TY - JOUR AU - Voss, T. C. AU - Hager, G. L. PY - 2014 DA - 2014// TI - Dynamic regulation of transcriptional states by chromatin and transcription factors JO - Nat Rev Genet. VL - 15 UR - https://doi.org/10.1038/nrg3623 DO - 10.1038/nrg3623 ID - Voss2014 ER - TY - JOUR AU - Spitz, F. AU - Furlong, E. E. M. PY - 2012 DA - 2012// TI - Transcription factors: from enhancer binding to developmental control JO - Nat Rev Genet. VL - 13 UR - https://doi.org/10.1038/nrg3207 DO - 10.1038/nrg3207 ID - Spitz2012 ER - TY - JOUR AU - Brkljacic, J. AU - Grotewold, E. PY - 1860 DA - 1860// TI - Combinatorial control of plant gene expression JO - Biochim Biophys Acta Gene Regul Mech VL - 2017 ID - Brkljacic1860 ER - TY - JOUR AU - Sexton, B. S. AU - Druliner, B. R. AU - Vera, D. L. AU - Avey, D. AU - Zhu, F. AU - Dennis, J. H. PY - 2016 DA - 2016// TI - Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response JO - Oncotarget. VL - 7 UR - https://doi.org/10.18632/oncotarget.6841 DO - 10.18632/oncotarget.6841 ID - Sexton2016 ER - TY - JOUR AU - Birney, E. AU - Stamatoyannopoulos, J. A. AU - Dutta, A. AU - Guigó, 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 - Yue, F. AU - Cheng, Y. AU - Breschi, A. AU - Vierstra, J. AU - Wu, W. AU - Ryba, T. PY - 2014 DA - 2014// TI - A comparative encyclopedia of DNA elements in the mouse genome JO - Nature. VL - 515 UR - https://doi.org/10.1038/nature13992 DO - 10.1038/nature13992 ID - Yue2014 ER - TY - JOUR AU - Maher, K. A. AU - Bajic, M. AU - Kajala, K. AU - Reynoso, M. AU - Pauluzzi, G. AU - West, D. A. PY - 2018 DA - 2018// TI - Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules JO - Plant Cell VL - 30 UR - https://doi.org/10.1105/tpc.17.00581 DO - 10.1105/tpc.17.00581 ID - Maher2018 ER - TY - JOUR AU - Zhang, W. AU - Wu, Y. AU - Schnable, J. C. AU - Zeng, Z. AU - Freeling, M. AU - Crawford, G. E. PY - 2012 DA - 2012// TI - High-resolution mapping of open chromatin in the rice genome JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.131342.111 DO - 10.1101/gr.131342.111 ID - Zhang2012 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 - 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 - STD TI - Lu Z, Marand AP, Ricci WA, Ethridge CL, Zhang X, Schmitz RJ. The prevalence, evolution and chromatin signatures of plant regulatory elements. Nat Plants. 2019; Available from: https://doi.org/10.1038/s41477-019-0548-z. ID - ref10 ER - TY - JOUR AU - Lane, A. K. AU - Niederhuth, C. E. AU - Ji, L. AU - Schmitz, R. J. PY - 2014 DA - 2014// TI - pENCODE: a plant encyclopedia of DNA elements JO - Annu Rev Genet VL - 48 UR - https://doi.org/10.1146/annurev-genet-120213-092443 DO - 10.1146/annurev-genet-120213-092443 ID - Lane2014 ER - TY - JOUR AU - Buenrostro, J. D. AU - Giresi, P. G. AU - Zaba, L. C. AU - Chang, H. Y. AU - Greenleaf, W. J. PY - 2013 DA - 2013// TI - Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position JO - Nat Methods VL - 10 UR - https://doi.org/10.1038/nmeth.2688 DO - 10.1038/nmeth.2688 ID - Buenrostro2013 ER - TY - JOUR AU - Boyle, A. P. AU - Song, L. AU - Lee, B. -. K. AU - London, D. AU - Keefe, D. AU - Birney, E. PY - 2011 DA - 2011// TI - High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.112656.110 DO - 10.1101/gr.112656.110 ID - Boyle2011 ER - TY - JOUR AU - Henikoff, J. G. AU - Belsky, J. A. AU - Krassovsky, K. AU - MacAlpine, D. M. AU - Henikoff, S. PY - 2011 DA - 2011// TI - Epigenome characterization at single base-pair resolution JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1110731108 DO - 10.1073/pnas.1110731108 ID - Henikoff2011 ER - TY - JOUR AU - Iwafuchi-Doi, M. AU - Donahue, G. AU - Kakumanu, A. AU - Watts, J. A. AU - Mahony, S. AU - Pugh, B. F. PY - 2016 DA - 2016// TI - The Pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation JO - Mol Cell VL - 62 UR - https://doi.org/10.1016/j.molcel.2016.03.001 DO - 10.1016/j.molcel.2016.03.001 ID - Iwafuchi-Doi2016 ER - TY - JOUR AU - Oka, R. AU - Zicola, J. AU - Weber, B. AU - Anderson, S. N. AU - Hodgman, C. AU - Gent, J. I. PY - 2017 DA - 2017// TI - Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize JO - Genome Biol VL - 18 UR - https://doi.org/10.1186/s13059-017-1273-4 DO - 10.1186/s13059-017-1273-4 ID - Oka2017 ER - TY - JOUR AU - Rodgers-Melnick, E. AU - Vera, D. L. AU - Bass, H. W. AU - Buckler, E. S. PY - 2016 DA - 2016// TI - Open chromatin reveals the functional maize genome JO - Proc Natl Acad Sci U S A VL - 113 UR - https://doi.org/10.1073/pnas.1525244113 DO - 10.1073/pnas.1525244113 ID - Rodgers-Melnick2016 ER - TY - JOUR AU - Sullivan, A. M. AU - Arsovski, A. A. AU - Lempe, J. AU - Bubb, K. L. AU - Weirauch, M. T. AU - Sabo, P. J. PY - 2014 DA - 2014// TI - Mapping and dynamics of regulatory DNA and transcription factor networks in a. thaliana JO - Cell Rep VL - 8 UR - https://doi.org/10.1016/j.celrep.2014.08.019 DO - 10.1016/j.celrep.2014.08.019 ID - Sullivan2014 ER - TY - JOUR AU - Vera, D. L. AU - Madzima, T. F. AU - Labonne, J. D. AU - Alam, M. P. AU - Hoffman, G. G. AU - Girimurugan, S. B. PY - 2014 DA - 2014// TI - Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize JO - Plant Cell VL - 26 UR - https://doi.org/10.1105/tpc.114.130609 DO - 10.1105/tpc.114.130609 ID - Vera2014 ER - TY - JOUR AU - Zhao, H. AU - Zhang, W. AU - Zhang, T. AU - Lin, Y. AU - Hu, Y. AU - Fang, C. PY - 2020 DA - 2020// TI - Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana JO - Genome Biol VL - 21 UR - https://doi.org/10.1186/s13059-020-1927-5 DO - 10.1186/s13059-020-1927-5 ID - Zhao2020 ER - TY - JOUR AU - Schaub, M. A. AU - Boyle, A. P. AU - Kundaje, A. AU - Batzoglou, S. AU - Snyder, M. PY - 2012 DA - 2012// TI - Linking disease associations with regulatory information in the human genome JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.136127.111 DO - 10.1101/gr.136127.111 ID - Schaub2012 ER - TY - JOUR AU - Maurano, M. T. AU - Humbert, R. AU - Rynes, E. AU - Thurman, R. E. AU - Haugen, E. AU - Wang, H. PY - 2012 DA - 2012// TI - Systematic localization of common disease-associated variation in regulatory DNA JO - Science. VL - 337 UR - https://doi.org/10.1126/science.1222794 DO - 10.1126/science.1222794 ID - Maurano2012 ER - TY - JOUR AU - Sandmann, T. AU - Girardot, C. AU - Brehme, M. AU - Tongprasit, W. AU - Stolc, V. AU - Furlong, E. E. M. PY - 2007 DA - 2007// TI - A core transcriptional network for early mesoderm development in Drosophila melanogaster JO - Genes Dev VL - 21 UR - https://doi.org/10.1101/gad.1509007 DO - 10.1101/gad.1509007 ID - Sandmann2007 ER - TY - JOUR AU - Borok, M. J. AU - Tran, D. A. AU - Ho, M. C. W. AU - Drewell, R. A. PY - 2010 DA - 2010// TI - Dissecting the regulatory switches of development: lessons from enhancer evolution in Drosophila JO - Development. VL - 137 UR - https://doi.org/10.1242/dev.036160 DO - 10.1242/dev.036160 ID - Borok2010 ER - TY - JOUR AU - Hirsch, N. AU - Eshel, R. AU - Bar Yaacov, R. AU - Shahar, T. AU - Shmulevich, F. AU - Dahan, I. PY - 2018 DA - 2018// TI - Unraveling the transcriptional regulation of TWIST1 in limb development JO - PLoS Genet VL - 14 UR - https://doi.org/10.1371/journal.pgen.1007738 DO - 10.1371/journal.pgen.1007738 ID - Hirsch2018 ER - TY - JOUR AU - Weber, B. AU - Zicola, J. AU - Oka, R. AU - Stam, M. PY - 2016 DA - 2016// TI - Plant enhancers: a call for discovery JO - Trends Plant Sci VL - 21 UR - https://doi.org/10.1016/j.tplants.2016.07.013 DO - 10.1016/j.tplants.2016.07.013 ID - Weber2016 ER - TY - JOUR AU - Clark, R. M. AU - Wagler, T. N. AU - Quijada, P. AU - Doebley, J. PY - 2006 DA - 2006// TI - A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture JO - Nat Genet VL - 38 UR - https://doi.org/10.1038/ng1784 DO - 10.1038/ng1784 ID - Clark2006 ER - TY - JOUR AU - Studer, A. AU - Zhao, Q. AU - Ross-Ibarra, J. AU - Doebley, J. PY - 2011 DA - 2011// TI - Identification of a functional transposon insertion in the maize domestication gene tb1 JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.942 DO - 10.1038/ng.942 ID - Studer2011 ER - TY - JOUR AU - Wills, D. M. AU - Whipple, C. J. AU - Takuno, S. AU - Kursel, L. E. AU - Shannon, L. M. AU - Ross-Ibarra, J. PY - 2013 DA - 2013// TI - From many, one: genetic control of prolificacy during maize domestication JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003604 DO - 10.1371/journal.pgen.1003604 ID - Wills2013 ER - TY - JOUR AU - Lu, Z. AU - Hofmeister, B. T. AU - Vollmers, C. AU - DuBois, R. M. AU - Schmitz, R. J. PY - 2017 DA - 2017// TI - Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1179 DO - 10.1093/nar/gkw1179 ID - Lu2017 ER - TY - STD TI - Ricci WA, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, et al. Widespread long-range cis-regulatory elements in the maize genome. Nat Plants. 2019; Available from: https://doi.org/10.1038/s41477-019-0547-0. ID - ref31 ER - TY - JOUR AU - Eveland, A. L. AU - Goldshmidt, A. AU - Pautler, M. AU - Morohashi, K. AU - Liseron-Monfils, C. AU - Lewis, M. W. PY - 2014 DA - 2014// TI - Regulatory modules controlling maize inflorescence architecture JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.166397.113 DO - 10.1101/gr.166397.113 ID - Eveland2014 ER - TY - JOUR AU - Bommert, P. AU - Nagasawa, N. S. AU - Jackson, D. PY - 2013 DA - 2013// TI - Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus JO - Nat Genet VL - 45 UR - https://doi.org/10.1038/ng.2534 DO - 10.1038/ng.2534 ID - Bommert2013 ER - TY - JOUR AU - Turpin, Z. M. AU - Vera, D. L. AU - Savadel, S. D. AU - Lung, P. -. Y. AU - Wear, E. E. AU - Mickelson-Young, L. PY - 2018 DA - 2018// TI - Chromatin structure profile data from DNS-seq: differential nuclease sensitivity mapping of four reference tissues of B73 maize (Zea mays L) JO - Data Brief VL - 20 UR - https://doi.org/10.1016/j.dib.2018.08.015 DO - 10.1016/j.dib.2018.08.015 ID - Turpin2018 ER - TY - JOUR AU - Pautler, M. AU - Eveland, A. L. AU - LaRue, T. AU - Yang, F. AU - Weeks, R. AU - Lunde, C. PY - 2015 DA - 2015// TI - FASCIATED EAR4 encodes a bZIP transcription factor that regulates shoot meristem size in maize JO - Plant Cell VL - 27 UR - https://doi.org/10.1105/tpc.114.132506 DO - 10.1105/tpc.114.132506 ID - Pautler2015 ER - TY - JOUR AU - Bolduc, N. AU - Yilmaz, A. AU - Mejia-Guerra, M. K. AU - Morohashi, K. AU - O’Connor, D. AU - Grotewold, E. PY - 2012 DA - 2012// TI - Unraveling the KNOTTED1 regulatory network in maize meristems JO - Genes Dev VL - 26 UR - https://doi.org/10.1101/gad.193433.112 DO - 10.1101/gad.193433.112 ID - Bolduc2012 ER - TY - JOUR AU - Pass, D. A. AU - Sornay, E. AU - Marchbank, A. AU - Crawford, M. R. AU - Paszkiewicz, K. AU - Kent, N. A. PY - 2017 DA - 2017// TI - Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis JO - PLoS Genet VL - 13 UR - https://doi.org/10.1371/journal.pgen.1006988 DO - 10.1371/journal.pgen.1006988 ID - Pass2017 ER - TY - STD TI - Girimurugan SB, Liu Y, Lung PY, Vera D, Dennis J. iSeg: an efficient algorithm for segmentation of genomic and epigenomic data. bioRxiv. biorxiv.org; 2017; Available from: http://www.biorxiv.org/content/early/2017/09/05/184515.abstract. UR - http://www.biorxiv.org/content/early/2017/09/05/184515.abstract ID - ref38 ER - TY - JOUR AU - Baucom, R. S. AU - Estill, J. C. AU - Chaparro, C. AU - Upshaw, N. AU - Jogi, A. AU - Deragon, J. -. M. PY - 2009 DA - 2009// TI - Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000732 DO - 10.1371/journal.pgen.1000732 ID - Baucom2009 ER - TY - STD TI - Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O’Connor CH, et al. Transposable elements contribute to dynamic genome content in maize. Plant J. 2019; Available from: https://doi.org/10.1111/tpj.14489. ID - ref40 ER - TY - STD TI - Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, et al. Improved maize reference genome with single-molecule technologies. Nature. Nature Research; 2017 [cited 2017 Jun 12]; Available from: https://doi.org/10.1038/nature22971. ID - ref41 ER - TY - STD TI - Zhao H, Zhang W, Chen L, Wang L, Marand AP, Wu Y, et al. Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome. Plant Physiology. 2018. p. 2789–803. Available from: https://doi.org/10.1104/pp.17.01467. ID - ref42 ER - TY - JOUR AU - Warman, C. AU - Panda, K. AU - Vejlupkova, Z. AU - Hokin, S. AU - Unger-Wallace, E. AU - Cole, R. A. PY - 2020 DA - 2020// TI - High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements JO - PLoS Genet VL - 16 UR - https://doi.org/10.1371/journal.pgen.1008462 DO - 10.1371/journal.pgen.1008462 ID - Warman2020 ER - TY - JOUR AU - Doebley, J. AU - Stec, A. AU - Hubbard, L. PY - 1997 DA - 1997// TI - The evolution of apical dominance in maize JO - Nature. VL - 386 UR - https://doi.org/10.1038/386485a0 DO - 10.1038/386485a0 ID - Doebley1997 ER - TY - JOUR AU - Danisman, S. PY - 2016 DA - 2016// TI - TCP transcription factors at the Interface between environmental challenges and the Plant’s growth responses JO - Front Plant Sci VL - 7 UR - https://doi.org/10.3389/fpls.2016.01930 DO - 10.3389/fpls.2016.01930 ID - Danisman2016 ER - TY - JOUR AU - Wimalanathan, K. AU - Friedberg, I. AU - Andorf, C. M. AU - Lawrence-Dill, C. J. PY - 2018 DA - 2018// TI - Maize GO annotation—methods, evaluation, and review (maize-GAMER) JO - Plant Direct VL - 2 UR - https://doi.org/10.1002/pld3.52 DO - 10.1002/pld3.52 ID - Wimalanathan2018 ER - TY - JOUR AU - Satoh-Nagasawa, N. AU - Nagasawa, N. AU - Malcomber, S. AU - Sakai, H. AU - Jackson, D. PY - 2006 DA - 2006// TI - A trehalose metabolic enzyme controls inflorescence architecture in maize JO - Nature. VL - 441 UR - https://doi.org/10.1038/nature04725 DO - 10.1038/nature04725 ID - Satoh-Nagasawa2006 ER - TY - STD TI - Bommert P. thick tassel dwarf1 encodes a putative maize ortholog of the Arabidopsis CLAVATA1 leucine-rich repeat receptor-like kinase. Development. 2005. p. 1235–45. Available from: https://doi.org/10.1242/dev.01671. ID - ref48 ER - TY - JOUR AU - Bailey, T. L. PY - 2011 DA - 2011// TI - DREME: motif discovery in transcription factor ChIP-seq data JO - Bioinformatics. VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr261 DO - 10.1093/bioinformatics/btr261 ID - Bailey2011 ER - TY - JOUR AU - Natoli, G. AU - Andrau, J. -. C. PY - 2012 DA - 2012// TI - Noncoding transcription at enhancers: general principles and functional models JO - Annu Rev Genet VL - 46 UR - https://doi.org/10.1146/annurev-genet-110711-155459 DO - 10.1146/annurev-genet-110711-155459 ID - Natoli2012 ER - TY - JOUR AU - Gil, N. AU - Ulitsky, I. PY - 2018 DA - 2018// TI - Production of spliced Long noncoding RNAs specifies regions with increased enhancer activity JO - Cell Syst VL - 7 UR - https://doi.org/10.1016/j.cels.2018.10.009 DO - 10.1016/j.cels.2018.10.009 ID - Gil2018 ER - TY - JOUR AU - Chekanova, J. A. PY - 2015 DA - 2015// TI - Long non-coding RNAs and their functions in plants JO - Curr Opin Plant Biol VL - 27 UR - https://doi.org/10.1016/j.pbi.2015.08.003 DO - 10.1016/j.pbi.2015.08.003 ID - Chekanova2015 ER - TY - JOUR AU - Ariel, F. AU - Jegu, T. AU - Latrasse, D. AU - Romero-Barrios, N. AU - Christ, A. AU - Benhamed, M. PY - 2014 DA - 2014// TI - Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop JO - Mol Cell VL - 55 UR - https://doi.org/10.1016/j.molcel.2014.06.011 DO - 10.1016/j.molcel.2014.06.011 ID - Ariel2014 ER - TY - JOUR AU - Kim, D. -. H. AU - Sung, S. PY - 2017 DA - 2017// TI - Vernalization-triggered intragenic chromatin loop formation by Long noncoding RNAs JO - Dev Cell VL - 40 UR - https://doi.org/10.1016/j.devcel.2016.12.021 DO - 10.1016/j.devcel.2016.12.021 ID - Kim2017 ER - TY - JOUR AU - Böhmdorfer, G. AU - Wierzbicki, A. T. PY - 2015 DA - 2015// TI - Control of chromatin structure by Long noncoding RNA JO - Trends Cell Biol VL - 25 UR - https://doi.org/10.1016/j.tcb.2015.07.002 DO - 10.1016/j.tcb.2015.07.002 ID - Böhmdorfer2015 ER - TY - JOUR AU - Quattro, C. AU - Enrico Pè, M. AU - Bertolini, E. PY - 2017 DA - 2017// TI - Long noncoding RNAs in the model species Brachypodium distachyon JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/s41598-017-11206-z DO - 10.1038/s41598-017-11206-z ID - Quattro2017 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 - Genes Dev VL - 25 UR - https://doi.org/10.1101/gad.17446611 DO - 10.1101/gad.17446611 ID - Cabili2011 ER - TY - JOUR AU - Ulitsky, I. PY - 2016 DA - 2016// TI - Evolution to the rescue: using comparative genomics to understand long non-coding RNAs JO - Nat Rev Genet. VL - 17 UR - https://doi.org/10.1038/nrg.2016.85 DO - 10.1038/nrg.2016.85 ID - Ulitsky2016 ER - TY - JOUR PY - 2012 DA - 2012// TI - An integrated encyclopedia of DNA elements in the human genome JO - Nature. VL - 489 UR - https://doi.org/10.1038/nature11247 DO - 10.1038/nature11247 ID - ref59 ER - TY - JOUR AU - Li, Q. AU - Gent, J. I. AU - Zynda, G. AU - Song, J. AU - Makarevitch, I. AU - Hirsch, C. D. PY - 2015 DA - 2015// TI - RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome JO - Proc Natl Acad Sci U S A VL - 112 UR - https://doi.org/10.1073/pnas.1514680112 DO - 10.1073/pnas.1514680112 ID - Li2015 ER - TY - JOUR AU - Hsu, F. -. M. AU - Yen, M. -. R. AU - Wang, C. -. T. AU - Lin, C. -. Y. AU - Wang, C. -. J. R. AU - Chen, P. -. Y. PY - 2017 DA - 2017// TI - Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize JO - Epigenetics Chromatin VL - 10 UR - https://doi.org/10.1186/s13072-017-0148-y DO - 10.1186/s13072-017-0148-y ID - Hsu2017 ER - TY - JOUR AU - Bukowski, R. AU - Guo, X. AU - Lu, Y. AU - Zou, C. AU - He, B. AU - Rong, Z. PY - 2018 DA - 2018// TI - Construction of the third-generation Zea mays haplotype map JO - Gigascience. VL - 7 UR - https://doi.org/10.1093/gigascience/gix134 DO - 10.1093/gigascience/gix134 ID - Bukowski2018 ER - TY - JOUR AU - Yu, J. AU - Holland, J. B. AU - McMullen, M. D. AU - Buckler, E. S. PY - 2008 DA - 2008// TI - Genetic design and statistical power of nested association mapping in maize JO - Genetics. VL - 178 UR - https://doi.org/10.1534/genetics.107.074245 DO - 10.1534/genetics.107.074245 ID - Yu2008 ER - TY - JOUR AU - Carles, C. C. AU - Lertpiriyapong, K. AU - Reville, K. AU - Fletcher, J. C. PY - 2004 DA - 2004// TI - The ULTRAPETALA1 gene functions early in Arabidopsis development to restrict shoot apical meristem activity and acts through WUSCHEL to regulate floral meristem determinacy JO - Genetics. VL - 167 UR - https://doi.org/10.1534/genetics.104.028787 DO - 10.1534/genetics.104.028787 ID - Carles2004 ER - TY - JOUR AU - Barazesh, S. AU - McSteen, P. PY - 2008 DA - 2008// TI - Barren inflorescence1 functions in organogenesis during vegetative and inflorescence development in maize JO - Genetics. VL - 179 UR - https://doi.org/10.1534/genetics.107.084079 DO - 10.1534/genetics.107.084079 ID - Barazesh2008 ER - TY - JOUR AU - Gallavotti, A. AU - Long, J. A. AU - Stanfield, S. AU - Yang, X. AU - Jackson, D. AU - Vollbrecht, E. PY - 2010 DA - 2010// TI - The control of axillary meristem fate in the maize ramosa pathway JO - Development. VL - 137 UR - https://doi.org/10.1242/dev.051748 DO - 10.1242/dev.051748 ID - Gallavotti2010 ER - TY - JOUR AU - Flint-Garcia, S. A. AU - Thuillet, A. -. C. AU - Yu, J. AU - Pressoir, G. AU - Romero, S. M. AU - Mitchell, S. E. PY - 2005 DA - 2005// TI - Maize association population: a high-resolution platform for quantitative trait locus dissection JO - Plant J Wiley Online Library VL - 44 ID - Flint-Garcia2005 ER - TY - STD TI - Rice BR, Fernandes SB, Lipka AE. Multi-Trait Genome-wide Association Studies Reveal Loci Associated with Maize Inflorescence and Leaf Architecture. Plant Cell Physiol. 2020; Available from: https://doi.org/10.1093/pcp/pcaa039. ID - ref68 ER - TY - JOUR AU - Benjamini, Y. AU - Hochberg, Y. PY - 1995 DA - 1995// TI - Controlling the false discovery rate: a practical and powerful approach to multiple testing JO - J R Stat Soc Series B Stat Methodol VL - 57 ID - Benjamini1995 ER - TY - JOUR AU - Upadyayula, N. AU - Silva, H. S. AU - Bohn, M. O. AU - Rocheford, T. R. PY - 2006 DA - 2006// TI - Genetic and QTL analysis of maize tassel and ear inflorescence architecture JO - Theor Appl Genet VL - 112 UR - https://doi.org/10.1007/s00122-005-0133-x DO - 10.1007/s00122-005-0133-x ID - Upadyayula2006 ER - TY - JOUR AU - Vollbrecht, E. AU - Springer, P. S. AU - Goh, L. AU - Buckler, E. S. AU - Martienssen, R. PY - 2005 DA - 2005// TI - Architecture of floral branch systems in maize and related grasses JO - Nature. VL - 436 UR - https://doi.org/10.1038/nature03892 DO - 10.1038/nature03892 ID - Vollbrecht2005 ER - TY - JOUR AU - Springer, N. AU - León, N. AU - Grotewold, E. PY - 2019 DA - 2019// TI - Challenges of translating gene regulatory information into agronomic improvements JO - Trends Plant Sci VL - 24 UR - https://doi.org/10.1016/j.tplants.2019.07.004 DO - 10.1016/j.tplants.2019.07.004 ID - Springer2019 ER - TY - JOUR AU - Gage, J. L. AU - White, M. R. AU - Edwards, J. W. AU - Kaeppler, S. AU - Leon, N. PY - 2018 DA - 2018// TI - Selection signatures underlying dramatic male inflorescence transformation during modern hybrid maize breeding JO - Genetics. VL - 210 UR - https://doi.org/10.1534/genetics.118.301487 DO - 10.1534/genetics.118.301487 ID - Gage2018 ER - TY - JOUR AU - Dong, Z. AU - Xiao, Y. AU - Govindarajulu, R. AU - Feil, R. AU - Siddoway, M. L. AU - Nielsen, T. PY - 2019 DA - 2019// TI - The regulatory landscape of a core maize domestication module controlling bud dormancy and growth repression JO - Nat Commun VL - 10 UR - https://doi.org/10.1038/s41467-019-11774-w DO - 10.1038/s41467-019-11774-w ID - Dong2019 ER - TY - JOUR AU - Lewis, M. W. AU - Bolduc, N. AU - Hake, K. AU - Htike, Y. AU - Hay, A. AU - Candela, H. PY - 2014 DA - 2014// TI - Gene regulatory interactions at lateral organ boundaries in maize JO - Development. VL - 141 UR - https://doi.org/10.1242/dev.111955 DO - 10.1242/dev.111955 ID - Lewis2014 ER - TY - JOUR AU - Bai, F. AU - Reinheimer, R. AU - Durantini, D. AU - Kellogg, E. A. AU - Schmidt, R. J. PY - 2012 DA - 2012// TI - TCP transcription factor, BRANCH ANGLE DEFECTIVE 1 (BAD1), is required for normal tassel branch angle formation in maize JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1202439109 DO - 10.1073/pnas.1202439109 ID - Bai2012 ER - TY - JOUR AU - Chapman, M. A. AU - Tang, S. AU - Draeger, D. AU - Nambeesan, S. AU - Shaffer, H. AU - Barb, J. G. PY - 2012 DA - 2012// TI - Genetic analysis of floral symmetry in van Gogh’s sunflowers reveals independent recruitment of CYCLOIDEA genes in the Asteraceae JO - PLoS Genet VL - 8 UR - https://doi.org/10.1371/journal.pgen.1002628 DO - 10.1371/journal.pgen.1002628 ID - Chapman2012 ER - TY - JOUR AU - Jiao, Y. AU - Lee, Y. K. AU - Gladman, N. AU - Chopra, R. AU - Christensen, S. A. AU - Regulski, M. PY - 2018 DA - 2018// TI - MSD1 regulates pedicellate spikelet fertility in sorghum through the jasmonic acid pathway JO - Nat Commun VL - 9 UR - https://doi.org/10.1038/s41467-018-03238-4 DO - 10.1038/s41467-018-03238-4 ID - Jiao2018 ER - TY - JOUR AU - Almeida, D. M. AU - Gregorio, G. B. AU - Oliveira, M. M. AU - Saibo, N. J. M. PY - 2017 DA - 2017// TI - Five novel transcription factors as potential regulators of OsNHX1 gene expression in a salt tolerant rice genotype JO - Plant Mol Biol VL - 93 UR - https://doi.org/10.1007/s11103-016-0547-7 DO - 10.1007/s11103-016-0547-7 ID - Almeida2017 ER - TY - JOUR AU - Wang, S. -. T. AU - Sun, X. -. L. AU - Hoshino, Y. AU - Yu, Y. AU - Jia, B. AU - Sun, Z. -. W. PY - 2014 DA - 2014// TI - MicroRNA319 positively regulates cold tolerance by targeting OsPCF6 and OsTCP21 in Rice (Oryza sativa L.) JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0091357 DO - 10.1371/journal.pone.0091357 ID - Wang2014 ER - TY - JOUR AU - Steiner, E. AU - Efroni, I. AU - Gopalraj, M. AU - Saathoff, K. AU - Tseng, T. -. S. AU - Kieffer, M. PY - 2012 DA - 2012// TI - The Arabidopsis O-linked N-acetylglucosamine transferase SPINDLY interacts with class I TCPs to facilitate cytokinin responses in leaves and flowers JO - Plant Cell VL - 24 UR - https://doi.org/10.1105/tpc.111.093518 DO - 10.1105/tpc.111.093518 ID - Steiner2012 ER - TY - JOUR AU - Danisman, S. AU - Wal, F. AU - Dhondt, S. AU - Waites, R. AU - Folter, S. AU - Bimbo, A. PY - 2012 DA - 2012// TI - Arabidopsis class I and class II TCP transcription factors regulate jasmonic acid metabolism and leaf development antagonistically JO - Plant Physiol VL - 159 UR - https://doi.org/10.1104/pp.112.200303 DO - 10.1104/pp.112.200303 ID - Danisman2012 ER - TY - JOUR AU - Kosugi, S. AU - Ohashi, Y. PY - 2002 DA - 2002// TI - DNA binding and dimerization specificity and potential targets for the TCP protein family JO - Plant J VL - 30 UR - https://doi.org/10.1046/j.1365-313X.2002.01294.x DO - 10.1046/j.1365-313X.2002.01294.x ID - Kosugi2002 ER - TY - JOUR AU - Viola, I. L. AU - Uberti Manassero, N. G. AU - Ripoll, R. AU - Gonzalez, D. H. PY - 2011 DA - 2011// TI - The Arabidopsis class I TCP transcription factor AtTCP11 is a developmental regulator with distinct DNA-binding properties due to the presence of a threonine residue at position 15 of the TCP domain JO - Biochem J VL - 435 UR - https://doi.org/10.1042/BJ20101019 DO - 10.1042/BJ20101019 ID - Viola2011 ER - TY - JOUR AU - Li, C. AU - Potuschak, T. AU - Colón-Carmona, A. AU - Gutiérrez, R. A. AU - Doerner, P. PY - 2005 DA - 2005// TI - Arabidopsis TCP20 links regulation of growth and cell division control pathways JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0504039102 DO - 10.1073/pnas.0504039102 ID - Li2005 ER - TY - JOUR AU - Burdo, B. AU - Gray, J. AU - Goetting-Minesky, M. P. AU - Wittler, B. AU - Hunt, M. AU - Li, T. PY - 2014 DA - 2014// TI - The maize TFome--development of a transcription factor open reading frame collection for functional genomics JO - Plant J VL - 80 UR - https://doi.org/10.1111/tpj.12623 DO - 10.1111/tpj.12623 ID - Burdo2014 ER - TY - JOUR AU - Gaudinier, A. AU - Brady, S. M. PY - 2016 DA - 2016// TI - Mapping transcriptional networks in plants: data-driven discovery of novel biological mechanisms JO - Annu Rev Plant Biol VL - 67 UR - https://doi.org/10.1146/annurev-arplant-043015-112205 DO - 10.1146/annurev-arplant-043015-112205 ID - Gaudinier2016 ER - TY - JOUR AU - Park, P. J. PY - 2009 DA - 2009// TI - ChIP–seq: advantages and challenges of a maturing technology JO - Nat Rev Genet Nature Publishing Group VL - 10 UR - https://doi.org/10.1038/nrg2641 DO - 10.1038/nrg2641 ID - Park2009 ER - TY - JOUR AU - Galli, M. AU - Khakhar, A. AU - Lu, Z. AU - Chen, Z. AU - Sen, S. AU - Joshi, T. PY - 2018 DA - 2018// TI - The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family JO - Nat Commun VL - 9 UR - https://doi.org/10.1038/s41467-018-06977-6 DO - 10.1038/s41467-018-06977-6 ID - Galli2018 ER - TY - JOUR AU - Pisignano, G. AU - Pavlaki, I. AU - Murrell, A. PY - 2019 DA - 2019// TI - Being in a loop: how long non-coding RNAs organise genome architecture JO - Essays Biochem VL - 63 UR - https://doi.org/10.1042/EBC20180057 DO - 10.1042/EBC20180057 ID - Pisignano2019 ER - TY - STD TI - Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, et al. Long Noncoding RNAs with Enhancer-like Function in Human Cells. Cell. 2010. p. 46–58. Available from: https://doi.org/10.1016/j.cell.2010.09.001. ID - ref91 ER - TY - STD TI - Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature. 2016. p. 452–5. Available from: https://doi.org/10.1038/nature20149. ID - ref92 ER - TY - STD TI - Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F, et al. Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood. Nature. 2017. p. 343–6. Available from: https://doi.org/10.1038/nature23451. ID - ref93 ER - TY - JOUR AU - Marchese, F. P. AU - Raimondi, I. AU - Huarte, M. PY - 2017 DA - 2017// TI - The multidimensional mechanisms of long noncoding RNA function JO - Genome Biol VL - 18 UR - https://doi.org/10.1186/s13059-017-1348-2 DO - 10.1186/s13059-017-1348-2 ID - Marchese2017 ER - TY - JOUR AU - Mattioli, K. AU - Volders, P. -. J. AU - Gerhardinger, C. AU - Lee, J. C. AU - Maass, P. G. AU - Melé, M. PY - 2019 DA - 2019// TI - High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity JO - Genome Res VL - 29 UR - https://doi.org/10.1101/gr.242222.118 DO - 10.1101/gr.242222.118 ID - Mattioli2019 ER - TY - JOUR AU - Sigova, A. A. AU - Mullen, A. C. AU - Molinie, B. AU - Gupta, S. AU - Orlando, D. A. AU - Guenther, M. G. PY - 2013 DA - 2013// TI - Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells JO - Proc Natl Acad Sci U S A VL - 110 UR - https://doi.org/10.1073/pnas.1221904110 DO - 10.1073/pnas.1221904110 ID - Sigova2013 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 - Wang, B. AU - Tseng, E. AU - Regulski, M. AU - Clark, T. A. AU - Hon, T. AU - Jiao, Y. PY - 2016 DA - 2016// TI - Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms11708 DO - 10.1038/ncomms11708 ID - Wang2016 ER - TY - JOUR AU - Wang, K. C. AU - Yang, Y. W. AU - Liu, B. AU - Sanyal, A. AU - Corces-Zimmerman, R. AU - Chen, Y. PY - 2011 DA - 2011// TI - A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression JO - Nature. VL - 472 UR - https://doi.org/10.1038/nature09819 DO - 10.1038/nature09819 ID - Wang2011 ER - TY - STD TI - Tan JY, Smith AAT, Ferreira da Silva M, Matthey-Doret C, Rueedi R, Sönmez R, et al. cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture. Cell Rep. 2017;18:2280–8. ID - ref100 ER - TY - JOUR AU - Liu, X. AU - Galli, M. AU - Camehl, I. AU - Gallavotti, A. PY - 2019 DA - 2019// TI - RAMOSA1 ENHANCER LOCUS2-mediated transcriptional repression regulates vegetative and reproductive architecture JO - Plant Physiol VL - 179 UR - https://doi.org/10.1104/pp.18.00913 DO - 10.1104/pp.18.00913 ID - Liu2019 ER - TY - JOUR AU - Krzywinski, M. AU - Schein, J. AU - Birol, I. AU - Connors, J. AU - Gascoyne, R. AU - Horsman, D. PY - 2009 DA - 2009// TI - Circos: an information aesthetic for comparative genomics JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.092759.109 DO - 10.1101/gr.092759.109 ID - Krzywinski2009 ER - TY - JOUR AU - Zhang, Y. AU - Liu, T. AU - Meyer, C. A. AU - Eeckhoute, J. AU - Johnson, D. S. AU - Bernstein, B. E. PY - 2008 DA - 2008// TI - Model-based analysis of ChIP-Seq (MACS) JO - Genome Biol VL - 9 UR - https://doi.org/10.1186/gb-2008-9-9-r137 DO - 10.1186/gb-2008-9-9-r137 ID - Zhang2008 ER - TY - JOUR AU - Lawrence, M. AU - Huber, W. AU - Pages, H. AU - Aboyoun, P. AU - Carlson, M. AU - Gentleman, R. PY - 2013 DA - 2013// TI - Software for computing and annotating genomic ranges JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003118 DO - 10.1371/journal.pcbi.1003118 ID - Lawrence2013 ER - TY - JOUR AU - Zhao, H. AU - Sun, Z. AU - Wang, J. AU - Huang, H. AU - Kocher, J. -. P. AU - Wang, L. PY - 2014 DA - 2014// TI - CrossMap: a versatile tool for coordinate conversion between genome assemblies JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btt730 DO - 10.1093/bioinformatics/btt730 ID - Zhao2014 ER - TY - JOUR AU - Gel, B. AU - Díez-Villanueva, A. AU - Serra, E. AU - Buschbeck, M. AU - Peinado, M. A. AU - Malinverni, R. PY - 2016 DA - 2016// TI - regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests JO - Bioinformatics VL - 32 ID - Gel2016 ER - TY - JOUR AU - Kim, D. AU - Langmead, B. AU - Salzberg, S. L. PY - 2015 DA - 2015// TI - HISAT: a fast spliced aligner with low memory requirements JO - Nat Methods VL - 12 UR - https://doi.org/10.1038/nmeth.3317 DO - 10.1038/nmeth.3317 ID - Kim2015 ER - TY - JOUR AU - Pertea, M. AU - Pertea, G. M. AU - Antonescu, C. M. AU - Chang, T. -. C. AU - Mendell, J. T. AU - Salzberg, S. L. PY - 2015 DA - 2015// TI - StringTie enables improved reconstruction of a transcriptome from RNA-seq reads JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3122 DO - 10.1038/nbt.3122 ID - Pertea2015 ER - TY - JOUR AU - Kersey, P. J. AU - Allen, J. E. AU - Armean, I. AU - Boddu, S. AU - Bolt, B. J. AU - Carvalho-Silva, D. PY - 2016 DA - 2016// TI - Ensembl genomes 2016: more genomes, more complexity JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1209 DO - 10.1093/nar/gkv1209 ID - Kersey2016 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 Nature Publishing Group VL - 7 UR - https://doi.org/10.1038/nprot.2012.016 DO - 10.1038/nprot.2012.016 ID - Trapnell2012 ER - TY - JOUR AU - Schurch, N. J. AU - Schofield, P. AU - Gierliński, M. AU - Cole, C. AU - Sherstnev, A. AU - Singh, V. PY - 2016 DA - 2016// TI - How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? JO - RNA. VL - 22 UR - https://doi.org/10.1261/rna.053959.115 DO - 10.1261/rna.053959.115 ID - Schurch2016 ER - TY - JOUR AU - Bailey, T. L. AU - Boden, M. AU - Buske, F. A. AU - Frith, M. AU - Grant, C. E. AU - Clementi, L. PY - 2009 DA - 2009// TI - MEME SUITE: tools for motif discovery and searching JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp335 DO - 10.1093/nar/gkp335 ID - Bailey2009 ER - TY - CHAP AU - Quattro, C. AU - Mica, E. AU - Pè, M. E. AU - Bertolini, E. ED - Sablok, G. ED - Budak, H. ED - Ralph, P. J. PY - 2018 DA - 2018// TI - Brachypodium distachyon Long noncoding RNAs: genome-wide identification and expression analysis BT - Brachypodium genomics: methods and protocols PB - Springer New York CY - New York UR - https://doi.org/10.1007/978-1-4939-7278-4_3 DO - 10.1007/978-1-4939-7278-4_3 ID - Quattro2018 ER - TY - JOUR AU - Quinn, J. J. AU - Chang, H. Y. PY - 2016 DA - 2016// TI - Unique features of long non-coding RNA biogenesis and function JO - Nat Rev Genet VL - 17 UR - https://doi.org/10.1038/nrg.2015.10 DO - 10.1038/nrg.2015.10 ID - Quinn2016 ER - TY - JOUR AU - Finn, R. D. AU - Bateman, A. AU - Clements, J. AU - Coggill, P. AU - Eberhardt, R. Y. AU - Eddy, S. R. PY - 2014 DA - 2014// TI - Pfam: the protein families database JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1223 DO - 10.1093/nar/gkt1223 ID - Finn2014 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 - Nawrocki, E. P. AU - Burge, S. W. AU - Bateman, A. AU - Daub, J. AU - Eberhardt, R. Y. AU - Eddy, S. R. PY - 2015 DA - 2015// TI - Rfam 12.0: updates to the RNA families database JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1063 DO - 10.1093/nar/gku1063 ID - Nawrocki2015 ER - TY - JOUR AU - Zhang, L. AU - Chia, J. -. M. AU - Kumari, S. AU - Stein, J. C. AU - Liu, Z. AU - Narechania, A. PY - 2009 DA - 2009// TI - A genome-wide characterization of microRNA genes in maize JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000716 DO - 10.1371/journal.pgen.1000716 ID - Zhang2009 ER - TY - JOUR AU - Thompson, B. E. AU - Basham, C. AU - Hammond, R. AU - Ding, Q. AU - Kakrana, A. AU - Lee, T. -. F. PY - 2014 DA - 2014// TI - The dicer-like1 homolog fuzzy tassel is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize JO - Plant Cell VL - 26 UR - https://doi.org/10.1105/tpc.114.132670 DO - 10.1105/tpc.114.132670 ID - Thompson2014 ER - TY - JOUR AU - Prüfer, K. AU - Stenzel, U. AU - Dannemann, M. AU - Green, R. E. AU - Lachmann, M. AU - Kelso, J. PY - 2008 DA - 2008// TI - PatMaN: rapid alignment of short sequences to large databases JO - Bioinformatics. VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn223 DO - 10.1093/bioinformatics/btn223 ID - Prüfer2008 ER - TY - JOUR AU - Patro, R. AU - Duggal, G. AU - Love, M. I. AU - Irizarry, R. A. AU - Kingsford, C. PY - 2017 DA - 2017// TI - Salmon provides fast and bias-aware quantification of transcript expression JO - Nat Methods VL - 14 UR - https://doi.org/10.1038/nmeth.4197 DO - 10.1038/nmeth.4197 ID - Patro2017 ER - TY - JOUR AU - Soneson, C. AU - Love, M. I. AU - Robinson, M. D. PY - 2015 DA - 2015// TI - Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences JO - F1000Res. VL - 4 UR - https://doi.org/10.12688/f1000research.7563.1 DO - 10.12688/f1000research.7563.1 ID - Soneson2015 ER - TY - JOUR AU - Zhang, J. D. AU - Hatje, K. AU - Sturm, G. AU - Broger, C. AU - Ebeling, M. AU - Burtin, M. PY - 2017 DA - 2017// TI - Detect tissue heterogeneity in gene expression data with BioQC JO - BMC Genomics VL - 18 UR - https://doi.org/10.1186/s12864-017-3661-2 DO - 10.1186/s12864-017-3661-2 ID - Zhang2017 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 - JOUR AU - Langfelder, P. AU - Horvath, S. PY - 2008 DA - 2008// TI - WGCNA: an R package for weighted correlation network analysis JO - BMC Bioinformatics VL - 9 UR - https://doi.org/10.1186/1471-2105-9-559 DO - 10.1186/1471-2105-9-559 ID - Langfelder2008 ER - TY - JOUR AU - Xi, Y. AU - Li, W. PY - 2009 DA - 2009// TI - BSMAP: whole genome bisulfite sequence MAPping program JO - BMC Bioinformatics. VL - 10 UR - https://doi.org/10.1186/1471-2105-10-232 DO - 10.1186/1471-2105-10-232 ID - Xi2009 ER - TY - JOUR AU - Yu, G. AU - Wang, L. -. G. AU - Han, Y. AU - He, Q. -. Y. PY - 2012 DA - 2012// TI - clusterProfiler: an R package for comparing biological themes among gene clusters JO - OMICS. VL - 16 UR - https://doi.org/10.1089/omi.2011.0118 DO - 10.1089/omi.2011.0118 ID - Yu2012 ER - TY - JOUR AU - Jin, J. AU - Tian, F. AU - Yang, D. -. C. AU - Meng, Y. -. Q. AU - Kong, L. AU - Luo, J. PY - 2017 DA - 2017// TI - PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw982 DO - 10.1093/nar/gkw982 ID - Jin2017 ER - TY - JOUR AU - Wallace, J. G. AU - Bradbury, P. J. AU - Zhang, N. AU - Gibon, Y. AU - Stitt, M. AU - Buckler, E. S. PY - 2014 DA - 2014// TI - Association mapping across numerous traits reveals patterns of functional variation in maize JO - PLoS Genet VL - 10 UR - https://doi.org/10.1371/journal.pgen.1004845 DO - 10.1371/journal.pgen.1004845 ID - Wallace2014 ER - TY - JOUR AU - Buckler, E. S. AU - Holland, J. B. AU - Bradbury, P. J. AU - Acharya, C. B. AU - Brown, P. J. AU - Browne, C. PY - 2009 DA - 2009// TI - The genetic architecture of maize flowering time JO - Science. VL - 325 UR - https://doi.org/10.1126/science.1174276 DO - 10.1126/science.1174276 ID - Buckler2009 ER - TY - JOUR AU - Brown, P. J. AU - Upadyayula, N. AU - Mahone, G. S. AU - Tian, F. AU - Bradbury, P. J. AU - Myles, S. PY - 2011 DA - 2011// TI - Distinct genetic architectures for male and female inflorescence traits of maize JO - PLoS Genet VL - 7 UR - https://doi.org/10.1371/journal.pgen.1002383 DO - 10.1371/journal.pgen.1002383 ID - Brown2011 ER - TY - JOUR AU - Bradbury, P. J. AU - Zhang, Z. AU - Kroon, D. E. AU - Casstevens, T. M. AU - Ramdoss, Y. AU - Buckler, E. S. PY - 2007 DA - 2007// TI - TASSEL: software for association mapping of complex traits in diverse samples JO - Bioinformatics. VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm308 DO - 10.1093/bioinformatics/btm308 ID - Bradbury2007 ER - TY - JOUR AU - Churchill, G. A. AU - Doerge, R. W. PY - 1994 DA - 1994// TI - Empirical threshold values for quantitative trait mapping JO - Genetics Genetics Soc America VL - 138 ID - Churchill1994 ER - TY - JOUR AU - Ziegler, G. R. AU - Hartsock, R. H. AU - Baxter, I. PY - 2015 DA - 2015// TI - Zbrowse: an interactive GWAS results browser JO - PeerJ Comput Sci VL - 1 UR - https://doi.org/10.7717/peerj-cs.3 DO - 10.7717/peerj-cs.3 ID - Ziegler2015 ER - TY - STD TI - Parvathaneni RK, Bertolini E, et al. The regulatory landscape of early maize inflorescence development. MNase-seq and GWAS datasets. Gene Expression Omnibus. GSE136685. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136685 (2019). UR - https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136685 ID - ref135 ER -