A transcriptome-wide, organ-specific regulatory map of Dendrobium officinale, an important traditional Chinese orchid herb

[1]  Qiye Li,et al.  The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb. , 2015, Molecular plant.

[2]  R. Brys,et al.  Mycorrhizal networks and coexistence in species-rich orchid communities. , 2015, The New phytologist.

[3]  Ana Kozomara,et al.  miRBase: annotating high confidence microRNAs using deep sequencing data , 2013, Nucleic Acids Res..

[4]  Ming Chen,et al.  Identification of novel microRNA-like-coding sites on the long-stem microRNA precursors in Arabidopsis. , 2013, Gene.

[5]  Shilin Chen,et al.  Analysis of the Dendrobium officinale transcriptome reveals putative alkaloid biosynthetic genes and genetic markers. , 2013, Gene.

[6]  Huizhong Wang,et al.  Functional characterization of a novel tropinone reductase-like gene in Dendrobium nobile Lindl. , 2013, Journal of plant physiology.

[7]  Ming Chen,et al.  A reversed framework for the identification of microRNA-target pairs in plants , 2013, Briefings Bioinform..

[8]  Huizhong Wang,et al.  Development and characterization of 110 novel EST-SSR markers for Dendrobium officinale (Orchidaceae). , 2012, American journal of botany.

[9]  Y. Tong,et al.  Review of research on Dendrobium, a prized folk medicine , 2012, Applied Microbiology and Biotechnology.

[10]  Ming Chen,et al.  Construction of MicroRNA- and MicroRNA*-mediated regulatory networks in plants , 2011, RNA biology.

[11]  B. Blencowe,et al.  SnapShot: High-Throughput Sequencing Applications , 2011, Cell.

[12]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

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

[14]  P. May,et al.  Stars and Symbiosis: MicroRNA- and MicroRNA*-Mediated Transcript Cleavage Involved in Arbuscular Mycorrhizal Symbiosis1[W][OA] , 2011, Plant Physiology.

[15]  Hsien-Da Huang,et al.  Arabidopsis Argonaute 2 regulates innate immunity via miRNA393(∗)-mediated silencing of a Golgi-localized SNARE gene, MEMB12. , 2011, Molecular cell.

[16]  Fatih Ozsolak,et al.  RNA sequencing: advances, challenges and opportunities , 2011, Nature Reviews Genetics.

[17]  Doron Betel,et al.  Widespread regulatory activity of vertebrate microRNA* species. , 2011, RNA.

[18]  Ming Chen,et al.  Toward microRNA-mediated gene regulatory networks in plants , 2011, Briefings Bioinform..

[19]  Ping Wu,et al.  High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism. , 2010, Journal of experimental botany.

[20]  Weixiong Zhang,et al.  Multiple distinct small RNAs originate from the same microRNA precursors , 2010, Genome Biology.

[21]  Xuemei Chen,et al.  Small RNAs and their roles in plant development. , 2009, Annual review of cell and developmental biology.

[22]  Michel Schneider,et al.  The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. , 2009, Journal of proteomics.

[23]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[24]  O. Voinnet.  Origin, Biogenesis, and Activity of Plant MicroRNAs , 2009, Cell.

[25]  Yi Xing,et al.  The Bifunctional microRNA miR-9/miR-9* Regulates REST and CoREST and Is Downregulated in Huntington's Disease , 2008, The Journal of Neuroscience.

[26]  D. Bartel,et al.  Criteria for Annotation of Plant MicroRNAs , 2008, The Plant Cell Online.

[27]  Hong Duan,et al.  The regulatory activity of microRNA* species has substantial influence on microRNA and 3′ UTR evolution , 2008, Nature Structural &Molecular Biology.

[28]  J. Dearnaley.  Further advances in orchid mycorrhizal research , 2007, Mycorrhiza.

[29]  J. Vielle-Calzada,et al.  A Family of MicroRNAs Present in Plants and Animals[W][OA] , 2006, The Plant Cell Online.

[30]  D. Bartel,et al.  MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.

[31]  D. Bartel,et al.  AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. , 2006, Molecular cell.

[32]  Louette R. Johnson Lutjens.  Research , 2006 .

[33]  Yuanji Zhang,et al.  miRU: an automated plant miRNA target prediction server , 2005, Nucleic Acids Res..

[34]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[35]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[36]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[37]  Franck Vazquez,et al.  The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. , 2004, Genes & development.

[38]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[39]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[40]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[41]  G. Ruvkun,et al.  A uniform system for microRNA annotation. , 2003, RNA.

[42]  Hakluyt's Voyages,et al.  Annotation , 1936, Glasgow Medical Journal.

[43]  S. Cohen,et al.  microRNA functions. , 2007, Annual review of cell and developmental biology.

[44]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[45]  Gapped BLAST and PSI-BLAST: A new , 1997 .