-enriched gene regulatory network in the Arabidopsis root. Mol Syst Biol. 2011, 7: 459-
-
(2011)
Mol Syst Biol
, vol.7
, pp. 459
-
-
Brady, S.M.1
Zhang, L.2
Megraw, M.3
Martinez, N.J.4
Jiang, E.5
Yi, C.S.6
Liu, W.7
Zeng, A.8
Taylor-Teeples, M.9
Kim, D.10
Ahnert, S.11
Ohler, U.12
Ware, D.13
Walhout, A.J.14
Benfey, P.N.15
-
41
-
-
79954414840
-
A stress-free walk from Arabidopsis to crops
-
Chew YH, Halliday KJ: A stress-free walk from Arabidopsis to crops. Curr Opin Biotechnol. 2011, 22: 281-286.
-
(2011)
Curr Opin Biotechnol
, vol.22
, pp. 281-286
-
-
Chew, Y.H.1
Halliday, K.J.2
-
42
-
-
79954572897
-
Quantitative analysis and application of tip position modulation-scanning electrochemical microscopy
-
Edwards MA, Whitworth AL, Unwin PR: Quantitative analysis and application of tip position modulation-scanning electrochemical microscopy. Anal Chem. 2011, 83: 1977-1984.
-
(2011)
Anal Chem
, vol.83
, pp. 1977-1984
-
-
Edwards, M.A.1
Whitworth, A.L.2
Unwin, P.R.3
-
43
-
-
79960901603
-
Reconstructing regulatory network transitions
-
Petricka JJ, Benfey PN: Reconstructing regulatory network transitions. Trends Cell Biol. 2011, 21: 442-451.
-
(2011)
Trends Cell Biol
, vol.21
, pp. 442-451
-
-
Petricka, J.J.1
Benfey, P.N.2
-
44
-
-
0038376557
-
Viviparous1 alters global gene expression patterns through regulation of abscisic acid signaling
-
Suzuki M, Ketterling MG, Li QB, McCarty DR: Viviparous1 alters global gene expression patterns through regulation of abscisic acid signaling. Plant Physiol. 2003, 132: 1664-1677.
-
(2003)
Plant Physiol
, vol.132
, pp. 1664-1677
-
-
Suzuki, M.1
Ketterling, M.G.2
Li, Q.B.3
McCarty, D.R.4
-
45
-
-
14844337487
-
Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed
-
Nakabayashi K, Okamoto M, Koshiba T, Kamiya Y, Nambara E: Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J. 2005, 41: 697-709.
-
(2005)
Plant J
, vol.41
, pp. 697-709
-
-
Nakabayashi, K.1
Okamoto, M.2
Koshiba, T.3
Kamiya, Y.4
Nambara, E.5
-
46
-
-
32044464356
-
Transcriptional regulation of ABI3- and ABA-responsive genes including RD29B and RD29A in seeds, germinating embryos, and seedlings of Arabidopsis
-
Nakashima K, Fujita Y, Katsura K, Maruyama K, Narusaka Y, Seki M, Shinozaki K, Yamaguchi-Shinozaki K: Transcriptional regulation of ABI3- and ABA-responsive genes including RD29B and RD29A in seeds, germinating embryos, and seedlings of Arabidopsis. Plant Mol Biol. 2006, 60: 51-68.
-
(2006)
Plant Mol Biol
, vol.60
, pp. 51-68
-
-
Nakashima, K.1
Fujita, Y.2
Katsura, K.3
Maruyama, K.4
Narusaka, Y.5
Seki, M.6
Shinozaki, K.7
Yamaguchi-Shinozaki, K.8
-
47
-
-
37749012692
-
Seed after-ripening is a discrete developmental pathway associated with specific gene networks in Arabidopsis
-
Carrera E, Holman T, Medhurst A, Dietrich D, Footitt S, Theodoulou FL, Holdsworth MJ: Seed after-ripening is a discrete developmental pathway associated with specific gene networks in Arabidopsis. Plant J. 2008, 53: 214-224.
-
(2008)
Plant J
, vol.53
, pp. 214-224
-
-
Carrera, E.1
Holman, T.2
Medhurst, A.3
Dietrich, D.4
Footitt, S.5
Theodoulou, F.L.6
Holdsworth, M.J.7
-
48
-
-
28044460802
-
The WEREWOLF MYB protein directly regulates CAPRICE transcription during cell fate specification in the Arabidopsis root epidermis
-
Ryu KH: The WEREWOLF MYB protein directly regulates CAPRICE transcription during cell fate specification in the Arabidopsis root epidermis. Development. 2005, 132: 4765-4775.
-
(2005)
Development
, vol.132
, pp. 4765-4775
-
-
Ryu, K.H.1
-
49
-
-
79952043059
-
Direct targets of the transcription factors ABA-Insensitive(ABI)4 and ABI5 reveal synergistic action by ABI4 and several bZIP ABA response factors
-
Reeves WM, Lynch TJ, Mobin R, Finkelstein RR: Direct targets of the transcription factors ABA-Insensitive(ABI)4 and ABI5 reveal synergistic action by ABI4 and several bZIP ABA response factors. Plant Mol Biol. 2011, 75: 347-363.
-
(2011)
Plant Mol Biol
, vol.75
, pp. 347-363
-
-
Reeves, W.M.1
Lynch, T.J.2
Mobin, R.3
Finkelstein, R.R.4
-
50
-
-
78049446272
-
A central regulatory system largely controls transcriptional activation and repression responses to phosphate starvation in Arabidopsis
-
Bustos R, Castrillo G, Linhares F, Puga MI, Rubio V, Perez-Perez J, Solano R, Leyva A, Paz-Ares J: A central regulatory system largely controls transcriptional activation and repression responses to phosphate starvation in Arabidopsis. PLoS Genet. 2010, 6:
-
(2010)
PLoS Genet.
, vol.6
-
-
Bustos, R.1
Castrillo, G.2
Linhares, F.3
Puga, M.I.4
Rubio, V.5
Perez-Perez, J.6
Solano, R.7
Leyva, A.8
Paz-Ares, J.9
-
51
-
-
0033388858
-
In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment
-
Kuo MH, Allis CD: In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment. Methods. 1999, 19: 425-433.
-
(1999)
Methods
, vol.19
, pp. 425-433
-
-
Kuo, M.H.1
Allis, C.D.2
-
52
-
-
36048931028
-
Tagging of MADS domain proteins for chromatin immunoprecipitation
-
de Folter S, Urbanus SL, van Zuijlen LG, Kaufmann K, Angenent GC: Tagging of MADS domain proteins for chromatin immunoprecipitation. BMC Plant Biol. 2007, 7: 47-
-
(2007)
BMC Plant Biol
, vol.7
, pp. 47
-
-
de Folter, S.1
Urbanus, S.L.2
van Zuijlen, L.G.3
Kaufmann, K.4
Angenent, G.C.5
-
53
-
-
84865822704
-
Genome-wide identification of transcription factor-binding sites in plants using chromatin immunoprecipitation followed by microarray (ChIP-chip) or sequencing (ChIP-seq)
-
Zhu JY, Sun Y, Wang ZY: Genome-wide identification of transcription factor-binding sites in plants using chromatin immunoprecipitation followed by microarray (ChIP-chip) or sequencing (ChIP-seq). Methods Mol Biol. 2012, 876: 173-188.
-
(2012)
Methods Mol Biol
, vol.876
, pp. 173-188
-
-
Zhu, J.Y.1
Sun, Y.2
Wang, Z.Y.3
-
54
-
-
84859582058
-
Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
-
Lickwar CR, Mueller F, Hanlon SE, McNally JG, Lieb JD: Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature. 2012, 484: 251-255.
-
(2012)
Nature
, vol.484
, pp. 251-255
-
-
Lickwar, C.R.1
Mueller, F.2
Hanlon, S.E.3
McNally, J.G.4
Lieb, J.D.5
-
55
-
-
64749089220
-
Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis
-
Oh E, Kang H, Yamaguchi S, Park J, Lee D, Kamiya Y, Choi G: Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis. Plant Cell Online. 2009, 21: 403-419.
-
(2009)
Plant Cell Online
, vol.21
, pp. 403-419
-
-
Oh, E.1
Kang, H.2
Yamaguchi, S.3
Park, J.4
Lee, D.5
Kamiya, Y.6
Choi, G.7
-
56
-
-
84874624769
-
Identification of direct targets of FUSCA3, a key regulator of Arabidopsis seed development
-
Wang F, Perry SE: Identification of direct targets of FUSCA3, a key regulator of Arabidopsis seed development. Plant Physiol. 2013, 161: 1251-1264.
-
(2013)
Plant Physiol
, vol.161
, pp. 1251-1264
-
-
Wang, F.1
Perry, S.E.2
-
57
-
-
84870724752
-
Arabidopsis bZIP16 transcription factor integrates light and hormone signaling pathways to regulate early seedling development
-
Hsieh WP, Hsieh HL, Wu SH: Arabidopsis bZIP16 transcription factor integrates light and hormone signaling pathways to regulate early seedling development. Plant Cell. 2012, 24: 3997-4011.
-
(2012)
Plant Cell
, vol.24
, pp. 3997-4011
-
-
Hsieh, W.P.1
Hsieh, H.L.2
Wu, S.H.3
-
58
-
-
84866902488
-
Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon
-
Monke G, Seifert M, Keilwagen J, Mohr M, Grosse I, Hahnel U, Junker A, Weisshaar B, Conrad U, Baumlein H, Altschmied L: Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res. 2012, 40: 8240-8254.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 8240-8254
-
-
Monke, G.1
Seifert, M.2
Keilwagen, J.3
Mohr, M.4
Grosse, I.5
Hahnel, U.6
Junker, A.7
Weisshaar, B.8
Conrad, U.9
Baumlein, H.10
Altschmied, L.11
-
59
-
-
70849092086
-
Global identification of targets of the Arabidopsis MADS domain protein AGAMOUS-Like15
-
Zheng Y, Ren N, Wang H, Stromberg AJ, Perry SE: Global identification of targets of the Arabidopsis MADS domain protein AGAMOUS-Like15. Plant Cell. 2009, 21: 2563-2577.
-
(2009)
Plant Cell
, vol.21
, pp. 2563-2577
-
-
Zheng, Y.1
Ren, N.2
Wang, H.3
Stromberg, A.J.4
Perry, S.E.5
-
60
-
-
79960736391
-
Microarray-based identification of transcription factor target genes
-
Plant Transcription Factors. Edited by: Yuan L, Perry SE., Totowa, NJ: Humana Press
-
Gorte M, Horstman A, Page RB, Heidstra R, Stromberg A, Boutilier K: Microarray-based identification of transcription factor target genes. Plant Transcription Factors. Edited by: Yuan L, Perry SE. 2011, Totowa, NJ: Humana Press, 754: 119-141.
-
(2011)
, vol.754
, pp. 119-141
-
-
Gorte, M.1
Horstman, A.2
Page, R.B.3
Heidstra, R.4
Stromberg, A.5
Boutilier, K.6
-
61
-
-
84878313826
-
TARGET: A transient transformation system for genome-wide transcription factor target discovery
-
Bargmann BO, Marshall-Colon A, Efroni I, Ruffel S, Birnbaum KD, Coruzzi GM, Krouk G: TARGET: A transient transformation system for genome-wide transcription factor target discovery. Mol Plant. 2013, 6: 978-980.
-
(2013)
Mol Plant
, vol.6
, pp. 978-980
-
-
Bargmann, B.O.1
Marshall-Colon, A.2
Efroni, I.3
Ruffel, S.4
Birnbaum, K.D.5
Coruzzi, G.M.6
Krouk, G.7
|