Identification of novel small ncRNAs in pollen of tomato

NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome

(2015) Hamed Bostan et al.   BMC PLANT BIOLOGY

Identification of novel and conserved miRNAs involved in pollen development in Brassica campestris ssp. chinensis by high-throughput sequencing and degradome analysis

(2014) Jianxia Jiang et al.   BMC GENOMICS

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

A non-canonical plant microRNA target site

(2014) Cécile Brousse et al.   NUCLEIC ACIDS RESEARCH

HEAT-INDUCED TAS1 TARGET1 Mediates Thermotolerance via HEAT STRESS TRANSCRIPTION FACTOR A1a-Directed Pathways in Arabidopsis

(2014) S. Li et al.   PLANT CELL

Virus induced gene silencing of three putative prolyl 4-hydroxylases enhances plant growth in tomato (Solanum lycopersicum)

(2014) Sotirios Fragkostefanakis et al.   PLANT MOLECULAR BIOLOGY

Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens

(2014) C.-Y. Chang et al.   PLANT PHYSIOLOGY

Tomato Genomic Resources Database: An Integrated Repository of Useful Tomato Genomic Information for Basic and Applied Research

(2014) B. Venkata Suresh et al.   PLoS One

Perspectives on deciphering mechanisms underlying plant heat stress response and thermotolerance

(2014) Kamila Bokszczanin   Frontiers in Plant Science

Expression patterns of conserved microRNAs in the male gametophyte of loblolly pine (Pinus taeda)

(2014) Christina R. Quinn et al.   Plant Reproduction

tRNA modifications: Necessary for correct tRNA-derived fragments during the recovery from stress?

(2013) Zeljko Durdevic et al.   BIOESSAYS

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data

(2013) Sören Müller et al.   BIOINFORMATICS

Massive analysis of cDNA Ends (MACE) and miRNA expression profiling identifies proatherogenic pathways in chronic kidney disease

(2013) Adam M Zawada et al.   Epigenetics

OsPOP5, A Prolyl Oligopeptidase Family Gene from Rice Confers Abiotic Stress Tolerance in Escherichia coli

(2013) Cun-Mei Tan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Arabidopsis Non-Coding RNA Regulation in Abiotic Stress Responses

(2013) Akihiro Matsui et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Non-Coding RNAs: Multi-Tasking Molecules in the Cell

(2013) Anita Gomes et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis

(2013) Rumyana Karlova et al.   JOURNAL OF EXPERIMENTAL BOTANY

Cell-specific Analysis of the Tomato Pollen Proteome from Pollen Mother Cell to Mature Pollen Provides Evidence for Developmental Priming

(2013) Palak Chaturvedi et al.   JOURNAL OF PROTEOME RESEARCH

Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources

(2013) Julie M. Cridland et al.   MOLECULAR BIOLOGY AND EVOLUTION

The RdDM Pathway Is Required for Basal Heat Tolerance in Arabidopsis

(2013) Olga V. Popova et al.   Molecular Plant

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

NOT2 Proteins Promote Polymerase II-Dependent Transcription and Interact with Multiple MicroRNA Biogenesis Factors in Arabidopsis

(2013) L. Wang et al.   PLANT CELL

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

(2013) D. Staiger et al.   PLANT CELL

Heat stress induction ofmiR398triggers a regulatory loop that is critical for thermotolerance in Arabidopsis

(2013) Qingmei Guan et al.   PLANT JOURNAL

An Autoregulatory Loop Controlling Arabidopsis HsfA2 Expression: Role of Heat Shock-Induced Alternative Splicing

(2013) J. Liu et al.   PLANT PHYSIOLOGY

RNA-Seq of Arabidopsis Pollen Uncovers Novel Transcription and Alternative Splicing

(2013) A. E. Loraine et al.   PLANT PHYSIOLOGY

High-Throughput Sequencing of Small RNAs from Pollen and Silk and Characterization of miRNAs as Candidate Factors Involved in Pollen-Silk Interactions in Maize

(2013) Xiao Ming Li et al.   PLoS One

Small RNAs derived from the 5′ end of tRNA can inhibit protein translation in human cells

(2013) Andrew Sobala et al.   RNA Biology

Reprogramming of DNA Methylation in Pollen Guides Epigenetic Inheritance via Small RNA

(2012) Joseph P. Calarco et al.   CELL

A genome-wide analysis of the RNA helicase gene family in Solanum lycopersicum

(2012) Ruirui Xu et al.   GENE

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

Epigenetic Reprogramming in Plant Reproductive Lineages

(2012) J. F. Gutierrez-Marcos et al.   PLANT AND CELL PHYSIOLOGY

MicroRNA regulation of plant innate immune receptors

(2012) F. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant Small RNAs: Biogenesis, Mode of Action and Their Roles in Abiotic Stresses

(2012) Praveen Guleria et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

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

The plant heat stress transcription factor (Hsf) family: Structure, function and evolution

(2011) Klaus-Dieter Scharf et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes

(2011) Changbin Chen et al.   BMC PLANT BIOLOGY

Predicting miRNA-mediated gene silencing mode based on miRNA-target duplex features

(2011) Xiaofeng Song et al.   COMPUTERS IN BIOLOGY AND MEDICINE

The Response to Heat Shock and Oxidative Stress in Saccharomyces cerevisiae

(2011) K. A. Morano et al.   GENETICS

MicroRNA activity in the Arabidopsis male germline

(2011) Filipe Borges et al.   JOURNAL OF EXPERIMENTAL BOTANY

Function and Evolution of a MicroRNA That Regulates a Ca2+-ATPase and Triggers the Formation of Phased Small Interfering RNAs in Tomato Reproductive Growth

(2011) Ying Wang et al.   PLANT CELL

Evolution and Functional Diversification ofMIRNAGenes

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

The role of class A1 heat shock factors (HSFA1s) in response to heat and other stresses in Arabidopsis

(2011) HSIANG-CHIN LIU et al.   PLANT CELL AND ENVIRONMENT

Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns

(2011) Irina Mohorianu et al.   PLANT JOURNAL

MicroRNAs and their diverse functions in plants

(2011) Guiling Sun   PLANT MOLECULAR BIOLOGY

Expression of arabinogalactan proteins during tomato fruit ripening and in response to mechanical wounding, hypoxia and anoxia

(2011) Sotirios Fragkostefanakis et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

(2011) Li Wei et al.   GENOME BIOLOGY

TAS1trans-Acting siRNA Targets Are Differentially Regulated at Low Temperature, and TAS1trans-Acting siRNA Mediates Temperature-Controlled At1g51670 Expression

(2010) Kohei KUME et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa

(2010) Li Q Wei et al.   BMC GENOMICS

Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.)

(2010) Mingming Xin et al.   BMC PLANT BIOLOGY

Non-coding small RNAs responsive to abiotic stress in wheat (Triticum aestivum L.)

(2010) Yingyin Yao et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Comparison of hormonal responses to heat, drought and combined stress in tobacco plants with elevated proline content

(2010) Jana Dobra et al.   JOURNAL OF PLANT PHYSIOLOGY

Lowly Expressed Genes in Arabidopsis thaliana Bear the Signature of Possible Pseudogenization by Promoter Degradation

(2010) L. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Atlas of Rice Grain Filling-Related Metabolism under High Temperature: Joint Analysis of Metabolome and Transcriptome Demonstrated Inhibition of Starch Accumulation and Induction of Amino Acid Accumulation

(2010) Hiromoto Yamakawa et al.   PLANT AND CELL PHYSIOLOGY

Research on plant abiotic stress responses in the post-genome era: past, present and future

(2010) Takashi Hirayama et al.   PLANT JOURNAL

Hemin and Magnesium-Protoporphyrin IX Induce Global Changes in Gene Expression in Chlamydomonas reinhardtii

(2010) B. Voss et al.   PLANT PHYSIOLOGY

The laccase multigene family in Arabidopsis thaliana: towards addressing the mystery of their gene function(s)

(2010) Phanikanth V. Turlapati et al.   PLANTA

Regulatory RNAs derived from transfer RNA?

(2010) T. Pederson   RNA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Roles of Plant Small RNAs in Biotic Stress Responses

(2009) Virginia Ruiz-Ferrer et al.   Annual Review of Plant Biology

Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis

(2009) Yongxin Chen et al.   BMC GENOMICS

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

tRNA as an active chemical scaffold for diverse chemical transformations

(2009) Christopher S. Francklyn et al.   FEBS LETTERS

Computational and analytical framework for small RNA profiling by high-throughput sequencing

(2009) N. Fahlgren et al.   RNA

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

(2009) C. Cole et al.   RNA

Proline: a multifunctional amino acid

(2009) László Szabados et al.   TRENDS IN PLANT SCIENCE

Proline accumulation in plants: a review

(2008) Nathalie Verbruggen et al.   AMINO ACIDS

ISOL@: an Italian SOLAnaceae genomics resource

(2008) Maria Luisa Chiusano et al.   BMC BIOINFORMATICS

Identification of conserved microRNAs and their targets from Solanum lycopersicum Mill

(2008) Jianguang Zhang et al.   GENE

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

(2008) S. Moxon et al.   GENOME RESEARCH

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

Role of Arabidopsis CHL27 Protein for Photosynthesis, Chloroplast Development and Gene Expression Profiling

(2008) Woo Young Bang et al.   PLANT AND CELL PHYSIOLOGY

Criteria for Annotation of Plant MicroRNAs

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

The transcriptional co-activator PGC-1α up regulates apelin in human and mouse adipocytes

(2008) Anne Mazzucotelli et al.   REGULATORY PEPTIDES

tRNA cleavage is a conserved response to oxidative stress in eukaryotes

(2008) D. M. Thompson et al.   RNA

Widespread Translational Inhibition by Plant miRNAs and siRNAs

(2008) P. Brodersen et al.   SCIENCE

Small RNAs in tomato fruit and leaf development

(2007) A ITAYA et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms