TY - JOUR AU - Geertz, M. AU - Maerkl, S. J. PY - 2010 DA - 2010// TI - Experimental strategies for studying transcription factor–DNA binding specificities JO - Brief Funct Genomics VL - 9 UR - https://doi.org/10.1093/bfgp/elq023 DO - 10.1093/bfgp/elq023 ID - Geertz2010 ER - TY - JOUR AU - Li, Y. AU - Chen, C. -. Y. AU - Kaye, A. M. AU - Wasserman, W. W. PY - 2015 DA - 2015// TI - The identification of cis-regulatory elements: a review from a machine learning perspective JO - Biosystems VL - 138 UR - https://doi.org/10.1016/j.biosystems.2015.10.002 DO - 10.1016/j.biosystems.2015.10.002 ID - Li2015 ER - TY - JOUR AU - Macneil, L. T. AU - Walhout, A. J. M. PY - 2011 DA - 2011// TI - Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.097378.109 DO - 10.1101/gr.097378.109 ID - Macneil2011 ER - TY - JOUR AU - Carroll, S. B. PY - 2008 DA - 2008// TI - Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution JO - Cell VL - 134 UR - https://doi.org/10.1016/j.cell.2008.06.030 DO - 10.1016/j.cell.2008.06.030 ID - Carroll2008 ER - TY - JOUR AU - Yamaguchi-Shinozaki, K. AU - Shinozaki, K. PY - 2006 DA - 2006// TI - Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses JO - Annu Rev Plant Biol VL - 57 UR - https://doi.org/10.1146/annurev.arplant.57.032905.105444 DO - 10.1146/annurev.arplant.57.032905.105444 ID - Yamaguchi-Shinozaki2006 ER - TY - JOUR AU - Brady, S. M. AU - Orlando, D. A. AU - Lee, J. -. Y. AU - Wang, J. Y. AU - Koch, J. AU - Dinneny, J. R. PY - 2007 DA - 2007// TI - A high-resolution root spatiotemporal map reveals dominant expression patterns JO - Science VL - 318 UR - https://doi.org/10.1126/science.1146265 DO - 10.1126/science.1146265 ID - Brady2007 ER - TY - JOUR AU - Dinneny, J. R. AU - Long, T. A. AU - Wang, J. Y. AU - Jung, J. W. AU - Mace, D. AU - Pointer, S. PY - 2008 DA - 2008// TI - Cell identity mediates the response of Arabidopsis roots to abiotic stress JO - Science VL - 320 UR - https://doi.org/10.1126/science.1153795 DO - 10.1126/science.1153795 ID - Dinneny2008 ER - TY - JOUR AU - Kilian, J. AU - Whitehead, D. AU - Horak, J. AU - Wanke, D. AU - Weinl, S. AU - Batistic, O. PY - 2007 DA - 2007// TI - The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses JO - Plant J VL - 50 UR - https://doi.org/10.1111/j.1365-313X.2007.03052.x DO - 10.1111/j.1365-313X.2007.03052.x ID - Kilian2007 ER - TY - JOUR AU - Rebeiz, M. AU - Patel, N. H. AU - Hinman, V. F. PY - 2015 DA - 2015// TI - Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development JO - Annu Rev Genomics Hum Genet. VL - 16 UR - https://doi.org/10.1146/annurev-genom-091212-153423 DO - 10.1146/annurev-genom-091212-153423 ID - Rebeiz2015 ER - TY - JOUR AU - Provart, N. J. AU - Alonso, J. AU - Assmann, S. M. AU - Bergmann, D. AU - Brady, S. M. AU - Brkljacic, J. PY - 2016 DA - 2016// TI - 50 years of Arabidopsis research: highlights and future directions JO - New Phytol VL - 209 UR - https://doi.org/10.1111/nph.13687 DO - 10.1111/nph.13687 ID - Provart2016 ER - TY - JOUR AU - Fournier-Level, A. AU - Korte, A. AU - Cooper, M. D. AU - Nordborg, M. AU - Schmitt, J. AU - Wilczek, A. M. PY - 2011 DA - 2011// TI - A map of local adaptation in Arabidopsis thaliana JO - Science VL - 334 UR - https://doi.org/10.1126/science.1209271 DO - 10.1126/science.1209271 ID - Fournier-Level2011 ER - TY - STD TI - Weigel D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol. 2012; http://www.plantphysiol.org/content/158/1/2.short UR - http://www.plantphysiol.org/content/158/1/2.short ID - ref12 ER - TY - JOUR PY - 2016 DA - 2016// TI - 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana JO - Cell VL - 166 UR - https://doi.org/10.1016/j.cell.2016.05.063 DO - 10.1016/j.cell.2016.05.063 ID - ref13 ER - TY - JOUR AU - Chang, C. AU - Bowman, J. L. AU - Meyerowitz, E. M. PY - 2016 DA - 2016// TI - Field guide to plant model systems JO - Cell VL - 167 UR - https://doi.org/10.1016/j.cell.2016.08.031 DO - 10.1016/j.cell.2016.08.031 ID - Chang2016 ER - TY - STD TI - NCBI. Genome List. https://www.ncbi.nlm.nih.gov/genome/browse/#!/overview/brassicaceae. Accessed Dec 12 2017. UR - https://www.ncbi.nlm.nih.gov/genome/browse/%23!/overview/brassicaceae ID - ref15 ER - TY - JOUR AU - Cheng, F. AU - Liu, S. AU - Wu, J. AU - Fang, L. AU - Sun, S. AU - Liu, B. PY - 2011 DA - 2011// TI - BRAD, the genetics and genomics database for Brassica plants JO - BMC Plant Biol VL - 11 UR - https://doi.org/10.1186/1471-2229-11-136 DO - 10.1186/1471-2229-11-136 ID - Cheng2011 ER - TY - JOUR AU - Lehti-Shiu, M. D. AU - Panchy, N. AU - Wang, P. AU - Uygun, S. AU - Shiu, S. -. H. PY - 1860 DA - 1860// TI - Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families JO - Biochim Biophys Acta VL - 2017 ID - Lehti-Shiu1860 ER - TY - JOUR AU - Lister, R. AU - Gregory, B. D. AU - Ecker, J. R. PY - 2009 DA - 2009// TI - Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond JO - Curr Opin Plant Biol VL - 12 UR - https://doi.org/10.1016/j.pbi.2008.11.004 DO - 10.1016/j.pbi.2008.11.004 ID - Lister2009 ER - TY - JOUR AU - Taylor-Teeples, M. AU - Lin, L. AU - de Lucas, M. AU - Turco, G. AU - Toal, T. W. AU - Gaudinier, A. PY - 2015 DA - 2015// TI - An Arabidopsis gene regulatory network for secondary cell wall synthesis JO - Nature VL - 517 UR - https://doi.org/10.1038/nature14099 DO - 10.1038/nature14099 ID - Taylor-Teeples2015 ER - TY - STD TI - Song L, Huang S-SC, Wise A, Castanon R, Nery JR, Chen H, et al. A transcription factor hierarchy defines an environmental stress response network. Science. 2016;354 Available from: https://doi.org/10.1126/science.aag1550 ID - ref20 ER - TY - JOUR AU - O’Malley, R. C. AU - Huang, S. -. S. C. AU - Song, L. AU - Lewsey, M. G. AU - Bartlett, A. AU - Nery, J. R. PY - 2016 DA - 2016// TI - Cistrome and epicistrome features shape the regulatory DNA landscape JO - Cell VL - 165 UR - https://doi.org/10.1016/j.cell.2016.04.038 DO - 10.1016/j.cell.2016.04.038 ID - O’Malley2016 ER - TY - JOUR AU - Wilkins, O. AU - Hafemeister, C. AU - Plessis, A. AU - Holloway-Phillips, M. -. M. AU - Pham, G. M. AU - Nicotra, A. B. PY - 2016 DA - 2016// TI - EGRINs (environmental gene regulatory influence networks) in rice that function in the response to water deficit, high temperature, and agricultural environments JO - Plant Cell VL - 28 UR - https://doi.org/10.1105/tpc.16.00158 DO - 10.1105/tpc.16.00158 ID - Wilkins2016 ER - TY - JOUR AU - Walley, J. W. AU - Sartor, R. C. AU - Shen, Z. AU - Schmitz, R. J. AU - Wu, K. J. AU - Urich, M. A. PY - 2016 DA - 2016// TI - Integration of omic networks in a developmental atlas of maize JO - Science VL - 353 UR - https://doi.org/10.1126/science.aag1125 DO - 10.1126/science.aag1125 ID - Walley2016 ER - TY - JOUR AU - Miao, Z. AU - Han, Z. AU - Zhang, T. AU - Chen, S. AU - Ma, C. PY - 2017 DA - 2017// TI - A systems approach to a spatio-temporal understanding of the drought stress response in maize JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/s41598-017-06929-y DO - 10.1038/s41598-017-06929-y ID - Miao2017 ER - TY - JOUR AU - Johnson, A. D. PY - 2017 DA - 2017// TI - The rewiring of transcription circuits in evolution JO - Curr Opin Genet Dev VL - 47 UR - https://doi.org/10.1016/j.gde.2017.09.004 DO - 10.1016/j.gde.2017.09.004 ID - Johnson2017 ER - TY - JOUR AU - Thompson, D. AU - Regev, A. AU - Roy, S. PY - 2015 DA - 2015// TI - Comparative analysis of gene regulatory networks: from network reconstruction to evolution JO - Annu Rev Cell Dev Biol VL - 31 UR - https://doi.org/10.1146/annurev-cellbio-100913-012908 DO - 10.1146/annurev-cellbio-100913-012908 ID - Thompson2015 ER - TY - JOUR AU - Lasky, J. R. AU - Des Marais, D. L. AU - Lowry, D. B. AU - Povolotskaya, I. AU - McKay, J. K. AU - Richards, J. H. PY - 2014 DA - 2014// TI - Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana JO - Mol Biol Evol VL - 31 UR - https://doi.org/10.1093/molbev/msu170 DO - 10.1093/molbev/msu170 ID - Lasky2014 ER - TY - JOUR AU - Zsögön, A. AU - Cermak, T. AU - Voytas, D. AU - Peres, L. E. P. PY - 2017 DA - 2017// TI - Genome editing as a tool to achieve the crop ideotype and de novo domestication of wild relatives: case study in tomato JO - Plant Sci VL - 256 UR - https://doi.org/10.1016/j.plantsci.2016.12.012 DO - 10.1016/j.plantsci.2016.12.012 ID - Zsögön2017 ER - TY - JOUR AU - Rodríguez-Leal, D. AU - Lemmon, Z. H. AU - Man, J. AU - Bartlett, M. E. AU - Lippman, Z. B. PY - 2017 DA - 2017// TI - Engineering quantitative trait variation for crop improvement by genome editing JO - Cell VL - 171 UR - https://doi.org/10.1016/j.cell.2017.08.030 DO - 10.1016/j.cell.2017.08.030 ID - Rodríguez-Leal2017 ER - TY - JOUR AU - Nemhauser, J. L. AU - Torii, K. U. PY - 2016 DA - 2016// TI - Plant synthetic biology for molecular engineering of signalling and development JO - Nat Plants VL - 2 UR - https://doi.org/10.1038/nplants.2016.10 DO - 10.1038/nplants.2016.10 ID - Nemhauser2016 ER - TY - JOUR AU - Pierre-Jerome, E. AU - Jang, S. S. AU - Havens, K. A. AU - Nemhauser, J. L. AU - Klavins, E. PY - 2014 DA - 2014// TI - Recapitulation of the forward nuclear auxin response pathway in yeast JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1324147111 DO - 10.1073/pnas.1324147111 ID - Pierre-Jerome2014 ER - TY - JOUR AU - Pierre-Jerome, E. AU - Moss, B. L. AU - Lanctot, A. AU - Hageman, A. AU - Nemhauser, J. L. PY - 2016 DA - 2016// TI - Functional analysis of molecular interactions in synthetic auxin response circuits JO - Proc Natl Acad Sci U S A VL - 113 UR - https://doi.org/10.1073/pnas.1604379113 DO - 10.1073/pnas.1604379113 ID - Pierre-Jerome2016 ER - TY - STD TI - Rubiolo M, Milone DH, Stegmayer G. Extreme learning machines for reverse engineering of gene regulatory networks from expression time series. Bioinformatics. 2017; https://doi.org/10.1093/bioinformatics/btx730 ID - ref33 ER - TY - JOUR AU - Sinha, N. R. AU - Rowland, S. D. AU - Ichihashi, Y. PY - 2016 DA - 2016// TI - Using gene networks in EvoDevo analyses JO - Curr Opin Plant Biol VL - 33 UR - https://doi.org/10.1016/j.pbi.2016.06.016 DO - 10.1016/j.pbi.2016.06.016 ID - Sinha2016 ER - TY - JOUR AU - Wittkopp, P. J. AU - Kalay, G. PY - 2011 DA - 2011// TI - Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence JO - Nat Rev Genet VL - 13 UR - https://doi.org/10.1038/nrg3095 DO - 10.1038/nrg3095 ID - Wittkopp2011 ER - TY - JOUR AU - Braguy, J. AU - Zurbriggen, M. D. PY - 2016 DA - 2016// TI - Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms JO - Plant J VL - 87 UR - https://doi.org/10.1111/tpj.13218 DO - 10.1111/tpj.13218 ID - Braguy2016 ER - TY - JOUR AU - Samodelov, S. L. AU - Zurbriggen, M. D. PY - 2017 DA - 2017// TI - Quantitatively understanding plant signaling: novel theoretical–experimental approaches JO - Trends Plant Sci VL - 22 UR - https://doi.org/10.1016/j.tplants.2017.05.006 DO - 10.1016/j.tplants.2017.05.006 ID - Samodelov2017 ER - TY - JOUR AU - Pereira, A. PY - 2016 DA - 2016// TI - Plant abiotic stress challenges from the changing environment JO - Front Plant Sci VL - 7 ID - Pereira2016 ER - TY - JOUR AU - Munns, R. AU - Tester, M. PY - 2008 DA - 2008// TI - Mechanisms of salinity tolerance JO - Annu Rev Plant Biol VL - 59 UR - https://doi.org/10.1146/annurev.arplant.59.032607.092911 DO - 10.1146/annurev.arplant.59.032607.092911 ID - Munns2008 ER - TY - JOUR AU - Zhu, J. -. K. PY - 2016 DA - 2016// TI - Abiotic stress signaling and responses in plants JO - Cell VL - 167 UR - https://doi.org/10.1016/j.cell.2016.08.029 DO - 10.1016/j.cell.2016.08.029 ID - Zhu2016 ER - TY - JOUR AU - Dinneny, J. R. PY - 2015 DA - 2015// TI - Traversing organizational scales in plant salt-stress responses JO - Curr Opin Plant Biol VL - 23 UR - https://doi.org/10.1016/j.pbi.2014.10.009 DO - 10.1016/j.pbi.2014.10.009 ID - Dinneny2015 ER - TY - JOUR AU - Feng, W. AU - Lindner, H. AU - Robbins, N. E. AU - Dinneny, J. R. PY - 2016 DA - 2016// TI - Growing out of stress: the role of cell- and organ-scale growth control in plant water-stress responses JO - Plant Cell VL - 28 UR - https://doi.org/10.1105/tpc.16.00182 DO - 10.1105/tpc.16.00182 ID - Feng2016 ER - TY - JOUR AU - Hasegawa, P. M. AU - Bressan, R. A. AU - Zhu, J. -. K. AU - Bohnert, H. J. PY - 2000 DA - 2000// TI - Plant cellular and molecular responses to high salinity JO - Annu Rev Plant Physiol Plant Mol Biol VL - 51 UR - https://doi.org/10.1146/annurev.arplant.51.1.463 DO - 10.1146/annurev.arplant.51.1.463 ID - Hasegawa2000 ER - TY - JOUR AU - Rellán-Álvarez, R. AU - Lobet, G. AU - Dinneny, J. R. PY - 2016 DA - 2016// TI - Environmental control of root system biology JO - Annu Rev Plant Biol VL - 67 UR - https://doi.org/10.1146/annurev-arplant-043015-111848 DO - 10.1146/annurev-arplant-043015-111848 ID - Rellán-Álvarez2016 ER - TY - BOOK AU - Brophy, J. A. N. AU - LaRue, T. PY - 2017 DA - 2017// TI - Dinneny JR PB - Understanding and engineering plant form CY - Semin Cell Dev Biol ID - Brophy2017 ER - TY - JOUR AU - Zhu, J. -. K. PY - 2002 DA - 2002// TI - Salt and drought stress signal transduction in plants JO - Annu Rev Plant Biol VL - 53 UR - https://doi.org/10.1146/annurev.arplant.53.091401.143329 DO - 10.1146/annurev.arplant.53.091401.143329 ID - Zhu2002 ER - TY - JOUR AU - Des Marais, D. L. AU - Juenger, T. E. PY - 2010 DA - 2010// TI - Pleiotropy, plasticity, and the evolution of plant abiotic stress tolerance JO - Ann N Y Acad Sci VL - 1206 UR - https://doi.org/10.1111/j.1749-6632.2010.05703.x DO - 10.1111/j.1749-6632.2010.05703.x ID - Des Marais2010 ER - TY - JOUR AU - Nicotra, A. B. AU - Atkin, O. K. AU - Bonser, S. P. AU - Davidson, A. M. AU - Finnegan, E. J. AU - Mathesius, U. PY - 2010 DA - 2010// TI - Plant phenotypic plasticity in a changing climate JO - Trends Plant Sci VL - 15 UR - https://doi.org/10.1016/j.tplants.2010.09.008 DO - 10.1016/j.tplants.2010.09.008 ID - Nicotra2010 ER - TY - JOUR AU - Zou, C. AU - Sun, K. AU - Mackaluso, J. D. AU - Seddon, A. E. AU - Jin, R. AU - Thomashow, M. F. PY - 2011 DA - 2011// TI - Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1103202108 DO - 10.1073/pnas.1103202108 ID - Zou2011 ER - TY - JOUR AU - Birnbaum, K. AU - Shasha, D. E. AU - Wang, J. Y. AU - Jung, J. W. AU - Lambert, G. M. AU - Galbraith, D. W. PY - 2003 DA - 2003// TI - A gene expression map of the Arabidopsis root JO - Science VL - 302 UR - https://doi.org/10.1126/science.1090022 DO - 10.1126/science.1090022 ID - Birnbaum2003 ER - TY - JOUR AU - Walker, L. AU - Boddington, C. AU - Jenkins, D. AU - Wang, Y. AU - Grønlund, J. T. AU - Hulsmans, J. PY - 2017 DA - 2017// TI - Changes in gene expression in space and time orchestrate environmentally mediated shaping of root architecture JO - Plant Cell VL - 29 UR - https://doi.org/10.1105/tpc.16.00961 DO - 10.1105/tpc.16.00961 ID - Walker2017 ER - TY - JOUR AU - Sonawane, A. R. AU - Platig, J. AU - Fagny, M. AU - Chen, C. -. Y. AU - Paulson, J. N. AU - Lopes-Ramos, C. M. PY - 2017 DA - 2017// TI - Understanding tissue-specific gene regulation JO - Cell Rep VL - 21 UR - https://doi.org/10.1016/j.celrep.2017.10.001 DO - 10.1016/j.celrep.2017.10.001 ID - Sonawane2017 ER - TY - JOUR AU - Uygun, S. AU - Seddon, A. E. AU - Azodi, C. B. AU - Shiu, S. -. H. PY - 2017 DA - 2017// TI - Predictive models of spatial transcriptional response to high salinity JO - Plant Physiol VL - 174 UR - https://doi.org/10.1104/pp.16.01828 DO - 10.1104/pp.16.01828 ID - Uygun2017 ER - TY - JOUR AU - Krishnan, A. AU - Gupta, C. AU - Ambavaram, M. M. R. AU - Pereira, A. PY - 2017 DA - 2017// TI - RECoN: Rice environment Coexpression network for systems level analysis of abiotic-stress response JO - Front Plant Sci VL - 8 UR - https://doi.org/10.3389/fpls.2017.01640 DO - 10.3389/fpls.2017.01640 ID - Krishnan2017 ER - TY - JOUR AU - Wu, H. -. J. AU - Zhang, Z. AU - Wang, J. -. Y. AU - Oh, D. -. H. AU - Dassanayake, M. AU - Liu, B. PY - 2012 DA - 2012// TI - Insights into salt tolerance from the genome of Thellungiella salsuginea JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1209954109 DO - 10.1073/pnas.1209954109 ID - Wu2012 ER - TY - JOUR AU - Orsini, F. AU - D’Urzo, M. P. AU - Inan, G. AU - Serra, S. AU - Oh, D. -. H. AU - Mickelbart, M. V. PY - 2010 DA - 2010// TI - A comparative study of salt tolerance parameters in 11 wild relatives of Arabidopsis thaliana JO - J Exp Bot VL - 61 UR - https://doi.org/10.1093/jxb/erq188 DO - 10.1093/jxb/erq188 ID - Orsini2010 ER - TY - JOUR AU - Oh, D. -. H. AU - Hong, H. AU - Lee, S. Y. AU - Yun, D. -. J. AU - Bohnert, H. J. AU - Dassanayake, M. PY - 2014 DA - 2014// TI - Genome structures and transcriptomes signify niche adaptation for the multiple-ion-tolerant extremophyte Schrenkiella parvula JO - Plant Physiol VL - 164 UR - https://doi.org/10.1104/pp.113.233551 DO - 10.1104/pp.113.233551 ID - Oh2014 ER - TY - JOUR AU - Dassanayake, M. AU - Oh, D. -. H. AU - Hong, H. AU - Bohnert, H. J. AU - Cheeseman, J. M. PY - 2011 DA - 2011// TI - Transcription strength and halophytic lifestyle JO - Trends Plant Sci VL - 16 UR - https://doi.org/10.1016/j.tplants.2010.10.006 DO - 10.1016/j.tplants.2010.10.006 ID - Dassanayake2011 ER - TY - JOUR AU - Oh, D. -. H. AU - Dassanayake, M. AU - Haas, J. S. AU - Kropornika, A. AU - Wright, C. AU - d’Urzo, M. P. PY - 2010 DA - 2010// TI - Genome structures and halophyte-specific gene expression of the extremophile Thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and Arabidopsis JO - Plant Physiol VL - 154 UR - https://doi.org/10.1104/pp.110.163923 DO - 10.1104/pp.110.163923 ID - Oh2010 ER - TY - JOUR AU - Oh, D. -. H. PY - 2012 DA - 2012// TI - Dassanayake M, Bohnert HJ JO - Cheeseman JM Life at the extreme: lessons from the genome Genome Biol VL - 13 ID - Oh2012 ER -