Transcriptome-Wide Characterization of miRNA-Directed and Non-miRNA-Directed Endonucleolytic Cleavage Using Degradome Analysis Under Low Ambient Temperature in Phalaenopsis aphrodite subsp. formosana

miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs

(2012) Fuliang Xie et al.   PLANT MOLECULAR BIOLOGY

Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids

(2011) Yu-Yun Hsiao et al.   BMC GENOMICS

Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

(2011) Qing-Xin Song et al.   BMC PLANT BIOLOGY

Genome-wide characterization of new and drought stress responsive microRNAs in Populus euphratica

(2011) Bosheng Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification of miRNAs and Their Target Genes Using Deep Sequencing and Degradome Analysis in Trifoliate Orange [Poncirus trifoliate (L.) Raf]

(2011) Jin-Zhi Zhang et al.   MOLECULAR BIOTECHNOLOGY

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

(2011) Cameron P. Bracken et al.   NUCLEIC ACIDS RESEARCH

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing

(2011) Anitha D. Jayaprakash et al.   NUCLEIC ACIDS RESEARCH

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

De Novo Assembly of Expressed Transcripts and Global Analysis of the Phalaenopsis aphrodite Transcriptome

(2011) Chun-lin Su et al.   PLANT AND CELL PHYSIOLOGY

Characterization of Oncidium ‘Gower Ramsey’ Transcriptomes using 454 GS-FLX Pyrosequencing and Their Application to the Identification of Genes Associated with Flowering Time

(2011) Yu-Yun Chang et al.   PLANT AND CELL PHYSIOLOGY

Stars and Symbiosis: MicroRNA- and MicroRNA*-Mediated Transcript Cleavage Involved in Arbuscular Mycorrhizal Symbiosis

(2011) E. A. Devers et al.   PLANT PHYSIOLOGY

Sequencing-Based Approaches Reveal Low Ambient Temperature-Responsive and Tissue-Specific MicroRNAs in Phalaenopsis Orchid

(2011) Feng-Ming An et al.   PLoS One

Long noncoding RNA: unveiling hidden layer of gene regulatory networks

(2011) Eun-Deok Kim et al.   TRENDS IN PLANT SCIENCE

Profiling of cold-stress-responsive miRNAs in rice by microarrays

(2010) De-Kang Lv et al.   GENE

Tryptophan Residues Promote Membrane Association for a Plant Lipid Glycosyltransferase Involved in Phosphate Stress

(2010) Changrong Ge et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis

(2010) Hanna Lee et al.   NUCLEIC ACIDS RESEARCH

TCP Transcription Factors Regulate the Activities of ASYMMETRIC LEAVES1 and miR164, as Well as the Auxin Response, during Differentiation of Leaves in Arabidopsis

(2010) T. Koyama et al.   PLANT CELL

Transcriptome-wide identification of microRNA targets in rice

(2010) Yong-Fang Li et al.   PLANT JOURNAL

miR156-Regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana

(2009) Jia-Wei Wang et al.   CELL

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

(2009) Marcelo A German et al.   Nature Protocols

Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome

(2009) C. Addo-Quaye et al.   RNA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Identification of cold-inducible microRNAs in plants by transcriptome analysis

(2008) X ZHOU et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

(2008) Charles Addo-Quaye et al.   CURRENT BIOLOGY

Cool-night temperature induces spike emergence and affects photosynthetic efficiency and metabolizable carbohydrate and organic acid pools in Phalaenopsis aphrodite

(2008) Wen-Huei Chen et al.   PLANT CELL REPORTS

Small-interfering RNAs from natural antisense transcripts derived from a cellulose synthase gene modulate cell wall biosynthesis in barley

(2008) M. A. Held et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA