Integrating transcriptome and microRNA analysis identifies genes and microRNAs for AHO-induced systemic acquired resistance in N. tabacum

Functional Roles of microRNAs in Agronomically Important Plants—Potential as Targets for Crop Improvement and Protection

(2017) Arnaud T. Djami-Tchatchou et al.   Frontiers in Plant Science

Transcriptome and metabolite analysis identifies nitrogen utilization genes in tea plant (Camellia sinensis)

(2017) Wei Li et al.   Scientific Reports

Integrated RNA-seq and sRNA-seq analysis reveals miRNA effects on secondary metabolism in Solanum tuberosum L

(2016) Yan Qiao et al.   MOLECULAR GENETICS AND GENOMICS

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Integrative Analysis of the microRNAome and Transcriptome Illuminates the Response of Susceptible Rice Plants to Rice Stripe Virus

(2016) Jian Yang et al.   PLoS One

Comparative transcriptomic analysis uncovers the complex genetic network for resistance to Sclerotinia sclerotiorum in Brassica napus

(2016) Jian Wu et al.   Scientific Reports

Salicylic acid signalling: new insights and prospects at a quarter-century milestone

(2015) X. Liu et al.   Essays in Biochemistry

Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genes

(2015) Xuewen Wang et al.   MOLECULAR GENETICS AND GENOMICS

OSC2 and CYP716A14v2 Catalyze the Biosynthesis of Triterpenoids for the Cuticle of Aerial Organs ofArtemisia annua

(2015) Tessa Moses et al.   PLANT CELL

Role of proline and pyrroline-5-carboxylate metabolism in plant defense against invading pathogens

(2015) Aarzoo Qamar   Frontiers in Plant Science

Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis)

(2015) Chao Zheng et al.   PLoS One

miRPlant: an integrated tool for identification of plant miRNA from RNA sequencing data

(2014) Jiyuan An et al.   BMC BIOINFORMATICS

Integrated analysis of miRNA and mRNA expression profiles in response to Cd exposure in rice seedlings

(2014) Mingfeng Tang et al.   BMC GENOMICS

Jasmonate-Triggered Plant Immunity

(2014) Marcelo L. Campos et al.   JOURNAL OF CHEMICAL ECOLOGY

Identification and consequences of miRNA–target interactions — beyond repression of gene expression

(2014) Jean Hausser et al.   NATURE REVIEWS GENETICS

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Signaling by small metabolites in systemic acquired resistance

(2014) Jyoti Shah et al.   PLANT JOURNAL

The tobacco genome sequence and its comparison with those of tomato and potato

(2014) Nicolas Sierro et al.   Nature Communications

Systemic Acquired Resistance: Turning Local Infection into Global Defense

(2013) Zheng Qing Fu et al.   Annual Review of Plant Biology

Impacts of pr-10a Overexpression at the Molecular and the Phenotypic Level

(2013) Lea Vaas et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Systemic Acquired Resistance (50 Years after Discovery): Moving from the Lab to the Field

(2013) Franco Gozzo et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Salicylic acid: an old hormone up to new tricks

(2013) Jon Lucas Boatwright et al.   MOLECULAR PLANT PATHOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs

(2013) Francesco Licausi et al.   NEW PHYTOLOGIST

Induction of Antiviral Responses by Acibenzolar-S-Methyl Against Cucurbit chlorotic yellows virus in Melon

(2013) Minoru Takeshita et al.   PHYTOPATHOLOGY

Target of tae-miR408, a chemocyanin-like protein gene (TaCLP1), plays positive roles in wheat response to high-salinity, heavy cupric stress and stripe rust

(2013) Hao Feng et al.   PLANT MOLECULAR BIOLOGY

Reduced Carbohydrate Availability Enhances the Susceptibility of Arabidopsis toward Colletotrichum higginsianum

(2013) T. Engelsdorf et al.   PLANT PHYSIOLOGY

The miR172 target TOE3 represses AGAMOUS expression during Arabidopsis floral patterning

(2013) Jae-Hoon Jung et al.   PLANT SCIENCE

Genome sequence of the date palm Phoenix dactylifera L

(2013) Ibrahim S. Al-Mssallem et al.   Nature Communications

Group A PP2Cs evolved in land plants as key regulators of intrinsic desiccation tolerance

(2013) Kenji Komatsu et al.   Nature Communications

Functional Evolution in the Plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) Gene Family

(2013) Jill C. Preston et al.   Frontiers in Plant Science

Comprehensive analysis of differential genes and miRNA profiles for discovery of topping-responsive genes in flue-cured tobacco roots

(2012) Yuancheng Qi et al.   FEBS Journal

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

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

(2011) Basel Khraiwesh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

psRNATarget: a plant small RNA target analysis server

(2011) Xinbin Dai et al.   NUCLEIC ACIDS RESEARCH

AGO1 and AGO2 Act Redundantly in miR408-Mediated Plantacyanin Regulation

(2011) Nicolas Maunoury et al.   PLoS One

Differential Expression of miRNAs in Response to Topping in Flue-Cured Tobacco (Nicotiana tabacum) Roots

(2011) Hongxiang Guo et al.   PLoS One

Abscisic Acid: Emergence of a Core Signaling Network

(2010) Sean R. Cutler et al.   Annual Review of Plant Biology

Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development

(2010) Amarjeet Singh et al.   BMC GENOMICS

SQUAMOSA Promoter-Binding Protein-Like Transcription Factors: Star Players for Plant Growth and Development

(2010) Xiaobo Chen et al.   Journal of Integrative Plant Biology

Post-Translational Derepression of Invertase Activity in Source Leaves via Down-Regulation of Invertase Inhibitor Expression Is Part of the Plant Defense Response

(2010) Katharina B. Bonfig et al.   Molecular Plant

Sugar transporters for intercellular exchange and nutrition of pathogens

(2010) Li-Qing Chen et al.   NATURE

Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks

(2010) Weixiong Zhang et al.   PLANT MOLECULAR BIOLOGY

Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum)

(2010) Taylor P. Frazier et al.   PLANTA

The microRNA156 and microRNA172 gene regulation cascades at post-germinative stages in Arabidopsis

(2010) Ruth C. Martin et al.   SEED SCIENCE RESEARCH

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Salicylic Acid, a Multifaceted Hormone to Combat Disease

(2009) A. Corina Vlot et al.   Annual Review of Phytopathology

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

Regulation and functional specialization of small RNA–target nodes during plant development

(2009) Ignacio Rubio-Somoza et al.   CURRENT OPINION IN PLANT BIOLOGY

Host small RNAs are big contributors to plant innate immunity

(2009) Chellappan Padmanabhan et al.   CURRENT OPINION IN PLANT BIOLOGY

Functional analyses of the ABI1-related protein phosphatase type 2C reveal evolutionarily conserved regulation of abscisic acid signaling between Arabidopsis and the moss Physcomitrella patens

(2009) Kenji Komatsu et al.   PLANT MOLECULAR BIOLOGY

Endogenous small RNAs and antibacterial immunity in plants

(2008) Hailing Jin   FEBS LETTERS

Biological and Molecular Analyses of the Acibenzolar-S-Methyl-Induced Systemic Acquired Resistance in Flue-Cured Tobacco AgainstTomato spotted wilt virus

(2008) B. Mandal et al.   PHYTOPATHOLOGY

3-Acetonyl-3-hydroxyoxindole: a new inducer of systemic acquired resistance in plants

(2008) Yanmei Li et al.   PLANT BIOTECHNOLOGY JOURNAL

Criteria for Annotation of Plant MicroRNAs

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