TY - JOUR AU - Bewley, J. D. PY - 1997 DA - 1997// TI - Seed germination and dormancy JO - Plant Cell VL - 9 UR - https://doi.org/10.1105/tpc.9.7.1055 DO - 10.1105/tpc.9.7.1055 ID - Bewley1997 ER - TY - STD TI - Bewley JD, Bradford K, Hilhorst H, Nonogaki H. Seeds: Physiology of development, germination and dormancy. 3rd ed. Springer; 2013. ID - ref2 ER - TY - JOUR AU - Alonso-Peral, M. M. AU - Li, J. AU - Li, Y. AU - Allen, R. S. AU - Schnippenkoetter, W. AU - Ohms, S. PY - 2010 DA - 2010// TI - The microRNA159-regulated GAMYB-like genes inhibit growth and promote programmed cell death in Arabidopsis JO - Plant Physiol VL - 154 UR - https://doi.org/10.1104/pp.110.160630 DO - 10.1104/pp.110.160630 ID - Alonso-Peral2010 ER - TY - JOUR AU - Das, S. S. AU - Karmakar, P. AU - Nandi, A. K. AU - Sanan-Mishra, N. PY - 2015 DA - 2015// TI - Small RNA mediated regulation of seed germination JO - Front Plant Sci VL - 6 ID - Das2015 ER - TY - JOUR AU - Liu, P. P. AU - Montgomery, T. A. AU - Fahlgren, N. AU - Kasschau, K. D. AU - Nonogaki, H. AU - Carrington, J. C. PY - 2007 DA - 2007// TI - Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages JO - Plant J VL - 52 UR - https://doi.org/10.1111/j.1365-313X.2007.03218.x DO - 10.1111/j.1365-313X.2007.03218.x ID - Liu2007 ER - TY - JOUR AU - Stamm, P. AU - Topham, A. T. AU - Mukhtar, N. K. AU - Jackson, M. D. AU - Tome, D. F. AU - Beynon, J. L. PY - 2017 DA - 2017// TI - The transcription factor ATHB5 affects GA-mediated plasticity in hypocotyl cell growth during seed germination JO - Plant Physiol VL - 173 UR - https://doi.org/10.1104/pp.16.01099 DO - 10.1104/pp.16.01099 ID - Stamm2017 ER - TY - JOUR AU - Xiao, W. AU - Custard, K. D. AU - Brown, R. C. AU - Lemmon, B. E. AU - Harada, J. J. AU - Goldberg, R. B. PY - 2006 DA - 2006// TI - DNA methylation is critical for Arabidopsis embryogenesis and seed viability JO - Plant Cell VL - 18 UR - https://doi.org/10.1105/tpc.105.038836 DO - 10.1105/tpc.105.038836 ID - Xiao2006 ER - TY - JOUR AU - Howell, K. A. AU - Narsai, R. AU - Carroll, A. AU - Ivanova, A. AU - Lohse, M. AU - Usadel, B. PY - 2009 DA - 2009// TI - Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process JO - Plant Physiol VL - 149 UR - https://doi.org/10.1104/pp.108.129874 DO - 10.1104/pp.108.129874 ID - Howell2009 ER - TY - JOUR AU - Nakabayashi, K. AU - Okamoto, M. AU - Koshiba, T. AU - Kamiya, Y. AU - Nambara, E. PY - 2005 DA - 2005// TI - Genome-wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed JO - Plant J VL - 41 UR - https://doi.org/10.1111/j.1365-313X.2005.02337.x DO - 10.1111/j.1365-313X.2005.02337.x ID - Nakabayashi2005 ER - TY - JOUR AU - Narsai, R. AU - Law, S. R. AU - Carrie, C. AU - Xu, L. AU - Whelan, J. PY - 2011 DA - 2011// TI - In depth temporal transcriptome profiling reveals a crucial developmental switch with roles for RNA processing and organelle metabolism that are essential for germination in Arabidopsis thaliana JO - Plant Physiol VL - 157 UR - https://doi.org/10.1104/pp.111.183129 DO - 10.1104/pp.111.183129 ID - Narsai2011 ER - TY - JOUR AU - Silva, A. T. AU - Ribone, P. A. AU - Chan, R. L. AU - Ligterink, W. AU - Hilhorst, H. W. PY - 2016 DA - 2016// TI - A predictive coexpression network identifies novel genes controlling the seed-to-seedling phase transition in Arabidopsis thaliana JO - Plant Physiol VL - 170 UR - https://doi.org/10.1104/pp.15.01704 DO - 10.1104/pp.15.01704 ID - Silva2016 ER - TY - JOUR AU - Okamoto, M. AU - Tatematsu, K. AU - Matsui, A. AU - Morosawa, T. AU - Ishida, J. AU - Tanaka, M. PY - 2010 DA - 2010// TI - Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays JO - Plant J VL - 62 UR - https://doi.org/10.1111/j.1365-313X.2010.04135.x DO - 10.1111/j.1365-313X.2010.04135.x ID - Okamoto2010 ER - TY - JOUR AU - Bassel, G. W. AU - Lan, H. AU - Glaab, E. AU - Gibbs, D. J. AU - Gerjets, T. AU - Krasnogor, N. PY - 2011 DA - 2011// TI - Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1100958108 DO - 10.1073/pnas.1100958108 ID - Bassel2011 ER - TY - JOUR AU - Hartmann, L. AU - Drewe-Boss, P. AU - Wiessner, T. AU - Wagner, G. AU - Geue, S. AU - Lee, H. C. PY - 2016 DA - 2016// TI - Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in Arabidopsis JO - Plant Cell VL - 28 UR - https://doi.org/10.1105/tpc.16.00508 DO - 10.1105/tpc.16.00508 ID - Hartmann2016 ER - TY - JOUR AU - Loraine, A. E. AU - McCormick, S. AU - Estrada, A. AU - Patel, K. AU - Qin, P. PY - 2013 DA - 2013// TI - RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing JO - Plant Physiol VL - 162 UR - https://doi.org/10.1104/pp.112.211441 DO - 10.1104/pp.112.211441 ID - Loraine2013 ER - TY - JOUR AU - Shikata, H. AU - Shibata, M. AU - Ushijima, T. AU - Nakashima, M. AU - Kong, S. G. AU - Matsuoka, K. PY - 2012 DA - 2012// TI - The RS domain of Arabidopsis splicing factor RRC1 is required for phytochrome B signal transduction JO - Plant J VL - 70 UR - https://doi.org/10.1111/j.1365-313X.2012.04937.x DO - 10.1111/j.1365-313X.2012.04937.x ID - Shikata2012 ER - TY - JOUR AU - Yan, K. AU - Liu, P. AU - Wu, C. A. AU - Yang, G. D. AU - Xu, R. AU - Guo, Q. H. PY - 2012 DA - 2012// TI - Stress-induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana JO - Mol Cell VL - 48 UR - https://doi.org/10.1016/j.molcel.2012.08.032 DO - 10.1016/j.molcel.2012.08.032 ID - Yan2012 ER - TY - JOUR AU - Rogers, K. AU - Chen, X. PY - 2013 DA - 2013// TI - Biogenesis, turnover, and mode of action of plant microRNAs JO - Plant Cell VL - 25 UR - https://doi.org/10.1105/tpc.113.113159 DO - 10.1105/tpc.113.113159 ID - Rogers2013 ER - TY - JOUR AU - Reyes, J. L. AU - Chua, N. H. PY - 2007 DA - 2007// TI - ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination JO - Plant J VL - 49 UR - https://doi.org/10.1111/j.1365-313X.2006.02980.x DO - 10.1111/j.1365-313X.2006.02980.x ID - Reyes2007 ER - TY - JOUR AU - Baldrich, P. AU - San, S. B. PY - 2016 DA - 2016// TI - MicroRNAs in rice innate immunity JO - Rice VL - 9 UR - https://doi.org/10.1186/s12284-016-0078-5 DO - 10.1186/s12284-016-0078-5 ID - Baldrich2016 ER - TY - JOUR AU - Curaba, J. AU - Singh, M. B. AU - Bhalla, P. L. PY - 2014 DA - 2014// TI - miRNAs in the crosstalk between phytohormone signalling pathways JO - J Exp Bot VL - 65 UR - https://doi.org/10.1093/jxb/eru002 DO - 10.1093/jxb/eru002 ID - Curaba2014 ER - TY - JOUR AU - Matzke, M. A. AU - Mosher, R. A. PY - 2014 DA - 2014// TI - RNA-directed DNA methylation: an epigenetic pathway of increasing complexity JO - Nat Rev Genet VL - 15 UR - https://doi.org/10.1038/nrg3683 DO - 10.1038/nrg3683 ID - Matzke2014 ER - TY - JOUR AU - Cuerda-Gil, D. AU - Slotkin, R. K. PY - 2016 DA - 2016// TI - Non-canonical RNA-directed DNA methylation JO - Nat Plants VL - 2 UR - https://doi.org/10.1038/nplants.2016.163 DO - 10.1038/nplants.2016.163 ID - Cuerda-Gil2016 ER - TY - JOUR AU - Kawakatsu, T. AU - Stuart, T. AU - Valdes, M. AU - Breakfield, N. AU - Schmitz, R. J. AU - Nery, J. R. PY - 2016 DA - 2016// TI - Unique cell-type-specific patterns of DNA methylation in the root meristem JO - Nat Plants VL - 2 UR - https://doi.org/10.1038/nplants.2016.58 DO - 10.1038/nplants.2016.58 ID - Kawakatsu2016 ER - TY - JOUR AU - Calarco, J. P. AU - Borges, F. AU - Donoghue, M. T. AU - Ex, F. AU - Jullien, P. E. AU - Lopes, T. PY - 2012 DA - 2012// TI - Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA JO - Cell VL - 151 UR - https://doi.org/10.1016/j.cell.2012.09.001 DO - 10.1016/j.cell.2012.09.001 ID - Calarco2012 ER - TY - JOUR AU - Ibarra, C. A. AU - Feng, X. AU - Schoft, V. K. AU - Hsieh, T. F. AU - Uzawa, R. AU - Rodrigues, J. A. PY - 2012 DA - 2012// TI - Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes JO - Science VL - 337 UR - https://doi.org/10.1126/science.1224839 DO - 10.1126/science.1224839 ID - Ibarra2012 ER - TY - JOUR AU - Park, K. AU - Kim, M. Y. AU - Vickers, M. AU - Park, J. S. AU - Hyun, Y. AU - Okamoto, T. PY - 2016 DA - 2016// TI - DNA demethylation is initiated in the central cells of Arabidopsis and rice JO - Proc Natl Acad Sci U S A VL - 113 UR - https://doi.org/10.1073/pnas.1619047114 DO - 10.1073/pnas.1619047114 ID - Park2016 ER - TY - JOUR AU - Deleris, A. AU - Halter, T. AU - Navarro, L. PY - 2016 DA - 2016// TI - DNA methylation and demethylation in plant immunity JO - Annu Rev Phytopathol VL - 54 UR - https://doi.org/10.1146/annurev-phyto-080615-100308 DO - 10.1146/annurev-phyto-080615-100308 ID - Deleris2016 ER - TY - JOUR AU - Hossain, M. S. AU - Kawakatsu, T. AU - Kim, K. D. AU - Zhang, N. AU - Nguyen, C. T. AU - Khan, S. M. PY - 2017 DA - 2017// TI - Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs JO - New Phytol VL - 214 UR - https://doi.org/10.1111/nph.14421 DO - 10.1111/nph.14421 ID - Hossain2017 ER - TY - JOUR AU - Secco, D. AU - Jabnoune, M. AU - Walker, H. AU - Shou, H. AU - Wu, P. AU - Poirier, Y. PY - 2013 DA - 2013// TI - Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery JO - Plant Cell VL - 25 UR - https://doi.org/10.1105/tpc.113.117325 DO - 10.1105/tpc.113.117325 ID - Secco2013 ER - TY - JOUR AU - Du, J. AU - Johnson, L. M. AU - Jacobsen, S. E. AU - Patel, D. J. PY - 2015 DA - 2015// TI - DNA methylation pathways and their crosstalk with histone methylation JO - Nat Rev Mol Cell Biol VL - 16 UR - https://doi.org/10.1038/nrm4043 DO - 10.1038/nrm4043 ID - Du2015 ER - TY - JOUR AU - Gouil, Q. AU - Baulcombe, D. C. PY - 2016 DA - 2016// TI - DNA methylation signatures of the plant chromomethyltransferases JO - PLoS Genet VL - 12 UR - https://doi.org/10.1371/journal.pgen.1006526 DO - 10.1371/journal.pgen.1006526 ID - Gouil2016 ER - TY - JOUR AU - Portis, E. AU - Acquadro, A. AU - Comino, C. AU - Lanteri, S. PY - 2004 DA - 2004// TI - Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP) JO - Plant Sci VL - 166 UR - https://doi.org/10.1016/j.plantsci.2003.09.004 DO - 10.1016/j.plantsci.2003.09.004 ID - Portis2004 ER - TY - JOUR AU - Meng, F. R. AU - Li, Y. C. AU - Yin, J. AU - Liu, H. AU - Chen, J. X. AU - Ni, F. Z. PY - 2012 DA - 2012// TI - Analysis of DNA methylation during the germination of wheat seeds JO - Biol Plant VL - 56 UR - https://doi.org/10.1007/s10535-012-0086-2 DO - 10.1007/s10535-012-0086-2 ID - Meng2012 ER - TY - JOUR AU - Narsai, R. AU - Secco, D. AU - Schultz, M. D. AU - Ecker, J. R. AU - Lister, R. AU - Whelan, J. PY - 2017 DA - 2017// TI - Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation JO - Plant J VL - 89 UR - https://doi.org/10.1111/tpj.13418 DO - 10.1111/tpj.13418 ID - Narsai2017 ER - TY - JOUR AU - Choi, Y. AU - Gehring, M. AU - Johnson, L. AU - Hannon, M. AU - Harada, J. J. AU - Goldberg, R. B. PY - 2002 DA - 2002// TI - DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in arabidopsis JO - Cell VL - 110 UR - https://doi.org/10.1016/S0092-8674(02)00807-3 DO - 10.1016/S0092-8674(02)00807-3 ID - Choi2002 ER - TY - JOUR AU - Ruhl, C. AU - Stauffer, E. AU - Kahles, A. AU - Wagner, G. AU - Drechsel, G. AU - Ratsch, G. PY - 2012 DA - 2012// TI - Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes JO - Plant Cell VL - 24 UR - https://doi.org/10.1105/tpc.112.103622 DO - 10.1105/tpc.112.103622 ID - Ruhl2012 ER - TY - JOUR AU - Zhang, X. N. AU - Mount, S. M. PY - 2009 DA - 2009// TI - Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development JO - Plant Physiol VL - 150 UR - https://doi.org/10.1104/pp.109.138180 DO - 10.1104/pp.109.138180 ID - Zhang2009 ER - TY - JOUR AU - Lopez-Molina, L. AU - Mongrand, S. AU - McLachlin, D. T. AU - Chait, B. T. AU - Chua, N. H. PY - 2002 DA - 2002// TI - ABI5 acts downstream of ABI3 to execute an ABA-dependent growth arrest during germination JO - Plant J VL - 32 UR - https://doi.org/10.1046/j.1365-313X.2002.01430.x DO - 10.1046/j.1365-313X.2002.01430.x ID - Lopez-Molina2002 ER - TY - JOUR AU - Chiang, G. C. AU - Barua, D. AU - Kramer, E. M. AU - Amasino, R. M. AU - Donohue, K. PY - 2009 DA - 2009// TI - Major flowering time gene, flowering locus C, regulates seed germination in Arabidopsis thaliana JO - Proc Natl Acad Sci U S A VL - 106 UR - https://doi.org/10.1073/pnas.0901367106 DO - 10.1073/pnas.0901367106 ID - Chiang2009 ER - TY - JOUR AU - Kendall, S. L. AU - Hellwege, A. AU - Marriot, P. AU - Whalley, C. AU - Graham, I. A. AU - Penfield, S. PY - 2011 DA - 2011// TI - Induction of dormancy in Arabidopsis summer annuals requires parallel regulation of DOG1 and hormone metabolism by low temperature and CBF transcription factors JO - Plant Cell VL - 23 UR - https://doi.org/10.1105/tpc.111.087643 DO - 10.1105/tpc.111.087643 ID - Kendall2011 ER - TY - JOUR AU - Carvalho, R. F. AU - Carvalho, S. D. AU - Duque, P. PY - 2010 DA - 2010// TI - The plant-specific SR45 protein negatively regulates glucose and ABA signaling during early seedling development in Arabidopsis JO - Plant Physiol VL - 154 UR - https://doi.org/10.1104/pp.110.155523 DO - 10.1104/pp.110.155523 ID - Carvalho2010 ER - TY - JOUR AU - Xing, D. AU - Wang, Y. AU - Hamilton, M. AU - Ben-Hur, A. AU - Reddy, A. S. PY - 2015 DA - 2015// TI - Transcriptome-wide identification of RNA targets of Arabidopsis SERINE/ARGININE-RICH45 uncovers the unexpected roles of this RNA binding protein in RNA processing JO - Plant Cell VL - 27 UR - https://doi.org/10.1105/tpc.15.00641 DO - 10.1105/tpc.15.00641 ID - Xing2015 ER - TY - JOUR AU - Schulze, S. AU - Schafer, B. N. AU - Parizotto, E. A. AU - Voinnet, O. AU - Theres, K. PY - 2010 DA - 2010// TI - LOST MERISTEMS genes regulate cell differentiation of central zone descendants in Arabidopsis shoot meristems JO - Plant J VL - 64 UR - https://doi.org/10.1111/j.1365-313X.2010.04359.x DO - 10.1111/j.1365-313X.2010.04359.x ID - Schulze2010 ER - TY - JOUR AU - Schulz, M. H. AU - Devanny, W. E. AU - Gitter, A. AU - Zhong, S. AU - Ernst, J. AU - Bar-Joseph, Z. PY - 2012 DA - 2012// TI - DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data JO - BMC Syst Biol VL - 6 UR - https://doi.org/10.1186/1752-0509-6-104 DO - 10.1186/1752-0509-6-104 ID - Schulz2012 ER - TY - JOUR AU - O’Malley, R. C. AU - Huang, 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 - 166 UR - https://doi.org/10.1016/j.cell.2016.08.063 DO - 10.1016/j.cell.2016.08.063 ID - O’Malley2016 ER - TY - JOUR AU - Olsen, A. N. AU - Ernst, H. A. AU - Leggio, L. L. AU - Skriver, K. PY - 2005 DA - 2005// TI - NAC transcription factors: structurally distinct, functionally diverse JO - Trends Plant Sci VL - 10 UR - https://doi.org/10.1016/j.tplants.2004.12.010 DO - 10.1016/j.tplants.2004.12.010 ID - Olsen2005 ER - TY - JOUR AU - Finkelstein, R. R. AU - Lynch, T. J. PY - 2000 DA - 2000// TI - The Arabidopsis abscisic acid response gene ABI5 encodes a basic leucine zipper transcription factor JO - Plant Cell VL - 12 UR - https://doi.org/10.1105/tpc.12.4.599 DO - 10.1105/tpc.12.4.599 ID - Finkelstein2000 ER - TY - JOUR AU - Huang, Y. AU - Feng, C. Z. AU - Ye, Q. AU - Wu, W. H. AU - Chen, Y. F. PY - 2016 DA - 2016// TI - Arabidopsis WRKY6 transcription factor acts as a positive regulator of abscisic acid signaling during seed germination and early seedling development JO - PLoS Genet VL - 12 UR - https://doi.org/10.1371/journal.pgen.1005833 DO - 10.1371/journal.pgen.1005833 ID - Huang2016 ER - TY - JOUR AU - Johannesson, H. AU - Wang, Y. AU - Hanson, J. AU - Engstrom, P. PY - 2003 DA - 2003// TI - The Arabidopsis thaliana homeobox gene ATHB5 is a potential regulator of abscisic acid responsiveness in developing seedlings JO - Plant Mol Biol VL - 51 UR - https://doi.org/10.1023/A:1022567625228 DO - 10.1023/A:1022567625228 ID - Johannesson2003 ER - TY - JOUR AU - Choi, H. AU - Jeong, S. AU - Kim, D. S. AU - Na, H. J. AU - Ryu, J. S. AU - Lee, S. S. PY - 2014 DA - 2014// TI - The homeodomain-leucine zipper ATHB23, a phytochrome B-interacting protein, is important for phytochrome B-mediated red light signaling JO - Physiol Plant VL - 150 UR - https://doi.org/10.1111/ppl.12087 DO - 10.1111/ppl.12087 ID - Choi2014 ER - TY - JOUR AU - Yanagisawa, S. PY - 2004 DA - 2004// TI - Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants JO - Plant Cell Physiol VL - 45 UR - https://doi.org/10.1093/pcp/pch055 DO - 10.1093/pcp/pch055 ID - Yanagisawa2004 ER - TY - JOUR AU - Santopolo, S. AU - Boccaccini, A. AU - Lorrai, R. AU - Ruta, V. AU - Capauto, D. AU - Minutello, E. PY - 2015 DA - 2015// TI - DOF AFFECTING GERMINATION 2 is a positive regulator of light-mediated seed germination and is repressed by DOF AFFECTING GERMINATION 1 JO - BMC Plant Biol VL - 15 UR - https://doi.org/10.1186/s12870-015-0453-1 DO - 10.1186/s12870-015-0453-1 ID - Santopolo2015 ER - TY - JOUR AU - Rushton, P. J. AU - Somssich, I. E. AU - Ringler, P. AU - Shen, Q. J. PY - 2010 DA - 2010// TI - WRKY transcription factors JO - Trends Plant Sci VL - 15 UR - https://doi.org/10.1016/j.tplants.2010.02.006 DO - 10.1016/j.tplants.2010.02.006 ID - Rushton2010 ER - TY - JOUR AU - Rueda-Romero, P. AU - Barrero-Sicilia, C. AU - Gomez-Cadenas, A. AU - Carbonero, P. AU - Onate-Sanchez, L. PY - 2012 DA - 2012// TI - Arabidopsis thaliana DOF6 negatively affects germination in non-after-ripened seeds and interacts with TCP14 JO - J Exp Bot VL - 63 UR - https://doi.org/10.1093/jxb/err388 DO - 10.1093/jxb/err388 ID - Rueda-Romero2012 ER - TY - CHAP AU - O’Malley, R. C. AU - Barragan, C. C. AU - Ecker, J. R. ED - Alonso, J. M. ED - Stepanova, A. N. PY - 2015 DA - 2015// TI - A User’s guide to the Arabidopsis T-DNA insertion mutant collections BT - Plant functional genomics: methods and protocols PB - Springer New York CY - New York ID - O’Malley2015 ER - TY - JOUR AU - Bueso, E. AU - Munoz-Bertomeu, J. AU - Campos, F. AU - Brunaud, V. AU - Martinez, L. AU - Sayas, E. PY - 2014 DA - 2014// TI - ARABIDOPSIS THALIANA HOMEOBOX25 uncovers a role for Gibberellins in seed longevity JO - Plant Physiol VL - 164 UR - https://doi.org/10.1104/pp.113.232223 DO - 10.1104/pp.113.232223 ID - Bueso2014 ER - TY - JOUR AU - Skirycz, A. AU - Radziejwoski, A. AU - Busch, W. AU - Hannah, M. A. AU - Czeszejko, J. AU - Kwasniewski, M. PY - 2008 DA - 2008// TI - The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana JO - Plant J VL - 56 UR - https://doi.org/10.1111/j.1365-313X.2008.03641.x DO - 10.1111/j.1365-313X.2008.03641.x ID - Skirycz2008 ER - TY - JOUR AU - Willemsen, V. AU - Bauch, M. AU - Bennett, T. AU - Campilho, A. AU - Wolkenfelt, H. AU - Xu, J. PY - 2008 DA - 2008// TI - The NAC domain transcription factors FEZ and SOMBRERO control the orientation of cell division plane in Arabidopsis root stem cells JO - Dev Cell VL - 15 UR - https://doi.org/10.1016/j.devcel.2008.09.019 DO - 10.1016/j.devcel.2008.09.019 ID - Willemsen2008 ER - TY - JOUR AU - Green, K. A. AU - Prigge, M. J. AU - Katzman, R. B. AU - Clark, S. E. PY - 2005 DA - 2005// TI - CORONA, a member of the class III homeodomain leucine zipper gene family in Arabidopsis, regulates stem cell specification and organogenesis JO - Plant Cell VL - 17 UR - https://doi.org/10.1105/tpc.104.026179 DO - 10.1105/tpc.104.026179 ID - Green2005 ER - TY - JOUR AU - Martinez, G. AU - Kohler, C. PY - 2017 DA - 2017// TI - Role of small RNAs in epigenetic reprogramming during plant sexual reproduction JO - Curr Opin Plant Biol VL - 36 UR - https://doi.org/10.1016/j.pbi.2016.12.006 DO - 10.1016/j.pbi.2016.12.006 ID - Martinez2017 ER - TY - JOUR AU - Chou, C. H. AU - Chang, N. W. AU - Shrestha, S. AU - Hsu, S. D. AU - Lin, Y. L. AU - Lee, W. H. PY - 2016 DA - 2016// TI - miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1258 DO - 10.1093/nar/gkv1258 ID - Chou2016 ER - TY - JOUR AU - Jha, A. AU - Shankar, R. PY - 2014 DA - 2014// TI - MiRNAting control of DNA methylation JO - J Biosci VL - 39 UR - https://doi.org/10.1007/s12038-014-9437-9 DO - 10.1007/s12038-014-9437-9 ID - Jha2014 ER - TY - JOUR AU - German, M. A. AU - Pillay, M. AU - Jeong, D. H. AU - Hetawal, A. AU - Luo, S. AU - Janardhanan, P. PY - 2008 DA - 2008// TI - Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends JO - Nat Biotechnol VL - 26 UR - https://doi.org/10.1038/nbt1417 DO - 10.1038/nbt1417 ID - German2008 ER - TY - JOUR AU - Meinke, D. AU - Muralla, R. AU - Sweeney, C. AU - Dickerman, A. PY - 2008 DA - 2008// TI - Identifying essential genes in Arabidopsis thaliana JO - Trends Plant Sci VL - 13 UR - https://doi.org/10.1016/j.tplants.2008.06.003 DO - 10.1016/j.tplants.2008.06.003 ID - Meinke2008 ER - TY - JOUR AU - Zhao, J. H. AU - Fang, Y. Y. AU - Duan, C. G. AU - Fang, R. X. AU - Ding, S. W. AU - Guo, H. S. PY - 2016 DA - 2016// TI - Genome-wide identification of endogenous RNA-directed DNA methylation loci associated with abundant 21-nucleotide siRNAs in Arabidopsis JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep36247 DO - 10.1038/srep36247 ID - Zhao2016 ER - TY - JOUR AU - Nonogaki, H. PY - 2010 DA - 2010// TI - MicroRNA gene regulation cascades during early stages of plant development JO - Plant Cell Physiol VL - 51 UR - https://doi.org/10.1093/pcp/pcq154 DO - 10.1093/pcp/pcq154 ID - Nonogaki2010 ER - TY - JOUR AU - Penfield, S. AU - Springthorpe, V. PY - 2012 DA - 2012// TI - Understanding chilling responses in Arabidopsis seeds and their contribution to life history JO - Philos Trans R Soc Lond B Biol Sci VL - 367 UR - https://doi.org/10.1098/rstb.2011.0186 DO - 10.1098/rstb.2011.0186 ID - Penfield2012 ER - TY - JOUR AU - Law, S. R. AU - Narsai, R. AU - Taylor, N. L. AU - Delannoy, E. AU - Carrie, C. AU - Giraud, E. PY - 2012 DA - 2012// TI - Nucleotide and RNA metabolism prime translational initiation in the earliest events of mitochondrial biogenesis during Arabidopsis germination JO - Plant Physiol VL - 158 UR - https://doi.org/10.1104/pp.111.192351 DO - 10.1104/pp.111.192351 ID - Law2012 ER - TY - JOUR AU - Jiang, Z. AU - Xu, G. AU - Jing, Y. AU - Tang, W. AU - Lin, R. PY - 2016 DA - 2016// TI - Phytochrome B and REVEILLE1/2-mediated signalling controls seed dormancy and germination in Arabidopsis JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms12377 DO - 10.1038/ncomms12377 ID - Jiang2016 ER - TY - JOUR AU - Neff, M. M. PY - 2012 DA - 2012// TI - Light-mediated seed germination: connecting phytochrome B to gibberellic acid JO - Dev Cell VL - 22 UR - https://doi.org/10.1016/j.devcel.2012.04.003 DO - 10.1016/j.devcel.2012.04.003 ID - Neff2012 ER - TY - JOUR AU - Bourbousse, C. AU - Mestiri, I. AU - Zabulon, G. AU - Bourge, M. AU - Formiggini, F. AU - Koini, M. A. PY - 2015 DA - 2015// TI - Light signaling controls nuclear architecture reorganization during seedling establishment JO - Proc Natl Acad Sci U S A VL - 112 UR - https://doi.org/10.1073/pnas.1503512112 DO - 10.1073/pnas.1503512112 ID - Bourbousse2015 ER - TY - JOUR AU - Yu, H. AU - Kumar, P. P. PY - 2003 DA - 2003// TI - Post-transcriptional gene silencing in plants by RNA JO - Plant Cell Rep VL - 22 UR - https://doi.org/10.1007/s00299-003-0699-1 DO - 10.1007/s00299-003-0699-1 ID - Yu2003 ER - TY - JOUR AU - Xu, R. AU - Wang, Y. AU - Zheng, H. AU - Lu, W. AU - Wu, C. AU - Huang, J. PY - 2015 DA - 2015// TI - Salt-induced transcription factor MYB74 is regulated by the RNA-directed DNA methylation pathway in Arabidopsis JO - J Exp Bot VL - 66 UR - https://doi.org/10.1093/jxb/erv312 DO - 10.1093/jxb/erv312 ID - Xu2015 ER - TY - JOUR AU - Alonso, J. M. AU - Stepanova, A. N. AU - Leisse, T. J. AU - Kim, C. J. AU - Chen, H. AU - Shinn, P. PY - 2003 DA - 2003// TI - Genome-wide insertional mutagenesis of Arabidopsis thaliana JO - Science VL - 301 UR - https://doi.org/10.1126/science.1086391 DO - 10.1126/science.1086391 ID - Alonso2003 ER - TY - JOUR AU - Ulker, B. AU - Li, Y. AU - Rosso, M. G. AU - Logemann, E. AU - Somssich, I. E. AU - Weisshaar, B. PY - 2008 DA - 2008// TI - T-DNA-mediated transfer of Agrobacterium tumefaciens chromosomal DNA into plants JO - Nat Biotechnol VL - 26 UR - https://doi.org/10.1038/nbt.1491 DO - 10.1038/nbt.1491 ID - Ulker2008 ER - TY - JOUR AU - Baulcombe, D. C. AU - Saunders, G. R. AU - Bevan, M. W. AU - Mayo, M. A. AU - Harrison, B. D. PY - 1986 DA - 1986// TI - Expression of biologically active viral satellite RNA from the nuclear genome of transformed plants JO - Nature VL - 321 UR - https://doi.org/10.1038/321446a0 DO - 10.1038/321446a0 ID - Baulcombe1986 ER - TY - JOUR AU - Kim, S. AU - Kim, M. S. AU - Kim, Y. M. AU - Yeom, S. I. AU - Cheong, K. AU - Kim, K. T. PY - 2015 DA - 2015// TI - Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.) JO - DNA Res VL - 22 UR - https://doi.org/10.1093/dnares/dsu035 DO - 10.1093/dnares/dsu035 ID - Kim2015 ER - TY - JOUR AU - Liao, Y. AU - Smyth, G. K. AU - Shi, W. PY - 2014 DA - 2014// TI - featureCounts: an efficient general purpose program for assigning sequence reads to genomic features JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btt656 DO - 10.1093/bioinformatics/btt656 ID - Liao2014 ER - TY - JOUR AU - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - STD TI - Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–19. ID - ref81 ER - TY - JOUR AU - Pimentel, H. AU - Sturmfels, P. AU - Bray, N. AU - Melsted, P. AU - Pachter, L. PY - 2016 DA - 2016// TI - The Lair: a resource for exploratory analysis of published RNA-Seq data JO - BMC Bioinforma VL - 17 UR - https://doi.org/10.1186/s12859-016-1357-2 DO - 10.1186/s12859-016-1357-2 ID - Pimentel2016 ER - TY - JOUR AU - Trapnell, C. AU - Roberts, A. AU - Goff, L. AU - Pertea, G. AU - Kim, D. AU - Kelley, D. R. PY - 2012 DA - 2012// TI - Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks JO - Nat Protoc VL - 7 UR - https://doi.org/10.1038/nprot.2012.016 DO - 10.1038/nprot.2012.016 ID - Trapnell2012 ER - TY - JOUR AU - Zhu, L. J. AU - Gazin, C. AU - Lawson, N. D. AU - Pages, H. AU - Lin, S. M. AU - Lapointe, D. S. PY - 2010 DA - 2010// TI - ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data JO - BMC Bioinforma VL - 11 UR - https://doi.org/10.1186/1471-2105-11-237 DO - 10.1186/1471-2105-11-237 ID - Zhu2010 ER - TY - JOUR AU - Axtell, M. J. PY - 2013 DA - 2013// TI - ShortStack: comprehensive annotation and quantification of small RNA genes JO - RNA VL - 19 UR - https://doi.org/10.1261/rna.035279.112 DO - 10.1261/rna.035279.112 ID - Axtell2013 ER - TY - JOUR AU - Langmead, B. AU - Trapnell, C. AU - Pop, M. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - Ultrafast and memory-efficient alignment of short DNA sequences to the human genome JO - Genome Biol VL - 10 UR - https://doi.org/10.1186/gb-2009-10-3-r25 DO - 10.1186/gb-2009-10-3-r25 ID - Langmead2009 ER - TY - JOUR AU - Urich, M. A. AU - Nery, J. R. AU - Lister, R. AU - Schmitz, R. J. AU - Ecker, J. R. PY - 2015 DA - 2015// TI - MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing JO - Nat Protoc VL - 10 UR - https://doi.org/10.1038/nprot.2014.114 DO - 10.1038/nprot.2014.114 ID - Urich2015 ER - TY - JOUR AU - Krueger, F. AU - Andrews, S. R. PY - 2011 DA - 2011// TI - Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr167 DO - 10.1093/bioinformatics/btr167 ID - Krueger2011 ER - TY - JOUR AU - Hsieh, T. F. AU - Ibarra, C. A. AU - Silva, P. AU - Zemach, A. AU - Eshed-Williams, L. AU - Fischer, R. L. PY - 2009 DA - 2009// TI - Genome-wide demethylation of Arabidopsis endosperm JO - Science VL - 324 UR - https://doi.org/10.1126/science.1172417 DO - 10.1126/science.1172417 ID - Hsieh2009 ER - TY - JOUR AU - Stroud, H. AU - Do, T. AU - Du, J. AU - Zhong, X. AU - Feng, S. AU - Johnson, L. PY - 2014 DA - 2014// TI - Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis JO - Nat Struct Mol Biol VL - 21 UR - https://doi.org/10.1038/nsmb.2735 DO - 10.1038/nsmb.2735 ID - Stroud2014 ER -