TY - JOUR AU - Struhl, K. PY - 2007 DA - 2007// TI - Transcriptional noise and the fidelity of initiation by RNA polymerase II JO - Nat Struct Mol Biol VL - 14 UR - https://doi.org/10.1038/nsmb0207-103 DO - 10.1038/nsmb0207-103 ID - Struhl2007 ER - TY - JOUR AU - Ponjavic, J. AU - Ponting, C. P. AU - Lunter, G. PY - 2007 DA - 2007// TI - Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.6036807 DO - 10.1101/gr.6036807 ID - Ponjavic2007 ER - TY - JOUR AU - Kim, Y. J. AU - Zheng, B. L. AU - Yu, Y. AU - Won, S. Y. AU - Mo, B. X. AU - Chen, X. M. PY - 2011 DA - 2011// TI - The role of mediator in small and long noncoding RNA production in Arabidopsis thaliana JO - EMBO J VL - 30 UR - https://doi.org/10.1038/emboj.2011.3 DO - 10.1038/emboj.2011.3 ID - Kim2011 ER - TY - JOUR AU - Wilusz, J. E. AU - Sunwoo, H. AU - Spector, D. L. PY - 2009 DA - 2009// TI - Long noncoding RNAs: functional surprises from the RNA world JO - Gene Dev VL - 23 UR - https://doi.org/10.1101/gad.1800909 DO - 10.1101/gad.1800909 ID - Wilusz2009 ER - TY - JOUR AU - Brosnan, C. A. AU - Voinnet, O. PY - 2009 DA - 2009// TI - The long and the short of noncoding RNAs JO - Curr Opin Cell Biol VL - 21 UR - https://doi.org/10.1016/j.ceb.2009.04.001 DO - 10.1016/j.ceb.2009.04.001 ID - Brosnan2009 ER - TY - JOUR AU - Rinn, J. L. AU - Chang, H. Y. PY - 2012 DA - 2012// TI - Genome regulation by long noncoding RNAs JO - Annu Rev Biochem VL - 81 UR - https://doi.org/10.1146/annurev-biochem-051410-092902 DO - 10.1146/annurev-biochem-051410-092902 ID - Rinn2012 ER - TY - JOUR AU - Cabili, M. N. AU - Trapnell, C. AU - Goff, L. AU - Koziol, M. AU - Tazon-Vega, B. AU - Regev, A. PY - 2011 DA - 2011// TI - Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses JO - Gene Dev VL - 25 UR - https://doi.org/10.1101/gad.17446611 DO - 10.1101/gad.17446611 ID - Cabili2011 ER - TY - JOUR AU - Ponting, C. P. AU - Oliver, P. L. AU - Reik, W. PY - 2009 DA - 2009// TI - Evolution and functions of long noncoding RNAs JO - Cell VL - 136 UR - https://doi.org/10.1016/j.cell.2009.02.006 DO - 10.1016/j.cell.2009.02.006 ID - Ponting2009 ER - TY - JOUR AU - Yamada, K. AU - Lim, J. AU - Dale, J. M. AU - Chen, H. M. AU - Shinn, P. AU - Palm, C. J. PY - 2003 DA - 2003// TI - Empirical analysis of transcriptional activity in the Arabidopsis genome JO - Science VL - 302 UR - https://doi.org/10.1126/science.1088305 DO - 10.1126/science.1088305 ID - Yamada2003 ER - TY - JOUR AU - Wang, X. J. AU - Gaasterland, T. AU - Chua, N. H. PY - 2005 DA - 2005// TI - Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana JO - Genome Biol VL - 6 UR - https://doi.org/10.1186/gb-2005-6-4-r30 DO - 10.1186/gb-2005-6-4-r30 ID - Wang2005 ER - TY - JOUR AU - Kornienko, A. E. AU - Guenzl, P. M. AU - Barlow, D. P. AU - Pauler, F. M. PY - 2013 DA - 2013// TI - Gene regulation by the act of long non-coding RNA transcription JO - BMC Biol VL - 11 UR - https://doi.org/10.1186/1741-7007-11-59 DO - 10.1186/1741-7007-11-59 ID - Kornienko2013 ER - TY - JOUR AU - Liu, J. AU - Wang, H. AU - Chua, N. H. PY - 2015 DA - 2015// TI - Long noncoding RNA transcriptome of plants JO - Plant Biotechnol J ID - Liu2015 ER - TY - JOUR AU - Rinn, J. L. AU - Kertesz, M. AU - Wang, J. K. AU - Squazzo, S. L. AU - Xu, X. AU - Brugmann, S. A. PY - 2007 DA - 2007// TI - Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs JO - Cell VL - 129 UR - https://doi.org/10.1016/j.cell.2007.05.022 DO - 10.1016/j.cell.2007.05.022 ID - Rinn2007 ER - TY - JOUR AU - Zhao, J. AU - Sun, B. K. AU - Erwin, J. A. AU - Song, J. J. AU - Lee, J. T. PY - 2008 DA - 2008// TI - Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome JO - Science VL - 322 UR - https://doi.org/10.1126/science.1163045 DO - 10.1126/science.1163045 ID - Zhao2008 ER - TY - JOUR AU - Sleutels, F. AU - Zwart, R. AU - Barlow, D. P. PY - 2002 DA - 2002// TI - The non-coding Air RNA is required for silencing autosomal imprinted genes JO - Nature VL - 415 UR - https://doi.org/10.1038/415810a DO - 10.1038/415810a ID - Sleutels2002 ER - TY - JOUR AU - Derrien, T. AU - Johnson, R. AU - Bussotti, G. AU - Tanzer, A. AU - Djebali, S. AU - Tilgner, H. PY - 2012 DA - 2012// TI - The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.132159.111 DO - 10.1101/gr.132159.111 ID - Derrien2012 ER - TY - JOUR AU - Birney, E. AU - Stamatoyannopoulos, J. A. AU - Dutta, A. AU - Guigo, R. AU - Gingeras, T. R. AU - Margulies, E. H. PY - 2007 DA - 2007// TI - Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project JO - Nature VL - 447 UR - https://doi.org/10.1038/nature05874 DO - 10.1038/nature05874 ID - Birney2007 ER - TY - JOUR AU - Wierzbicki, A. T. PY - 2012 DA - 2012// TI - The role of long non-coding RNA in transcriptional gene silencing JO - Curr Opin Plant Biol VL - 15 UR - https://doi.org/10.1016/j.pbi.2012.08.008 DO - 10.1016/j.pbi.2012.08.008 ID - Wierzbicki2012 ER - TY - JOUR AU - Lucia, F. AU - Dean, C. PY - 2011 DA - 2011// TI - Long non-coding RNAs and chromatin regulation JO - Curr Opin Plant Biol VL - 14 UR - https://doi.org/10.1016/j.pbi.2010.11.006 DO - 10.1016/j.pbi.2010.11.006 ID - Lucia2011 ER - TY - JOUR AU - Heo, J. B. AU - Sung, S. PY - 2011 DA - 2011// TI - Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA JO - Science VL - 331 UR - https://doi.org/10.1126/science.1197349 DO - 10.1126/science.1197349 ID - Heo2011 ER - TY - JOUR AU - Swiezewski, S. AU - Liu, F. Q. AU - Magusin, A. AU - Dean, C. PY - 2009 DA - 2009// TI - Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target JO - Nature VL - 462 UR - https://doi.org/10.1038/nature08618 DO - 10.1038/nature08618 ID - Swiezewski2009 ER - TY - JOUR AU - Franco-Zorrilla, J. M. AU - Valli, A. AU - Todesco, M. AU - Mateos, I. AU - Puga, M. I. AU - Rubio-Somoza, I. PY - 2007 DA - 2007// TI - Target mimicry provides a new mechanism for regulation of microRNA activity JO - Nat Genet VL - 39 UR - https://doi.org/10.1038/ng2079 DO - 10.1038/ng2079 ID - Franco-Zorrilla2007 ER - TY - JOUR AU - Shin, H. AU - Shin, H. S. AU - Chen, R. AU - Harrison, M. J. PY - 2006 DA - 2006// TI - Loss of At4 function impacts phosphate distribution between the roots and the shoots during phosphate starvation JO - Plant J VL - 45 UR - https://doi.org/10.1111/j.1365-313X.2005.02629.x DO - 10.1111/j.1365-313X.2005.02629.x ID - Shin2006 ER - TY - JOUR AU - MacIntosh, G. C. AU - Wilkerson, C. AU - Green, P. J. PY - 2001 DA - 2001// TI - Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs JO - Plant Physiol VL - 127 UR - https://doi.org/10.1104/pp.010501 DO - 10.1104/pp.010501 ID - MacIntosh2001 ER - TY - JOUR AU - Ben Amor, B. AU - Wirth, S. AU - Merchan, F. AU - Laporte, P. AU - d’Aubenton-Carafa, Y. AU - Hirsch, J. PY - 2009 DA - 2009// TI - Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.080275.108 DO - 10.1101/gr.080275.108 ID - Ben Amor2009 ER - TY - JOUR AU - Liu, J. AU - Jung, C. AU - Xu, J. AU - Wang, H. AU - Deng, S. L. AU - Bernad, L. PY - 2012 DA - 2012// TI - Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis JO - Plant Cell VL - 24 UR - https://doi.org/10.1105/tpc.112.102855 DO - 10.1105/tpc.112.102855 ID - Liu2012 ER - TY - JOUR AU - Matsui, A. AU - Ishida, J. AU - Morosawa, T. AU - Mochizuki, Y. AU - Kaminuma, E. AU - Endo, T. A. PY - 2008 DA - 2008// TI - Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array JO - Plant Cell Physiol VL - 49 UR - https://doi.org/10.1093/pcp/pcn101 DO - 10.1093/pcp/pcn101 ID - Matsui2008 ER - TY - JOUR AU - Ding, J. H. AU - Lu, Q. AU - Ouyang, Y. D. AU - Mao, H. L. AU - Zhang, P. B. AU - Yao, J. L. PY - 2012 DA - 2012// TI - A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice JO - P Natl Acad Sci USA VL - 109 UR - https://doi.org/10.1073/pnas.1121374109 DO - 10.1073/pnas.1121374109 ID - Ding2012 ER - TY - JOUR AU - Boerner, S. AU - McGinnis, K. M. PY - 2012 DA - 2012// TI - Computational identification and functional predictions of long noncoding RNA in Zea mays JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0043047 DO - 10.1371/journal.pone.0043047 ID - Boerner2012 ER - TY - JOUR AU - Li, L. AU - Eichten, S. R. AU - Shimizu, R. AU - Petsch, K. AU - Yeh, C. T. AU - Wu, W. PY - 2014 DA - 2014// TI - Genome-wide discovery and characterization of maize long non-coding RNAs JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/gb-2014-15-2-r40 DO - 10.1186/gb-2014-15-2-r40 ID - Li2014 ER - TY - JOUR AU - Zhang, W. AU - Han, Z. X. AU - Guo, Q. L. AU - Liu, Y. AU - Zheng, Y. X. AU - Wu, F. L. PY - 2014 DA - 2014// TI - Identification of maize long non-coding RNAs responsive to drought stress JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0098958 DO - 10.1371/journal.pone.0098958 ID - Zhang2014 ER - TY - JOUR AU - Young, N. D. AU - Debelle, F. AU - Oldroyd, G. E. D. AU - Geurts, R. AU - Cannon, S. B. AU - Udvardi, M. K. PY - 2011 DA - 2011// TI - The Medicago genome provides insight into the evolution of rhizobial symbioses JO - Nature VL - 480 ID - Young2011 ER - TY - JOUR AU - Branca, A. AU - Paape, T. D. AU - Zhou, P. AU - Briskine, R. AU - Farmer, A. D. AU - Mudge, J. PY - 2011 DA - 2011// TI - Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula JO - P Natl Acad Sci USA VL - 108 UR - https://doi.org/10.1073/pnas.1104032108 DO - 10.1073/pnas.1104032108 ID - Branca2011 ER - TY - JOUR AU - Benedito, V. A. AU - Torres-Jerez, I. AU - Murray, J. D. AU - Andriankaja, A. AU - Allen, S. AU - Kakar, K. PY - 2008 DA - 2008// TI - A gene expression atlas of the model legume Medicago truncatula JO - Plant J VL - 55 UR - https://doi.org/10.1111/j.1365-313X.2008.03519.x DO - 10.1111/j.1365-313X.2008.03519.x ID - Benedito2008 ER - TY - JOUR AU - Campalans, A. AU - Kondorosi, A. AU - Crespi, M. PY - 2004 DA - 2004// TI - Enod40, a short open reading frame-containing mRNA, induces cytoplasmic localization of a nuclear RNA binding protein in Medicago truncatula JO - Plant Cell VL - 16 UR - https://doi.org/10.1105/tpc.019406 DO - 10.1105/tpc.019406 ID - Campalans2004 ER - TY - JOUR AU - Burleigh, S. H. AU - Harrison, M. J. PY - 1997 DA - 1997// TI - A novel gene whose expression in Medicago truncatula roots is suppressed in response to colonization by vesicular-arbuscular mycorrhizal (VAM) fungi and to phosphate nutrition JO - Plant Mol Biol VL - 34 UR - https://doi.org/10.1023/A:1005841119665 DO - 10.1023/A:1005841119665 ID - Burleigh1997 ER - TY - JOUR AU - Wen, J. AU - Parker, B. J. AU - Weiller, G. F. PY - 2007 DA - 2007// TI - In Silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula JO - In Silico Biol VL - 7 ID - Wen2007 ER - TY - JOUR AU - Ewing, B. AU - Green, P. PY - 1998 DA - 1998// TI - Base-calling of automated sequencer traces using phred JO - II Error probabilities Genome Res VL - 8 ID - Ewing1998 ER - TY - JOUR AU - Trapnell, C. AU - Pachter, L. AU - Salzberg, S. L. PY - 2009 DA - 2009// TI - TopHat: discovering splice junctions with RNA-Seq JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp120 DO - 10.1093/bioinformatics/btp120 ID - Trapnell2009 ER - TY - JOUR AU - Trapnell, C. AU - Williams, B. A. AU - Pertea, G. AU - Mortazavi, A. AU - Kwan, G. AU - Baren, M. J. PY - 2010 DA - 2010// TI - Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation JO - Nat Biotechnol VL - 28 UR - https://doi.org/10.1038/nbt.1621 DO - 10.1038/nbt.1621 ID - Trapnell2010 ER - TY - JOUR AU - Wang, H. AU - Chung, P. J. AU - Liu, J. AU - Jang, I. C. AU - Kean, M. J. AU - Xu, J. PY - 2014 DA - 2014// TI - Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.165555.113 DO - 10.1101/gr.165555.113 ID - Wang2014 ER - TY - JOUR AU - Xie, C. Y. AU - Yuan, J. AU - Li, H. AU - Li, M. AU - Zhao, G. G. AU - Bu, D. C. PY - 2014 DA - 2014// TI - NONCODEv4: exploring the world of long non-coding RNA genes JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1222 DO - 10.1093/nar/gkt1222 ID - Xie2014 ER - TY - JOUR AU - Mercer, T. R. AU - Dinger, M. E. AU - Mattick, J. S. PY - 2009 DA - 2009// TI - Long non-coding RNAs: insights into functions JO - Nat Rev Genet VL - 10 UR - https://doi.org/10.1038/nrg2521 DO - 10.1038/nrg2521 ID - Mercer2009 ER - TY - JOUR AU - Yu, W. Q. AU - Gius, D. AU - Onyango, P. AU - Muldoon-Jacobs, K. AU - Karp, J. AU - Feinberg, A. P. PY - 2008 DA - 2008// TI - Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA JO - Nature VL - 451 UR - https://doi.org/10.1038/nature06468 DO - 10.1038/nature06468 ID - Yu2008 ER - TY - JOUR AU - Pauli, A. AU - Valen, E. AU - Lin, M. F. AU - Garber, M. AU - Vastenhouw, N. L. AU - Levin, J. Z. PY - 2012 DA - 2012// TI - Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.133009.111 DO - 10.1101/gr.133009.111 ID - Pauli2012 ER - TY - JOUR AU - Studer, A. J. AU - Gandin, A. AU - Kolbe, A. R. AU - Wang, L. AU - Cousins, A. B. AU - Brutnell, T. P. PY - 2014 DA - 2014// TI - A limited role for carbonic anhydrase in C4 photosynthesis as revealed by a ca1ca2 double mutant in maize JO - Plant Physiol VL - 165 UR - https://doi.org/10.1104/pp.114.237602 DO - 10.1104/pp.114.237602 ID - Studer2014 ER - TY - JOUR AU - Xiong, L. M. AU - Schumaker, K. S. AU - Zhu, J. K. PY - 2002 DA - 2002// TI - Cell signaling during cold, drought, and salt stress JO - Plant Cell VL - 14 UR - https://doi.org/10.1105/tpc.010278 DO - 10.1105/tpc.010278 ID - Xiong2002 ER - TY - JOUR AU - Mittler, R. PY - 2002 DA - 2002// TI - Oxidative stress, antioxidants and stress tolerance JO - Trends Plant Sci VL - 7 UR - https://doi.org/10.1016/S1360-1385(02)02312-9 DO - 10.1016/S1360-1385(02)02312-9 ID - Mittler2002 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 - Yamaguchi, T. AU - Aharon, G. S. AU - Sottosanto, J. B. AU - Blumwald, E. PY - 2005 DA - 2005// TI - Vacuolar Na+/H+ antiporter cation selectivity is regulated by calmodulin from within the vacuole in a Ca2+- and pH-dependent manner JO - P Natl Acad Sci USA VL - 102 UR - https://doi.org/10.1073/pnas.0504437102 DO - 10.1073/pnas.0504437102 ID - Yamaguchi2005 ER - TY - JOUR AU - Collins, F. S. AU - Lander, E. S. AU - Rogers, J. AU - Waterston, R. H. AU - Conso, I. H. G. S. PY - 2004 DA - 2004// TI - Finishing the euchromatic sequence of the human genome JO - Nature VL - 431 UR - https://doi.org/10.1038/nature03001 DO - 10.1038/nature03001 ID - Collins2004 ER - TY - JOUR AU - Carninci, P. AU - Kasukawa, T. AU - Katayama, S. AU - Gough, J. AU - Frith, M. C. AU - Maeda, N. PY - 2005 DA - 2005// TI - The transcriptional landscape of the mammalian genome JO - Science VL - 309 UR - https://doi.org/10.1126/science.1112014 DO - 10.1126/science.1112014 ID - Carninci2005 ER - TY - JOUR AU - Wang, T. Z. AU - Zhang, J. L. AU - Tian, Q. Y. AU - Zhao, M. G. AU - Zhang, W. H. PY - 2013 DA - 2013// TI - A Medicago truncatula EF-hand family gene, MtCaMP1, is involved in drought and salt stress tolerance JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0058952 DO - 10.1371/journal.pone.0058952 ID - Wang2013 ER - TY - JOUR AU - Zelicourt, A. AU - Diet, A. AU - Marion, J. AU - Laffont, C. AU - Ariel, F. AU - Moison, M. L. PY - 2012 DA - 2012// TI - Dual involvement of a Medicago truncatula NAC transcription factor in root abiotic stress response and symbiotic nodule senescence JO - Plant J VL - 70 UR - https://doi.org/10.1111/j.1365-313X.2011.04859.x DO - 10.1111/j.1365-313X.2011.04859.x ID - Zelicourt2012 ER - TY - JOUR AU - Xie, C. AU - Zhang, R. X. AU - Qu, Y. T. AU - Miao, Z. Y. AU - Zhang, Y. Q. AU - Shen, X. Y. PY - 2012 DA - 2012// TI - Overexpression of MtCAS31 enhances drought tolerance in transgenic Arabidopsis by reducing stomatal density JO - New Phytol VL - 195 UR - https://doi.org/10.1111/j.1469-8137.2012.04136.x DO - 10.1111/j.1469-8137.2012.04136.x ID - Xie2012 ER - TY - JOUR AU - Ge, L. AU - Peng, J. AU - Berbel, A. AU - Madueno, F. AU - Chen, R. PY - 2014 DA - 2014// TI - Regulation of compound leaf development by PHANTASTICA in Medicago truncatula JO - Plant Physiol VL - 164 UR - https://doi.org/10.1104/pp.113.229914 DO - 10.1104/pp.113.229914 ID - Ge2014 ER - TY - JOUR AU - Lelandais-Briere, C. AU - Naya, L. AU - Sallet, E. AU - Calenge, F. AU - Frugier, F. AU - Hartmann, C. PY - 2009 DA - 2009// TI - Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules JO - Plant Cell VL - 21 UR - https://doi.org/10.1105/tpc.109.068130 DO - 10.1105/tpc.109.068130 ID - Lelandais-Briere2009 ER - TY - JOUR AU - Wang, T. Z. AU - Chen, L. AU - Zhao, M. G. AU - Tian, Q. Y. AU - Zhang, W. H. PY - 2011 DA - 2011// TI - Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-367 DO - 10.1186/1471-2164-12-367 ID - Wang2011 ER - TY - JOUR AU - Zhou, Z. S. AU - Zeng, H. Q. AU - Liu, Z. P. AU - Yang, Z. M. PY - 2012 DA - 2012// TI - Genome-wide identification of Medicago truncatula microRNAs and their targets reveals their differential regulation by heavy metal JO - Plant Cell Environ VL - 35 UR - https://doi.org/10.1111/j.1365-3040.2011.02418.x DO - 10.1111/j.1365-3040.2011.02418.x ID - Zhou2012 ER - TY - JOUR AU - Shuai, P. AU - Liang, D. AU - Tang, S. AU - Zhang, Z. AU - Ye, C. Y. AU - Su, Y. PY - 2014 DA - 2014// TI - Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa JO - J Exp Bot VL - 65 UR - https://doi.org/10.1093/jxb/eru256 DO - 10.1093/jxb/eru256 ID - Shuai2014 ER - TY - JOUR AU - Liu, Q. AU - Kasuga, M. AU - Sakuma, Y. AU - Abe, H. AU - Miura, S. AU - Yamaguchi-Shinozaki, K. PY - 1998 DA - 1998// TI - Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis JO - Plant Cell VL - 10 UR - https://doi.org/10.1105/tpc.10.8.1391 DO - 10.1105/tpc.10.8.1391 ID - Liu1998 ER - TY - JOUR AU - Jaglo-Ottosen, K. R. AU - Gilmour, S. J. AU - Zarka, D. G. AU - Schabenberger, O. AU - Thomashow, M. F. PY - 1998 DA - 1998// TI - Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance JO - Science VL - 280 UR - https://doi.org/10.1126/science.280.5360.104 DO - 10.1126/science.280.5360.104 ID - Jaglo-Ottosen1998 ER - TY - JOUR AU - Liu, J. P. AU - Zhu, J. K. PY - 1998 DA - 1998// TI - A calcium sensor homolog required for plant salt tolerance JO - Science VL - 280 UR - https://doi.org/10.1126/science.280.5371.1943 DO - 10.1126/science.280.5371.1943 ID - Liu1998 ER - TY - JOUR AU - Qiu, Q. S. AU - Guo, Y. AU - Dietrich, M. A. AU - Schumaker, K. S. AU - Zhu, J. K. PY - 2002 DA - 2002// TI - Regulation of SOS1, a plasma membrane Na+/H+ exchanger in Arabidopsis thaliana, by SOS2 and SOS3 JO - P Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.122224699 DO - 10.1073/pnas.122224699 ID - Qiu2002 ER - TY - JOUR AU - Liu, R. AU - Zhu, J. K. PY - 2014 DA - 2014// TI - Non-coding RNAs as potent tools for crop improvement JO - Natl Sci Rev VL - 1 UR - https://doi.org/10.1093/nsr/nwu006 DO - 10.1093/nsr/nwu006 ID - Liu2014 ER - TY - JOUR AU - Zhu, Q. H. AU - Stephen, S. AU - Taylor, J. AU - Helliwell, C. A. AU - Wang, M. B. PY - 2014 DA - 2014// TI - Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana JO - New Phytol VL - 201 UR - https://doi.org/10.1111/nph.12537 DO - 10.1111/nph.12537 ID - Zhu2014 ER - TY - JOUR AU - Zhang, L. M. AU - Liu, X. G. AU - Qu, X. N. AU - Yu, Y. AU - Han, S. P. AU - Dou, Y. PY - 2013 DA - 2013// TI - Early transcriptomic adaptation to Na2CO3 stress altered the expression of a quarter of the total genes in the maize genome and exhibited shared and distinctive profiles with NaCl and high pH stresses JO - J Integr Plant Biol VL - 55 UR - https://doi.org/10.1111/jipb.12100 DO - 10.1111/jipb.12100 ID - Zhang2013 ER - TY - JOUR AU - Borodina, T. AU - Adjaye, J. AU - Sultan, M. PY - 2011 DA - 2011// TI - A strand-specific library preparation protocol for RNA sequencing JO - Methods Enzymol VL - 500 ID - Borodina2011 ER - TY - JOUR AU - Kong, L. AU - Zhang, Y. AU - Ye, Z. Q. AU - Liu, X. Q. AU - Zhao, S. Q. AU - Wei, L. PY - 2007 DA - 2007// TI - CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm391 DO - 10.1093/nar/gkm391 ID - Kong2007 ER - TY - JOUR AU - Anders, S. AU - Huber, W. PY - 2010 DA - 2010// TI - Differential expression analysis for sequence count data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-10-r106 DO - 10.1186/gb-2010-11-10-r106 ID - Anders2010 ER - TY - JOUR AU - Robinson, J. T. AU - Thorvaldsdottir, H. AU - Winckler, W. AU - Guttman, M. AU - Lander, E. S. AU - Getz, G. PY - 2011 DA - 2011// TI - Integrative genomics viewer JO - Nat Biotechnol VL - 29 UR - https://doi.org/10.1038/nbt.1754 DO - 10.1038/nbt.1754 ID - Robinson2011 ER - TY - JOUR AU - Liao, Q. AU - Liu, C. N. AU - Yuan, X. Y. AU - Kang, S. L. AU - Miao, R. Y. AU - Xiao, H. PY - 2011 DA - 2011// TI - Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1348 DO - 10.1093/nar/gkq1348 ID - Liao2011 ER - TY - JOUR AU - Ashburner, M. AU - Ball, C. A. AU - Blake, J. A. AU - Botstein, D. AU - Butler, H. AU - Cherry, J. M. PY - 2000 DA - 2000// TI - Gene ontology: tool for the unification of biology JO - Nat Genet VL - 25 UR - https://doi.org/10.1038/75556 DO - 10.1038/75556 ID - Ashburner2000 ER - TY - JOUR AU - Conesa, A. AU - Gotz, S. AU - Garcia-Gomez, J. M. AU - Terol, J. AU - Talon, M. AU - Robles, M. PY - 2005 DA - 2005// TI - Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti610 DO - 10.1093/bioinformatics/bti610 ID - Conesa2005 ER - TY - JOUR AU - Shannon, P. AU - Markiel, A. AU - Ozier, O. AU - Baliga, N. S. AU - Wang, J. T. AU - Ramage, D. PY - 2003 DA - 2003// TI - Cytoscape: a software environment for integrated models of biomolecular interaction networks JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1239303 DO - 10.1101/gr.1239303 ID - Shannon2003 ER -