Differential microRNA expression, microRNA arm switching, and microRNA:long noncoding RNA interaction in response to salinity stress in soybean

R-Loop Mediated trans Action of the APOLO Long Noncoding RNA

(2020) Federico Ariel et al.   MOLECULAR CELL

Long Non-coding RNA in Plants in the Era of Reference Sequences

(2020) Hikmet Budak et al.   Frontiers in Plant Science

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

(2020) Wenyan Nong et al.   Nature Communications

Genome-wide identification of microRNAs and phased siRNAs in soybean roots under long-term salt stress

(2020) Qian Wang et al.   Genes & Genomics

LncMirNet: Predicting LncRNA–miRNA Interaction Based on Deep Learning of Ribonucleic Acid Sequences

(2020) Sen Yang et al.   MOLECULES

microRNA strand selection: Unwinding the rules

(2020) Jeffrey C. Medley et al.   Wiley Interdisciplinary Reviews-RNA

Exploration of miRNA-mediated fertility regulation network of cytoplasmic male sterility during flower bud development in soybean

(2019) Xianlong Ding et al.   3 Biotech

A reference-grade wild soybean genome

(2019) Min Xie et al.   Nature Communications

Homeostasis in the soybean miRNA396–GRF network is essential for productive soybean cyst nematode infections

(2019) Jason B Noon et al.   JOURNAL OF EXPERIMENTAL BOTANY

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon

(2019) Alejandro Sanz-Carbonell et al.   BMC PLANT BIOLOGY

Conserved miRNAs modulate the expression of potential transcription factors of isoflavonoid biosynthetic pathway in soybean seeds

(2019) Om Prakash Gupta et al.   MOLECULAR BIOLOGY REPORTS

Systematic identification and analysis of heat‐stress‐responsive lncRNAs, circRNAs and miRNAs with associated co‐expression and ceRNA networks in cucumber ( Cucumis sativus L.)

(2019) Xueying He et al.   PHYSIOLOGIA PLANTARUM

Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing

(2019) Yu et al.   Genes

Overexpression of soybean miR169c confers increased drought stress sensitivity in transgenic Arabidopsis thaliana

(2019) Yuehua Yu et al.   PLANT SCIENCE

Mechanisms and Functions of Long Non-Coding RNAs at Multiple Regulatory Levels

(2019) Xiaopei Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Analysis of Soybean Long Non-Coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts

(2019) Xiao Lin et al.   PLANT PHYSIOLOGY

psRNATarget: a plant small RNA target analysis server (2017 release)

(2018) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Transcriptomic reprogramming in soybean seedlings under salt stress

(2018) Ailin Liu et al.   PLANT CELL AND ENVIRONMENT

miRNA-Mediated Interactions in and between Plants and Insects

(2018) Chade Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Novel phosphate deficiency-responsive long non-coding RNAs in the legume model plant Medicago truncatula

(2017) Tianzuo Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families

(2017) Ioanna Kalvari et al.   NUCLEIC ACIDS RESEARCH

MicroRNAs regulate the sesquiterpenoid hormonal pathway in Drosophila and other arthropods

(2017) Zhe Qu et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Calcium-Dependent Protein Kinase in Ginger Binds with Importin-α through Its Junction Domain for Nuclear Localization, and Further Interacts with NAC Transcription Factor

(2017) Padmanabhan Jayanthi Vivek et al.   Frontiers in Plant Science

A long noncoding RNA involved in rice reproductive development by negatively regulating osa-miR160

(2017) Meng Wang et al.   Science Bulletin

Small RNA profiles in soybean primary root tips under water deficit

(2016) Yun Zheng et al.   BMC Systems Biology

Novel and conserved microRNAs in soybean floral whorls

(2016) F.R. Kulcheski et al.   GENE

Normalization for Relative Quantification of mRNA and microRNA in Soybean Exposed to Various Abiotic Stresses

(2016) Weican Liu et al.   PLoS One

Genome-Wide Small RNA Analysis of Soybean Reveals Auxin-Responsive microRNAs that are Differentially Expressed in Response to Salt Stress in Root Apex

(2016) Zhengxi Sun et al.   Frontiers in Plant Science

Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize

(2015) Chunyan Fan et al.   BMC GENOMICS

GmmiR156b overexpression delays flowering time in soybean

(2015) Dong Cao et al.   PLANT MOLECULAR BIOLOGY

MicroRNA Maturation and MicroRNA Target Gene Expression Regulation Are Severely Disrupted in Soybean dicer-like1 Double Mutants

(2015) Shaun J. Curtin et al.   G3-Genes Genomes Genetics

Flexible microRNA arm selection in rice

(2014) Wangxiong Hu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

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

Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop

(2014) Federico Ariel et al.   MOLECULAR CELL

AntisenseCOOLAIRmediates the coordinated switching of chromatin states atFLCduring vernalization

(2014) Tibor Csorba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean

(2014) Chu-Yu Ye et al.   Frontiers in Plant Science

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation

(2013) Feng Xu et al.   BMC GENOMICS

Identification and Dynamic Regulation of microRNAs Involved in Salt Stress Responses in Functional Soybean Nodules by High-Throughput Sequencing

(2013) Zhanghui Dong et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structure, evolution and function of the bi-directionally transcribed iab-4/iab-8 microRNA locus in arthropods

(2013) Jerome H. L. Hui et al.   NUCLEIC ACIDS RESEARCH

GmNFYA3, a target gene of miR169, is a positive regulator of plant tolerance to drought stress

(2013) Zhiyong Ni et al.   PLANT MOLECULAR BIOLOGY

Overexpression of gma-MIR394a confers tolerance to drought in transgenic Arabidopsis thaliana

(2012) Zhiyong Ni et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Expression Analysis of Nudix Hydrolase Genes in Chrysanthemum lavandulifolium

(2012) He Huang et al.   PLANT MOLECULAR BIOLOGY REPORTER

Characterization of the stress associated microRNAs in Glycine max by deep sequencing

(2011) Haiyan Li et al.   BMC PLANT BIOLOGY

MicroRNA evolution by arm switching

(2011) Sam Griffiths-Jones et al.   EMBO REPORTS

Arabidopsis Argonaute 2 Regulates Innate Immunity via miRNA393∗-Mediated Silencing of a Golgi-Localized SNARE Gene, MEMB12

(2011) Xiaoming Zhang et al.   MOLECULAR CELL

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

Functional Shifts in Insect microRNA Evolution

(2010) Antonio Marco et al.   Genome Biology and Evolution

Analysis of phosphorus-deficient responsive miRNAs and cis-elements from soybean (Glycine max L.)

(2010) Hou Qing Zeng et al.   JOURNAL OF PLANT PHYSIOLOGY

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA

(2010) J. B. Heo et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Labeled microRNA pull-down assay system: an experimental approach for high-throughput identification of microRNA-target mRNAs

(2009) Ren-Jun Hsu et al.   NUCLEIC ACIDS RESEARCH

Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing

(2009) L.-C. Hsieh et al.   PLANT PHYSIOLOGY

Salt Tolerance in Soybean

(2008) Tsui-Hung Phang et al.   Journal of Integrative Plant Biology

Regulatory Network of MicroRNA399 and PHO2 by Systemic Signaling

(2008) S.-I Lin et al.   PLANT PHYSIOLOGY

Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China

(2008) Yinghui Li et al.   THEORETICAL AND APPLIED GENETICS