Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing

An RNA-Seq based gene expression atlas of the common bean

(2014) Jamie A O’Rourke et al.   BMC GENOMICS

Whole-genome discovery of miRNAs and their targets in wheat (Triticum aestivum L.)

(2014) Fenglong Sun et al.   BMC PLANT BIOLOGY

Computational identification of miRNAs and their targets in Phaseolus vulgaris

(2014) J. Han et al.   GENETICS AND MOLECULAR RESEARCH

Identification of Cold-Responsive miRNAs and Their Target Genes in Nitrogen-Fixing Nodules of Soybean

(2014) Senlei Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Homeodomain leucine-zipper proteins and their role in synchronizing growth and development with the environment

(2014) Ronny Brandt et al.   Journal of Integrative Plant Biology

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

Soybean miR172c Targets the Repressive AP2 Transcription Factor NNC1 to ActivateENOD40Expression and Regulate Nodule Initiation

(2014) Youning Wang et al.   PLANT CELL

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

(2014) Siwaret Arikit et al.   PLANT CELL

Transcriptome Analysis of Salt Tolerant Common Bean (Phaseolus vulgaris L.) under Saline Conditions

(2014) Mahmut Can Hiz et al.   PLoS One

Regulation of Copper Homeostasis and Biotic Interactions by MicroRNA 398b in Common Bean

(2014) Loreto Naya et al.   PLoS One

MicroRNA319 Positively Regulates Cold Tolerance by Targeting OsPCF6 and OsTCP21 in Rice (Oryza sativa L.)

(2014) Sun-ting Wang et al.   PLoS One

Extending the sRNAome of Apple by Next-Generation Sequencing

(2014) Marike Visser et al.   PLoS One

miRNAs: Biogenesis, Origin and Evolution, Functions on Virus-Host Interaction

(2013) Yang Zhuo et al.   CELLULAR PHYSIOLOGY AND BIOCHEMISTRY

Two Common Bean Genotypes with Contrasting Response to Phosphorus Deficiency Show Variations in the microRNA 399-Mediated PvPHO2 Regulation within the PvPHR1 Signaling Pathway

(2013) Mario Ramírez et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

miR172 Regulates Soybean Nodulation

(2013) Zhe Yan et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

TOO MUCH LOVE, a Novel Kelch Repeat-Containing F-box Protein, Functions in the Long-Distance Regulation of the Legume–Rhizobium Symbiosis

(2013) Masahiro Takahara et al.   PLANT AND CELL PHYSIOLOGY

The Plant Cell Reviews Aspects of MicroRNA and PhasiRNA Regulatory Function

(2013) N. A. Eckardt   PLANT CELL

MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots

(2013) Rui Xia et al.   PLANT CELL

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

(2013) Q. Fei et al.   PLANT CELL

Global identification of miRNAs and targets in Populus euphratica under salt stress

(2013) Bosheng Li et al.   PLANT MOLECULAR BIOLOGY

Small RNA pathways and diversity in model legumes: lessons from genomics

(2013) Pilar Bustos-Sanmamed et al.   Frontiers in Plant Science

On the complexity of miRNA-mediated regulation in plants: novel insights into the genomic organization of plant miRNAs

(2012) Moreno Colaiacovo et al.   Biology Direct

Genome organization and characteristics of soybean microRNAs

(2012) Marie Turner et al.   BMC GENOMICS

Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.)

(2012) Ernesto Ormeño-Orrillo et al.   BMC GENOMICS

Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing

(2012) Pablo Pelaez et al.   BMC GENOMICS

Identification of expressed resistance gene-like sequences by data mining in 454-derived transcriptomic sequences of common bean (Phaseolus vulgaris L.)

(2012) Zhanji Liu et al.   BMC PLANT BIOLOGY

Emerging role for RNA-based regulation in plant immunity

(2012) Dorothee Staiger et al.   NEW PHYTOLOGIST

The D3 F-box protein is a key component in host strigolactone responses essential for arbuscular mycorrhizal symbiosis

(2012) Satoko Yoshida et al.   NEW PHYTOLOGIST

Two Direct Targets of Cytokinin Signaling Regulate Symbiotic Nodulation in Medicago truncatula

(2012) F. Ariel et al.   PLANT CELL

The microRNA miR171h modulates arbuscular mycorrhizal colonization ofMedicago truncatulaby targetingNSP2

(2012) Dominique Lauressergues et al.   PLANT JOURNAL

Two MicroRNAs Linked to Nodule Infection and Nitrogen-Fixing Ability in the Legume Lotus japonicus

(2012) A. De Luis et al.   PLANT PHYSIOLOGY

Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics

(2012) Chad Brocker et al.   PLANTA

Genome-wide analysis of microRNAs in rubber tree (Hevea brasiliensis L.) using high-throughput sequencing

(2012) Manassawe Lertpanyasampatha et al.   PLANTA

Identification of Nitrogen Starvation-Responsive MicroRNAs in Arabidopsis thaliana

(2012) Gang Liang et al.   PLoS One

Plant secondary siRNA production determined by microRNA-duplex structure

(2012) P. A. Manavella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Apple miRNAs and tasiRNAs with novel regulatory networks

(2012) Rui Xia et al.   GENOME BIOLOGY

Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing

(2011) Venu Kalavacharla et al.   BMC PLANT BIOLOGY

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

(2011) J. Zhai et al.   GENES & DEVELOPMENT

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Evolution and Functional Diversification ofMIRNAGenes

(2011) Josh T. Cuperus et al.   PLANT CELL

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis

(2011) Xianwei Song et al.   PLANT JOURNAL

Conservation and divergence in plant microRNAs

(2011) Matthew W. Jones-Rhoades   PLANT MOLECULAR BIOLOGY

The Phaseolus vulgaris miR159a precursor encodes a second differentially expressed microRNA

(2011) Cecilia Contreras-Cubas et al.   PLANT MOLECULAR BIOLOGY

Vive la différence: biogenesis and evolution of microRNAs in plants and animals

(2011) Michael J Axtell et al.   GENOME BIOLOGY

MicroRNA-mediated signaling involved in plant root development

(2010) Yijun Meng et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Identification of homologous microRNAs in 56 animal genomes

(2010) Sung-Chou Li et al.   GENOMICS

High-throughput degradome sequencing can be used to gain insights into microRNA precursor metabolism

(2010) Y. Meng et al.   JOURNAL OF EXPERIMENTAL BOTANY

MicroRNA expression profile in common bean (Phaseolus vulgaris) under nutrient deficiency stresses and manganese toxicity

(2010) Oswaldo Valdés-López et al.   NEW PHYTOLOGIST

Arabidopsis lyrataSmall RNAs: TransientMIRNAand Small Interfering RNA Loci within theArabidopsisGenus

(2010) Zhaorong Ma et al.   PLANT CELL

Bs1, a New Chimeric Gene Formed by Retrotransposon-Mediated Exon Shuffling in Maize

(2010) N. Elrouby et al.   PLANT PHYSIOLOGY

Misexpression of miR482, miR1512, and miR1515 Increases Soybean Nodulation

(2010) H. Li et al.   PLANT PHYSIOLOGY

Origin, Biogenesis, and Activity of Plant MicroRNAs

(2009) Olivier Voinnet   CELL

Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia

(2009) Yan-Qiong Zhang et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Identification of microRNA in the protist Trichomonas vaginalis

(2009) Wei-Chen Lin et al.   GENOMICS

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

Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress

(2009) Catalina Arenas-Huertero et al.   PLANT MOLECULAR BIOLOGY

Global Changes in the Transcript and Metabolic Profiles during Symbiotic Nitrogen Fixation in Phosphorus-Stressed Common Bean Plants

(2009) G. Hernandez et al.   PLANT PHYSIOLOGY

Distinct extremely abundant siRNAs associated with cosuppression in petunia

(2009) E. De Paoli et al.   RNA

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

Evolution of microRNAs and their targets: Are all microRNAs biologically relevant?

(2008) M AXTELL   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

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Specificity of ARGONAUTE7-miR390 Interaction and Dual Functionality in TAS3 Trans-Acting siRNA Formation

(2008) Taiowa A. Montgomery et al.   CELL

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

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

A rice serine carboxypeptidase-like gene OsBISCPL1 is involved in regulation of defense responses against biotic and oxidative stress

(2008) Huizhi Liu et al.   GENE

A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains

(2008) Q.-H. Zhu et al.   GENOME RESEARCH

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

(2008) R. D. Morin et al.   GENOME RESEARCH

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

Criteria for Annotation of Plant MicroRNAs

(2008) B. C. Meyers et al.   PLANT CELL

Essential role of MYB transcription factor: PvPHR1 and microRNA: PvmiR399 in phosphorus-deficiency signalling in common bean roots

(2008) OSWALDO VALDÉS-LÓPEZ et al.   PLANT CELL AND ENVIRONMENT

MicroRNA166 controls root and nodule development in Medicago truncatula

(2008) Adnane Boualem et al.   PLANT JOURNAL