TY - JOUR AU - Zhu, X. -. G. AU - Long, S. P. AU - Ort, D. R. PY - 2008 DA - 2008// TI - What is the maximum efficiency with which photosynthesis can convert solar energy into biomass? JO - Curr Opin Biotechnol VL - 19 UR - https://doi.org/10.1016/j.copbio.2008.02.004 DO - 10.1016/j.copbio.2008.02.004 ID - Zhu2008 ER - TY - STD TI - Raghavendra AS, Sage RF. C4 Photosynthesis and Related CO2 Concentrating Mechanisms. Volume 32. Springer Science & Business Media; Springer Netherlands, 2010. ID - ref2 ER - TY - JOUR AU - Covshoff, S. AU - Hibberd, J. M. PY - 2012 DA - 2012// TI - Integrating C4 photosynthesis into C3 crops to increase yield potential JO - Curr Opin Biotechnol VL - 23 UR - https://doi.org/10.1016/j.copbio.2011.12.011 DO - 10.1016/j.copbio.2011.12.011 ID - Covshoff2012 ER - TY - JOUR AU - Hibberd, J. M. AU - Covshoff, S. PY - 2010 DA - 2010// TI - The regulation of gene expression required for C4 photosynthesis JO - Annu Rev Plant Biol VL - 61 UR - https://doi.org/10.1146/annurev-arplant-042809-112238 DO - 10.1146/annurev-arplant-042809-112238 ID - Hibberd2010 ER - TY - JOUR AU - Sheen, J. PY - 1999 DA - 1999// TI - C4 gene expression JO - Annu Rev Plant Biol VL - 50 UR - https://doi.org/10.1146/annurev.arplant.50.1.187 DO - 10.1146/annurev.arplant.50.1.187 ID - Sheen1999 ER - TY - JOUR AU - Aubry, S. AU - Brown, N. J. AU - Hibberd, J. M. PY - 2011 DA - 2011// TI - The role of proteins in C3 plants prior to their recruitment into the C4 pathway JO - J Exp Bot VL - 62 UR - https://doi.org/10.1093/jxb/err012 DO - 10.1093/jxb/err012 ID - Aubry2011 ER - TY - JOUR AU - Langdale, J. A. PY - 2011 DA - 2011// TI - C4 cycles: past, present, and future research on C4 photosynthesis JO - Plant Cell VL - 23 UR - https://doi.org/10.1105/tpc.111.092098 DO - 10.1105/tpc.111.092098 ID - Langdale2011 ER - TY - JOUR AU - Caemmerer, S. AU - Quick, W. P. AU - Furbank, R. T. PY - 2012 DA - 2012// TI - The development of C4 rice: current progress and future challenges JO - Science VL - 336 UR - https://doi.org/10.1126/science.1220177 DO - 10.1126/science.1220177 ID - Caemmerer2012 ER - TY - JOUR AU - Roider, H. G. AU - Kanhere, A. AU - Manke, T. AU - Vingron, M. PY - 2007 DA - 2007// TI - Predicting transcription factor affinities to DNA from a biophysical model JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl565 DO - 10.1093/bioinformatics/btl565 ID - Roider2007 ER - TY - STD TI - Palumbo MJ, Newberg LA. Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data. Nucleic Acids Res. 2010;38: W268-274. ID - ref10 ER - TY - STD TI - Jia H, Li J. Finding transcription factor binding motifs for co-regulated genes by combining sequence overrepresentation with cross-species conservation. J Probab Stat. 2012;2012. http://dx.doi.org/10.1155/2012/830575 UR - http://dx.doi.org/10.1155/2012/830575 ID - ref11 ER - TY - JOUR AU - Zhang, X. AU - Zhao, X. -. M. AU - He, K. AU - Lu, L. AU - Cao, Y. AU - Liu, J. AU - Hao, J. -. K. AU - Liu, Z. -. P. AU - Chen, L. PY - 2012 DA - 2012// TI - Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/btr626 DO - 10.1093/bioinformatics/btr626 ID - Zhang2012 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - STD TI - Sundaram V, Cheng Y, Ma Z, Li D, Xing X, Edge P, Snyder MP, Wang T. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res. 2014;24:1963-76. ID - ref14 ER - TY - JOUR AU - Xie, M. AU - Hong, C. AU - Zhang, B. AU - Lowdon, R. F. AU - Xing, X. AU - Li, D. AU - Zhou, X. AU - Lee, H. J. AU - Maire, C. L. AU - Ligon, K. L. PY - 2013 DA - 2013// TI - DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2649 DO - 10.1038/ng.2649 ID - Xie2013 ER - TY - JOUR AU - Terashima, I. AU - Hanba, Y. T. AU - Tazoe, Y. AU - Vyas, P. AU - Yano, S. PY - 2006 DA - 2006// TI - Irradiance and phenotype: comparative eco-development of sun and shade leaves in relation to photosynthetic CO2 diffusion JO - J Exp Bot. VL - 57 UR - https://doi.org/10.1093/jxb/erj014 DO - 10.1093/jxb/erj014 ID - Terashima2006 ER - TY - JOUR AU - Wang, T. AU - Zeng, J. AU - Lowe, C. B. AU - Sellers, R. G. AU - Salama, S. R. AU - Yang, M. AU - Burgess, S. M. AU - Brachmann, R. K. AU - Haussler, D. PY - 2007 DA - 2007// TI - Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53 JO - Proc Natl Acad Sci VL - 104 UR - https://doi.org/10.1073/pnas.0703637104 DO - 10.1073/pnas.0703637104 ID - Wang2007 ER - TY - JOUR AU - Lynch, V. J. AU - Leclerc, R. D. AU - May, G. AU - Wagner, G. P. PY - 2011 DA - 2011// TI - Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.917 DO - 10.1038/ng.917 ID - Lynch2011 ER - TY - JOUR AU - Rebollo, R. AU - Romanish, M. T. AU - Mager, D. L. PY - 2012 DA - 2012// TI - Transposable elements: an abundant and natural source of regulatory sequences for host genes JO - Annu Rev Genet VL - 46 UR - https://doi.org/10.1146/annurev-genet-110711-155621 DO - 10.1146/annurev-genet-110711-155621 ID - Rebollo2012 ER - TY - JOUR AU - Jacques, P. -. E. AU - Jeyakani, J. AU - Bourque, G. PY - 2013 DA - 2013// TI - The majority of primate-specific regulatory sequences are derived from transposable elements JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003504 DO - 10.1371/journal.pgen.1003504 ID - Jacques2013 ER - TY - JOUR AU - Kapusta, A. AU - Kronenberg, Z. AU - Lynch, V. J. AU - Zhuo, X. AU - Ramsay, L. AU - Bourque, G. AU - Yandell, M. AU - Feschotte, C. PY - 2013 DA - 2013// TI - Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003470 DO - 10.1371/journal.pgen.1003470 ID - Kapusta2013 ER - TY - JOUR AU - Gowik, U. AU - Bräutigam, A. AU - Weber, K. L. AU - Weber, A. P. M. AU - Westhoff, P. PY - 2011 DA - 2011// TI - Evolution of C4 photosynthesis in the genus Flaveria: how many and which genes does it take to make C4? JO - Plant Cell VL - 23 UR - https://doi.org/10.1105/tpc.111.086264 DO - 10.1105/tpc.111.086264 ID - Gowik2011 ER - TY - JOUR AU - Sage, R. F. AU - Christin, P. A. AU - Edwards, E. J. PY - 2011 DA - 2011// TI - The C4 plant lineages of planet earth JO - J Exp Bot VL - 62 UR - https://doi.org/10.1093/jxb/err048 DO - 10.1093/jxb/err048 ID - Sage2011 ER - TY - JOUR AU - Christin, P. A. AU - Besnard, G. AU - Samaritani, E. AU - Duvall, M. R. AU - Hodkinson, T. R. AU - Savolainen, V. AU - Salamin, N. PY - 2008 DA - 2008// TI - Oligocene CO2 decline promoted C4 photosynthesis in grasses JO - Curr Biol VL - 18 UR - https://doi.org/10.1016/j.cub.2007.11.058 DO - 10.1016/j.cub.2007.11.058 ID - Christin2008 ER - TY - CHAP AU - Monson, R. K. ED - Sage, R. F. ED - Monson, R. K. PY - 1989 DA - 1989// TI - The origins of C4 genes and evolutionary pattern in the C4 metabolic phenotype BT - C4 plant biology PB - Academic Press CY - San Diego, CA, USA ID - Monson1989 ER - TY - JOUR AU - Kajala, K. AU - Brown, N. J. AU - Williams, B. P. AU - Borrill, P. AU - Taylor, L. E. AU - Hibberd, J. M. PY - 2012 DA - 2012// TI - Multiple Arabidopsis genes primed for recruitment into C4 photosynthesis JO - Plant J VL - 69 UR - https://doi.org/10.1111/j.1365-313X.2011.04769.x DO - 10.1111/j.1365-313X.2011.04769.x ID - Kajala2012 ER - TY - JOUR AU - Gowik, U. AU - Burscheidt, J. AU - Akyildiz, M. AU - Schlue, U. AU - Koczor, M. AU - Streubel, M. AU - Westhoff, P. PY - 2004 DA - 2004// TI - cis-regulatory elements for mesophyll-specific gene expression in the C4 plant Flaveria trinervia, the promoter of the C4 phosphoenolpyruvate carboxylase gene JO - Plant Cell VL - 16 UR - https://doi.org/10.1105/tpc.019729 DO - 10.1105/tpc.019729 ID - Gowik2004 ER - TY - JOUR AU - Brown, N. J. AU - Newell, C. A. AU - Stanley, S. AU - Chen, J. E. AU - Perrin, A. J. AU - Kajala, K. AU - Hibberd, J. M. PY - 2011 DA - 2011// TI - Independent and parallel recruitment of preexisting mechanisms underlying C4 photosynthesis JO - Science VL - 331 UR - https://doi.org/10.1126/science.1201248 DO - 10.1126/science.1201248 ID - Brown2011 ER - TY - JOUR AU - Enright, A. J. AU - Dongen, S. AU - Ouzounis, C. A. PY - 2002 DA - 2002// TI - An efficient algorithm for large-scale detection of protein families JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.7.1575 DO - 10.1093/nar/30.7.1575 ID - Enright2002 ER - TY - JOUR AU - Pavesi, G. AU - Mereghetti, P. AU - Zambelli, F. AU - Stefani, M. AU - Mauri, G. AU - Pesole, G. PY - 2006 DA - 2006// TI - MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes JO - Nucleic Acids Res. VL - 34 UR - https://doi.org/10.1093/nar/gkl285 DO - 10.1093/nar/gkl285 ID - Pavesi2006 ER - TY - JOUR AU - Li, P. AU - Ponnala, L. AU - Gandotra, N. AU - Wang, L. AU - Si, Y. AU - Tausta, S. L. AU - Kebrom, T. H. AU - Provart, N. AU - Patel, R. AU - Myers, C. R. PY - 2010 DA - 2010// TI - The developmental dynamics of the maize leaf transcriptome JO - Nat Genet VL - 42 UR - https://doi.org/10.1038/ng.703 DO - 10.1038/ng.703 ID - Li2010 ER - TY - JOUR AU - Bailey, T. L. AU - Gribskov, M. PY - 1998 DA - 1998// TI - Combining evidence using p-values: application to sequence homology searches JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.1.48 DO - 10.1093/bioinformatics/14.1.48 ID - Bailey1998 ER - TY - JOUR AU - Naito, K. AU - Zhang, F. AU - Tsukiyama, T. AU - Saito, H. AU - Hancock, C. N. AU - Richardson, A. O. AU - Okumoto, Y. AU - Tanisaka, T. AU - Wessler, S. R. PY - 2009 DA - 2009// TI - Unexpected consequences of a sudden and massive transposon amplification on rice gene expression JO - Nature VL - 461 UR - https://doi.org/10.1038/nature08479 DO - 10.1038/nature08479 ID - Naito2009 ER - TY - JOUR AU - Kuang, H. AU - Padmanabhan, C. AU - Li, F. AU - Kamei, A. AU - Bhaskar, P. B. AU - Ouyang, S. AU - Jiang, J. AU - Buell, C. R. AU - Baker, B. PY - 2009 DA - 2009// TI - Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: new functional implications for MITEs JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.078196.108 DO - 10.1101/gr.078196.108 ID - Kuang2009 ER - TY - JOUR AU - Yang, G. AU - Lee, Y. -. H. AU - Jiang, Y. AU - Shi, X. AU - Kertbundit, S. AU - Hall, T. C. PY - 2005 DA - 2005// TI - A two-edged role for the transposable element Kiddo in the rice ubiquitin2 promoter JO - Plant Cell VL - 17 UR - https://doi.org/10.1105/tpc.104.030528 DO - 10.1105/tpc.104.030528 ID - Yang2005 ER - TY - JOUR AU - Ouyang, S. AU - Buell, C. R. PY - 2004 DA - 2004// TI - The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh099 DO - 10.1093/nar/gkh099 ID - Ouyang2004 ER - TY - STD TI - Yu X, Zheng G, Shan L, Meng G, Vingron M, Liu Q, Zhu XG. Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana. Frontiers in Plant Sci. 5:273.doi: 10.3389/fpls.2014.00273. ID - ref37 ER - TY - JOUR AU - Mukherjee, K. AU - Choudhury, A. R. AU - Gupta, B. AU - Gupta, S. AU - Sengupta, D. N. PY - 2006 DA - 2006// TI - An ABRE-binding factor, OSBZ8, is highly expressed in salt tolerant cultivars than in salt sensitive cultivars of indica rice JO - BMC Plant Biol VL - 6 UR - https://doi.org/10.1186/1471-2229-6-18 DO - 10.1186/1471-2229-6-18 ID - Mukherjee2006 ER - TY - JOUR AU - Singh, K. AU - Dennis, E. S. AU - Ellis, J. G. AU - Llewellyn, D. J. AU - Tokuhisa, J. G. AU - Wahleithner, J. A. AU - Peacock, W. J. PY - 1990 DA - 1990// TI - OCSBF-1, a maize ocs enhancer binding factor: isolation and expression during development JO - Plant Cell VL - 2 UR - https://doi.org/10.1105/tpc.2.9.891 DO - 10.1105/tpc.2.9.891 ID - Singh1990 ER - TY - JOUR AU - Maddaloni, M. AU - Donini, G. AU - Balconi, C. AU - Rizzi, E. AU - Gallusci, P. AU - Forlani, F. AU - Lohmer, S. AU - Thompson, R. AU - Salamini, F. AU - Motto, M. PY - 1996 DA - 1996// TI - The transcriptional activator Opaque-2 controls the expression of a cytosolic form of pyruvate orthophosphate dikinase-1 in maize endosperms JO - Mol Gen Genet MGG VL - 250 ID - Maddaloni1996 ER - TY - JOUR AU - Song, Y. H. AU - Yoo, C. M. AU - Hong, A. P. AU - Kim, S. H. AU - Jeong, H. J. AU - Shin, S. Y. AU - Kim, H. J. AU - Yun, D. -. J. AU - Lim, C. O. AU - Bahk, J. D. PY - 2008 DA - 2008// TI - DNA-binding study identifies C-box and hybrid C/G-box or C/A-box motifs as high-affinity binding sites for STF1 and LONG HYPOCOTYL5 proteins JO - Plant Physiol VL - 146 UR - https://doi.org/10.1104/pp.107.113217 DO - 10.1104/pp.107.113217 ID - Song2008 ER - TY - JOUR AU - Verdier, J. AU - Thompson, R. D. PY - 2008 DA - 2008// TI - Transcriptional regulation of storage protein synthesis during dicotyledon seed filling JO - Plant Cell Physiol VL - 49 UR - https://doi.org/10.1093/pcp/pcn116 DO - 10.1093/pcp/pcn116 ID - Verdier2008 ER - TY - JOUR AU - Tabata, T. AU - Nakayama, T. AU - Mikami, K. AU - Iwabuchi, M. PY - 1991 DA - 1991// TI - HBP-1a and HBP-1b: leucine zipper-type transcription factors of wheat JO - EMBO J. VL - 10 ID - Tabata1991 ER - TY - JOUR AU - Sell, S. AU - Hehl, R. PY - 2014 DA - 2014// TI - Functional dissection of a small anaerobically induced bZIP transcription factor from tomato JO - Eur J Biochem VL - 271 UR - https://doi.org/10.1111/j.1432-1033.2004.04413.x DO - 10.1111/j.1432-1033.2004.04413.x ID - Sell2014 ER - TY - JOUR AU - Yoshida, T. AU - Fujita, Y. AU - Maruyama, K. AU - Mogami, J. AU - Todaka, D. AU - Shinozaki, K. AU - Yamaguchi-Shinozaki, K. PY - 2015 DA - 2015// TI - Four Arabidopsis AREB/ABF transcription factors function predominantly in gene expression downstream of SnRK2 kinases in abscisic acid signalling in response to osmotic stress JO - Plant Cell Environ VL - 38 UR - https://doi.org/10.1111/pce.12351 DO - 10.1111/pce.12351 ID - Yoshida2015 ER - TY - JOUR AU - Azakhsh, M. AU - Kirienko, A. N. AU - Zhukov, V. A. AU - Lebedeva, M. A. AU - Dolgikh, E. A. AU - Lutova, L. A. PY - 2015 DA - 2015// TI - KNOTTED1-LIKE HOMEOBOX 3: a new regulator of symbiotic nodule development JO - J Exp Bot. VL - 66 UR - https://doi.org/10.1093/jxb/erv414 DO - 10.1093/jxb/erv414 ID - Azakhsh2015 ER - TY - JOUR AU - Corral, J. M. AU - Vogel, H. AU - Aliyu, O. M. AU - Hensel, G. AU - Thiel, T. AU - Kumlehn, J. AU - Sharbel, T. F. PY - 2013 DA - 2013// TI - A conserved apomixis-specific polymorphism is correlated with exclusive exonuclease expression in premeiotic ovules of apomictic Boechera species JO - Plant Physiol VL - 163 UR - https://doi.org/10.1104/pp.113.222430 DO - 10.1104/pp.113.222430 ID - Corral2013 ER -