RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications
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Hong Ma | Genfeng Zhu | Lei Wang | Ji Qi | Yingxiang Wang | Haifeng Wang | H. Nian | Chen Cao | Qibin Ma | Qiaoying Zeng | Zhihao Cheng
[1] Zhixi Tian,et al. Global Dissection of Alternative Splicing in Paleopolyploid Soybean[W] , 2014, Plant Cell.
[2] Hong Ma,et al. The Arabidopsis RAD51 paralogs RAD51B, RAD51D and XRCC2 play partially redundant roles in somatic DNA repair and gene regulation. , 2014, The New phytologist.
[3] P. Bhalla,et al. An RNA-Seq Transcriptome Analysis of Histone Modifiers and RNA Silencing Genes in Soybean during Floral Initiation Process , 2013, PloS one.
[4] Hong Ma,et al. Flower Development under Drought Stress: Morphological and Transcriptomic Analyses Reveal Acute Responses and Long-Term Acclimation in Arabidopsis[C][W] , 2013, Plant Cell.
[5] Cristobal Uauy,et al. Separating homeologs by phasing in the tetraploid wheat transcriptome , 2013, Genome Biology.
[6] Zhongchi Liu,et al. Genome-Scale Transcriptomic Insights into Early-Stage Fruit Development in Woodland Strawberry Fragaria vesca[C][W] , 2013, Plant Cell.
[7] Hong Ma,et al. Deep mRNA Sequencing Analysis to Capture the Transcriptome Landscape of Zebrafish Embryos and Larvae , 2013, PloS one.
[8] L. Hileman,et al. Functional Evolution in the Plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family , 2013, Front. Plant Sci..
[9] Gary Stacey,et al. The fate of duplicated genes in a polyploid plant genome. , 2013, The Plant journal : for cell and molecular biology.
[10] M. Axtell,et al. miR156 and miR390 Regulate tasiRNA Accumulation and Developmental Timing in Physcomitrella patens[C][W][OA] , 2012, Plant Cell.
[11] Qian Wang,et al. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data , 2012, Bioinform..
[12] Chongsheng He,et al. Reprogramming of H3K27me3 Is Critical for Acquisition of Pluripotency from Cultured Arabidopsis Tissues , 2012, PLoS genetics.
[13] A. Murphy,et al. ER-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis , 2012, Nature Communications.
[14] P. Bhalla,et al. Comparative Genomic Analysis of Soybean Flowering Genes , 2012, PloS one.
[15] Yamile Marquez,et al. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis , 2012, Genome research.
[16] P. Benfey,et al. Cell type-specific transcriptional profiling: implications for metabolite profiling. , 2012, The Plant journal : for cell and molecular biology.
[17] David R. Kelley,et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks , 2012, Nature Protocols.
[18] Jeremy D. DeBarry,et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.
[19] P. Huijser,et al. Genomic organization, phylogenetic comparison and differential expression of the SBP-box family of transcription factors in tomato , 2012, Planta.
[20] Zhong Wang,et al. Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.
[21] G. Coupland,et al. The Arabidopsis SOC1-like genes AGL42, AGL71 and AGL72 promote flowering in the shoot apical and axillary meristems. , 2011, The Plant journal : for cell and molecular biology.
[22] F. Tax,et al. CLAVATA Signaling Pathway Receptors of Arabidopsis Regulate Cell Proliferation in Fruit Organ Formation as well as in Meristems , 2011, Genetics.
[23] Z. Gong,et al. Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. , 2011, Genome research.
[24] M. Kater,et al. Functional Analysis of All AGAMOUS Subfamily Members in Rice Reveals Their Roles in Reproductive Organ Identity Determination and Meristem Determinacy[W] , 2011, Plant Cell.
[25] Fangqing Zhao,et al. inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data , 2011, Nucleic Acids Res..
[26] Pingli Lu,et al. The transcriptome landscape of Arabidopsis male meiocytes from high-throughput sequencing: the complexity and evolution of the meiotic process. , 2011, The Plant journal : for cell and molecular biology.
[27] Vipin T. Sreedharan,et al. A spatial and temporal map of C. elegans gene expression. , 2011, Genome research.
[28] B. Graveley. The developmental transcriptome of Drosophila melanogaster , 2010, Nature.
[29] Robert Turgeon,et al. The developmental dynamics of the maize leaf transcriptome , 2010, Nature Genetics.
[30] Bo Wang,et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection , 2010, Nature Genetics.
[31] E. Wang,et al. Analysis and design of RNA sequencing experiments for identifying isoform regulation , 2010, Nature Methods.
[32] Xiaolong Yan,et al. The soybean root-specific protein kinase GmWNK1 regulates stress-responsive ABA signaling on the root system architecture. , 2010, The Plant journal : for cell and molecular biology.
[33] Rex T. Nelson,et al. RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome , 2010, BMC Plant Biology.
[34] Jianxin Ma,et al. Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. , 2010, The Plant journal : for cell and molecular biology.
[35] Xuehui Huang,et al. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. , 2010, Genome research.
[36] G. Stacey,et al. A Fluorescence in Situ Hybridization System for Karyotyping Soybean , 2010, Genetics.
[37] Dongqiao Shi,et al. Female gametophyte development in flowering plants. , 2010, Annual review of plant biology.
[38] Yunde Zhao. Auxin biosynthesis and its role in plant development. , 2010, Annual review of plant biology.
[39] Huanming Yang,et al. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. , 2010, Genome research.
[40] Zhou Du,et al. agriGO: a GO analysis toolkit for the agricultural community , 2010, Nucleic Acids Res..
[41] Trupti Joshi,et al. An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. , 2010, The Plant journal : for cell and molecular biology.
[42] G. Bassel,et al. The regulation of post-germinative transition from the cotyledon- to vegetative-leaf stages by microRNA-targeted SQUAMOSA PROMOTER-BINDING PROTEIN LIKE13 in Arabidopsis , 2010, Seed Science Research.
[43] Elliot M Meyerowitz,et al. Arabidopsis regeneration from multiple tissues occurs via a root development pathway. , 2010, Developmental cell.
[44] T. Sakurai,et al. Genome sequence of the palaeopolyploid soybean , 2010, Nature.
[45] Henry D. Priest,et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. , 2010, Genome research.
[46] Mariana Benítez,et al. Flower Development , 2010, The arabidopsis book.
[47] L. Østergaard,et al. Distinct and dynamic auxin activities during reproductive development. , 2009, Cold Spring Harbor perspectives in biology.
[48] G. Stacey,et al. Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection1[C][W][OA] , 2009, Plant Physiology.
[49] S. Jackson,et al. Molecular and Chromosomal Evidence for Allopolyploidy in Soybean1[OA] , 2009, Plant Physiology.
[50] Jing Zhang,et al. Subcellular homeostasis of phytohormone auxin is mediated by the ER-localized PIN5 transporter , 2009, Nature.
[51] Steffen Vanneste,et al. Auxin: A Trigger for Change in Plant Development , 2009, Cell.
[52] Hongyu Zhao,et al. A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies , 2009, Nature Genetics.
[53] M. Hayashi,et al. SQUAMOSA Promoter Binding Protein–Like7 Is a Central Regulator for Copper Homeostasis in Arabidopsis[W] , 2009, The Plant Cell Online.
[54] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[55] P. Bhalla,et al. Genome-wide analysis of gene expression in soybean shoot apical meristem , 2009, Plant Molecular Biology.
[56] P. Hogeweg,et al. Root System Architecture from Coupling Cell Shape to Auxin Transport , 2008, PLoS biology.
[57] Eric T. Wang,et al. Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.
[58] M. Stephens,et al. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.
[59] Marcel H. Schulz,et al. A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome , 2008, Science.
[60] Ryan D. Morin,et al. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. , 2008, BioTechniques.
[61] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[62] I. Goodhead,et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution , 2008, Nature.
[63] M. Gerstein,et al. The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.
[64] S. Ranade,et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing , 2008, Nature Methods.
[65] D. Bartel,et al. Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome , 2008, Current Biology.
[66] R. Lister,et al. Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis , 2008, Cell.
[67] Heinz Saedler,et al. The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis , 2008, Plant Molecular Biology.
[68] Chenwu Xu,et al. Comparative study of SBP-box gene family in Arabidopsis and rice. , 2008, Gene.
[69] Rex T. Nelson,et al. Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing , 2007, BMC Genomics.
[70] J. Skvarla,et al. Pollen wall development in flowering plants. , 2007, The New phytologist.
[71] N. Ori,et al. The role of hormones in shoot apical meristem function. , 2006, Current opinion in plant biology.
[72] Yunde Zhao,et al. Auxin biosynthesis by the YUCCA flavin monooxygenases controls the formation of floral organs and vascular tissues in Arabidopsis. , 2006, Genes & development.
[73] C. Dean,et al. The Timing of Developmental Transitions in Plants , 2006, Cell.
[74] R. Shoemaker,et al. Paleopolyploidy and gene duplication in soybean and other legumes. , 2006, Current opinion in plant biology.
[75] X. Gu,et al. Evolution of alternative splicing after gene duplication. , 2005, Genome research.
[76] Xinwen Liang,et al. Arabidopsis AtSPL14, a plant-specific SBP-domain transcription factor, participates in plant development and sensitivity to fumonisin B1. , 2005, The Plant journal : for cell and molecular biology.
[77] Sean R. Eddy,et al. Rfam: annotating non-coding RNAs in complete genomes , 2004, Nucleic Acids Res..
[78] M. Paz,et al. The association of culm anatomy with lodging susceptibility in modern spring wheat genotypes , 2004, Euphytica.
[79] A. Banerjee,et al. Assessment of conditions affecting Agrobacterium-mediated soybean transformation using the cotyledonary node explant , 2004, Euphytica.
[80] Jeroen Raes,et al. Duplication and divergence: the evolution of new genes and old ideas. , 2004, Annual review of genetics.
[81] Joseph R Ecker,et al. CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[82] S. Rhee,et al. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. , 2004, The Plant journal : for cell and molecular biology.
[83] Teuvo Kohonen,et al. Self-organized formation of topologically correct feature maps , 2004, Biological Cybernetics.
[84] Hong Ma,et al. The Arabidopsis MALE MEIOCYTE DEATH1 gene encodes a PHD-finger protein that is required for male meiosis. , 2003, The Plant cell.
[85] P. Huijser,et al. SPL8, an SBP-Box Gene That Affects Pollen Sac Development in Arabidopsis Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010678. , 2003, The Plant Cell Online.
[86] J. A. Buso,et al. BMC Plant Biology , 2003 .
[87] Thomas D. Schmittgen,et al. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.
[88] J. Reed,et al. Roles and activities of Aux/IAA proteins in Arabidopsis. , 2001, Trends in plant science.
[89] E. Liscum,et al. Arabidopsis NPH3: A NPH1 photoreceptor-interacting protein essential for phototropism. , 1999, Science.
[90] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[91] T. Kohonen. Self-organized formation of topographically correct feature maps , 1982 .
[92] Thomas D. Schmittgen,et al. Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2 2 DD C T Method , 2022 .