Whole transcriptome analysis and construction of a ceRNA regulatory network related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis)

[1]  Zhiyong Liu,et al.  Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis) , 2021, BMC genomics.

[2]  Z. Ding,et al.  Fulvic acid enhances drought resistance in tea plants by regulating the starch and sucrose metabolism and certain secondary metabolism. , 2021, Journal of proteomics.

[3]  Baoshan Wang,et al.  Current Understanding of bHLH Transcription Factors in Plant Abiotic Stress Tolerance , 2021, International journal of molecular sciences.

[4]  Hongyu Zhang,et al.  Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice , 2021, Plant Molecular Biology.

[5]  Hongyu Zhang,et al.  Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice , 2021, Planta.

[6]  Y. Hur,et al.  Molecular characterization of Arabidopsis thalianaLSH1 and LSH2 genes , 2020, Genes & Genomics.

[7]  D. Inzé,et al.  Molecular networks regulating cell division during Arabidopsis leaf growth , 2019, Journal of Experimental Botany.

[8]  M. Ohme-Takagi,et al.  Identification of TCP13 as an Upstream Regulator of ATHB12 during Leaf Development , 2019, Genes.

[9]  F. Ariel,et al.  Class I TCP transcription factors target the gibberellin biosynthesis gene GA20ox1 and the growth promoting genes HBI1 and PRE6 during thermomorphogenic growth in Arabidopsis. , 2019, Plant & cell physiology.

[10]  Youhuang Bai,et al.  Identification and characterization of pineapple leaf lncRNAs in crassulacean acid metabolism (CAM) photosynthesis pathway , 2019, Scientific Reports.

[11]  P. Harris,et al.  Developmental changes in collenchyma cell-wall polysaccharides in celery (Apium graveolens L.) petioles , 2019, BMC Plant Biology.

[12]  A. Xiong,et al.  Elevated gibberellin enhances lignin accumulation in celery (Apium graveolens L.) leaves , 2019, Protoplasma.

[13]  A. Xiong,et al.  Exogenous brassinosteroids altered cell length, gibberellin content, and cellulose deposition in promoting carrot petiole elongation. , 2018, Plant science : an international journal of experimental plant biology.

[14]  J. Bennetzen,et al.  Circular RNA architecture and differentiation during leaf bud to young leaf development in tea (Camellia sinensis) , 2018, Planta.

[15]  Jingjing Wang,et al.  Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development , 2018, BMC Genomics.

[16]  Jingjing Wang,et al.  Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development , 2018, BMC Genomics.

[17]  S. Fredericq,et al.  TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees , 2018, BMC Research Notes.

[18]  Huiyong Zhang,et al.  Constitutive Expression of miR408 Improves Biomass and Seed Yield in Arabidopsis , 2018, Front. Plant Sci..

[19]  William R Pearson,et al.  Finding Protein and Nucleotide Similarities with FASTA , 2003, Current protocols in bioinformatics.

[20]  H. Tsukaya,et al.  Regulation of plant growth and development by the GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR duo. , 2015, Journal of experimental botany.

[21]  A. Xiong,et al.  High-throughput sequencing of small RNAs and anatomical characteristics associated with leaf development in celery , 2015, Scientific Reports.

[22]  Steven L Salzberg,et al.  HISAT: a fast spliced aligner with low memory requirements , 2015, Nature Methods.

[23]  M. Bevan,et al.  The Ubiquitin Receptors DA1, DAR1, and DAR2 Redundantly Regulate Endoreduplication by Modulating the Stability of TCP14/15 in Arabidopsis , 2015, Plant Cell.

[24]  Alyssa C. Frazee,et al.  Ballgown bridges the gap between transcriptome assembly and expression analysis , 2015, Nature Biotechnology.

[25]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[26]  D. Inzé,et al.  Gibberellins and DELLAs: central nodes in growth regulatory networks. , 2014, Trends in plant science.

[27]  R. Pierik,et al.  Interactions between Auxin, Microtubules and XTHs Mediate Green Shade- Induced Petiole Elongation in Arabidopsis , 2014, PloS one.

[28]  Yueying Zhang,et al.  The Ubiquitin Receptor DA1 Regulates Seed and Organ Size by Modulating the Stability of the Ubiquitin-Specific Protease UBP15/SOD2 in Arabidopsis[W] , 2014, Plant Cell.

[29]  F. Madueño,et al.  Regulation of Compound Leaf Development by PHANTASTICA in Medicago truncatula1[C][W][OPEN] , 2013, Plant Physiology.

[30]  Yi Zhao,et al.  Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts , 2013, Nucleic acids research.

[31]  Chunjiang Zhou,et al.  Signal transduction in leaf senescence , 2013, Plant Molecular Biology.

[32]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[33]  Yijun Meng,et al.  Target mimics: an embedded layer of microRNA-involved gene regulatory networks in plants , 2012, BMC Genomics.

[34]  Sungtaeg Kang,et al.  Genetic map of lps3: a new short petiole gene in soybeans. , 2012, Genome.

[35]  L. Xiong,et al.  Gradual Increase of miR156 Regulates Temporal Expression Changes of Numerous Genes during Leaf Development in Rice1[C][W][OA] , 2012, Plant Physiology.

[36]  J. Parker,et al.  The impact of temperature on balancing immune responsiveness and growth in Arabidopsis. , 2011, Trends in plant science.

[37]  G. Horiguchi,et al.  Key Proliferative Activity in the Junction between the Leaf Blade and Leaf Petiole of Arabidopsis1[W][OA] , 2011, Plant Physiology.

[38]  P. Pandolfi,et al.  A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? , 2011, Cell.

[39]  Patrick Xuechun Zhao,et al.  psRNATarget: a plant small RNA target analysis server , 2011, Nucleic Acids Res..

[40]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[41]  Shan Lu,et al.  The cauliflower Orange gene enhances petiole elongation by suppressing expression of eukaryotic release factor 1. , 2011, The New phytologist.

[42]  K. Shinozaki,et al.  TCP Transcription Factors Regulate the Activities of ASYMMETRIC LEAVES1 and miR164, as Well as the Auxin Response, during Differentiation of Leaves in Arabidopsis[C][W] , 2010, Plant Cell.

[43]  D. Weigel,et al.  Control of cell proliferation in Arabidopsis thaliana by microRNA miR396 , 2010, Development.

[44]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[45]  C. Ponting,et al.  Genomic and Transcriptional Co-Localization of Protein-Coding and Long Non-Coding RNA Pairs in the Developing Brain , 2009, PLoS genetics.

[46]  S. Dhondt,et al.  Gibberellin Signaling Controls Cell Proliferation Rate in Arabidopsis , 2009, Current Biology.

[47]  Dongmei Liu,et al.  Ectopic expression of miR396 suppresses GRF target gene expression and alters leaf growth in Arabidopsis. , 2009, Physiologia plantarum.

[48]  R. Pierik,et al.  Auxin and Ethylene Regulate Elongation Responses to Neighbor Proximity Signals Independent of Gibberellin and DELLA Proteins in Arabidopsis1[C][W][OA] , 2009, Plant Physiology.

[49]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[50]  David L. Smith,et al.  Expression of three expansin genes during development and maturation of Kyoho grape berries. , 2007, Journal of plant physiology.

[51]  Jian-feng Zhang,et al.  A xyloglucan endotransglucosylase/hydrolase involves in growth of primary root and alters the deposition of cellulose in Arabidopsis , 2007, Planta.

[52]  J. Sheen,et al.  Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis , 2007, Nature Protocols.

[53]  Yong Zhang,et al.  CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine , 2007, Nucleic Acids Res..

[54]  Naama Menda,et al.  Regulation of LANCEOLATE by miR319 is required for compound-leaf development in tomato , 2007, Nature Genetics.

[55]  M. Matsuoka,et al.  Gibberellin receptor and its role in gibberellin signaling in plants. , 2007, Annual review of plant biology.

[56]  T. Demura,et al.  Overexpression of miR165 affects apical meristem formation, organ polarity establishment and vascular development in Arabidopsis. , 2007, Plant & cell physiology.

[57]  Hirokazu Tsukaya,et al.  Mechanism of leaf-shape determination. , 2006, Annual review of plant biology.

[58]  R. Pierik,et al.  Reaching out of the shade. , 2005, Current opinion in plant biology.

[59]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[60]  J. Benschop,et al.  Ethylene regulates fast apoplastic acidification and expansin A transcription during submergence-induced petiole elongation in Rumex palustris. , 2005, The Plant journal : for cell and molecular biology.

[61]  C. Helliwell,et al.  The Involvement of Gibberellin 20-Oxidase Genes in Phytochrome-Regulated Petiole Elongation of Arabidopsis , 2005, Plant Physiology.

[62]  Xiaochen Bo,et al.  TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA. , 2005, Bioinformatics.

[63]  Youn-sung Kim,et al.  microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. , 2005, The Plant journal : for cell and molecular biology.

[64]  S. McQueen-Mason,et al.  Changes in expansin activity and gene expression during ethylene-promoted leaflet abscission in Sambucus nigra. , 2005, Journal of experimental botany.

[65]  G. Horiguchi,et al.  Coordination of cell proliferation and cell expansion in the control of leaf size in Arabidopsis thaliana , 2005, Journal of Plant Research.

[66]  Michelle T. Juarez,et al.  microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity , 2004, Nature.

[67]  K. Shinozaki,et al.  Overexpression of LSH1, a member of an uncharacterised gene family, causes enhanced light regulation of seedling development. , 2004, The Plant journal : for cell and molecular biology.

[68]  K. Nishitani,et al.  A Surprising Diversity and Abundance of Xyloglucan Endotransglucosylase/Hydrolases in Rice. Classification and Expression Analysis1 , 2004, Plant Physiology.

[69]  H. Tsukaya.  Organ shape and size: a lesson from studies of leaf morphogenesis. , 2003, Current opinion in plant biology.

[70]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[71]  B Keller,et al.  Activation tagging of the LEAFY PETIOLE gene affects leaf petiole development in Arabidopsis thaliana. , 2000, Development.

[72]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..

[73]  P. Hedden,et al.  Modification of gibberellin production and plant development in Arabidopsis by sense and antisense expression of gibberellin 20-oxidase genes. , 1999, The Plant journal : for cell and molecular biology.

[74]  S. Clough,et al.  Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[75]  E. M. Meyerowitz,et al.  Arabidopsis thaliana , 2022, CABI Compendium.