Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

MicroRNA nomenclature and the need for a revised naming prescription

(2015) Hikmet Budak et al.   Briefings in Functional Genomics

Plant miRNAs: biogenesis, organization and origins

(2015) Hikmet Budak et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data—The Case of the GrassAegilops tauschiiComplex Genome

(2015) Hikmet Budak et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Stress responsive miRNAs and isomiRs in cereals

(2015) Hikmet Budak et al.   PLANT SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice

(2014) Yujie Fang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differential regulation of microRNAs in response to osmotic, salt and cold stresses in wheat

(2014) Om Prakash Gupta et al.   MOLECULAR BIOLOGY REPORTS

Advances in identification and validation of plant microRNAs and their target genes

(2014) Xin Sun et al.   PHYSIOLOGIA PLANTARUM

mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

(2014) A. Li et al.   PLANT CELL

ptr-MIR169 is a posttranscriptional repressor of PtrHAP2 during vegetative bud dormancy period of aspen (Populus tremuloides) trees

(2013) Rewati Potkar et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Biogenesis, evolution, and functions of plant microRNAs

(2013) P. P. Pashkovskiy et al.   BIOCHEMISTRY-MOSCOW

Response of miRNAs and their targets to salt and drought stresses in cotton (Gossypium hirsutum L.)

(2013) Min Wang et al.   GENE

Discovery of MicroRNA169 Gene Copies in Genomes of Flowering Plants through Positional Information

(2013) Martín Calviño et al.   Genome Biology and Evolution

MicroRNAs and Their Cross-Talks in Plant Development

(2013) Danfeng Jin et al.   Journal of Genetics and Genomics

Proteome changes in wild and modern wheat leaves upon drought stress by two-dimensional electrophoresis and nanoLC-ESI–MS/MS

(2013) Hikmet Budak et al.   PLANT MOLECULAR BIOLOGY

MicroRNA-mediated gene regulation: potential applications for plant genetic engineering

(2013) Man Zhou et al.   PLANT MOLECULAR BIOLOGY

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

(2013) Zhiyong Ni et al.   PLANT MOLECULAR BIOLOGY

Unique and Conserved MicroRNAs in Wheat Chromosome 5D Revealed by Next-Generation Sequencing

(2013) Kuaybe Yucebilgili Kurtoglu et al.   PLoS One

Drought Tolerance in Modern and Wild Wheat

(2013) Hikmet Budak et al.   TheScientificWorldJOURNAL

Analysis of biochemical variations and microRNA expression in wild (Ipomoea campanulata) and cultivated (Jacquemontia pentantha) species exposed to in vivo water stress

(2013) Vallabhi Ghorecha et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

Subgenomic analysis of microRNAs in polyploid wheat

(2012) Melda Kantar et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Addressing the Role of microRNAs in Reprogramming Leaf Growth during Drought Stress in Brachypodium distachyon

(2012) Edoardo Bertolini et al.   Molecular Plant

miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data

(2012) Jiyuan An et al.   NUCLEIC ACIDS RESEARCH

Effects of Aluminum Oxide Nanoparticles on the Growth, Development, and microRNA Expression of Tobacco (Nicotiana tabacum)

(2012) Caitlin E. Burklew et al.   PLoS One

Functions of microRNAs in plant stress responses

(2012) Ramanjulu Sunkar et al.   TRENDS IN PLANT SCIENCE

PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs

(2011) Ping Xuan et al.   BIOINFORMATICS

MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

(2011) Yonggan Wu et al.   BMC BIOINFORMATICS

In Medicago truncatula, water deficit modulates the transcript accumulation of components of small RNA pathways

(2011) Cláudio Capitão et al.   BMC PLANT BIOLOGY

Deep sequencing of small RNAs in plants: applied bioinformatics

(2011) D. J. Studholme   Briefings in Functional Genomics

Alteration in expression of hormone-related genes in wild emmer wheat roots associated with drought adaptation mechanisms

(2011) Tamar Krugman et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Wheat Hybridization and Polyploidization Results in Deregulation of Small RNAs

(2011) Michal Kenan-Eichler et al.   GENETICS

High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis

(2011) N. W. Breakfield et al.   GENOME RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

Dehydration Stress-Responsive miRNA in Brachypodium distachyon: Evident by Genome-Wide Screening of microRNAs Expression

(2011) Hikmet Budak et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Over-expression of microRNA169 confers enhanced drought tolerance to tomato

(2010) Xiaohui Zhang et al.   BIOTECHNOLOGY LETTERS

Multilevel regulation and signalling processes associated with adaptation to terminal drought in wild emmer wheat

(2010) Tamar Krugman et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa

(2010) Liguo Zhou et al.   JOURNAL OF EXPERIMENTAL BOTANY

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

miRNA expression patterns of Triticum dicoccoides in response to shock drought stress

(2010) Melda Kantar et al.   PLANTA

HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models

(2009) Sabah Kadri et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Dicer-like (DCL) proteins in plants

(2009) Qingpo Liu et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Transcriptome pathways unique to dehydration tolerant relatives of modern wheat

(2009) Neslihan Z. Ergen et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Genomic dissection of drought resistance in durum wheat × wild emmer wheat recombinant inbreed line population

(2009) ZVI PELEG et al.   PLANT CELL AND ENVIRONMENT

Drought and salt tolerances in wild relatives for wheat and barley improvement

(2009) EVIATAR NEVO et al.   PLANT CELL AND ENVIRONMENT

miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula

(2009) Inês Trindade et al.   PLANTA

Conserved microRNAs and their targets in model grass species Brachypodium distachyon

(2009) Turgay Unver et al.   PLANTA

Identification of novel and candidate miRNAs in rice by high throughput sequencing

(2008) Ramanjulu Sunkar et al.   BMC PLANT BIOLOGY

Wild emmer: genetic resources, gene mapping and potential for wheat improvement

(2008) Weilong Xie et al.   EUPHYTICA

Data mining for miRNAs and their targets in the Triticeae

(2008) Ani Dryanova et al.   GENOME

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance

(2008) W.-X. Li et al.   PLANT CELL

Sequencing over 13 000 expressed sequence tags from six subtractive cDNA libraries of wild and modern wheats following slow drought stress

(2008) NESLIHAN Z. ERGEN et al.   PLANT CELL AND ENVIRONMENT