Long non-coding RNAs are major contributors to transcriptome changes in sunflower meiocytes with different recombination rates

Identification of miRNAs with potential roles in regulation of anther development and male-sterility in 7B-1 male-sterile tomato mutant

(2015) Vahid Omidvar et al.   BMC GENOMICS

A BRCA1-interacting lncRNA regulates homologous recombination

(2015) V. Sharma et al.   EMBO REPORTS

The plant-specific protein FEHLSTART controls male meiotic entry, initializing meiotic synchronization in Arabidopsis

(2015) Junhua Li et al.   PLANT JOURNAL

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

(2015) Jixian Zhai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Battles and hijacks: noncoding transcription in plants

(2015) Federico Ariel et al.   TRENDS IN PLANT SCIENCE

The Chromatin Protein DUET/MMD1 Controls Expression of the Meiotic Gene TDM1 during Male Meiosis in Arabidopsis

(2015) Sébastien Andreuzza et al.   PLoS Genetics

Non-coding RNAs: The small mysteries of males

(2015) Michael J. Axtell   Nature Plants

Long Non-coding RNAs and Their Biological Roles in Plants

(2015) Xue Liu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Regulation of Transcription by Long Noncoding RNAs

(2014) Roberto Bonasio et al.   Annual Review of Genetics

Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.)

(2014) Ran Han et al.   BMC GENOMICS

The transcriptome landscape of early maize meiosis

(2014) Stefanie Dukowic-Schulze et al.   BMC PLANT BIOLOGY

A deep survey of alternative splicing in grape reveals changes in the splicing machinery related to tissue, stress condition and genotype

(2014) Nicola Vitulo et al.   BMC PLANT BIOLOGY

LncTar: a tool for predicting the RNA targets of long noncoding RNAs

(2014) Jianwei Li et al.   BRIEFINGS IN BIOINFORMATICS

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

Genome-Wide Identification of Long Intergenic Noncoding RNA Genes and Their Potential Association with Domestication in Pigs

(2014) Zhong-Yin Zhou et al.   Genome Biology and Evolution

Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa

(2014) Peng Shuai et al.   JOURNAL OF EXPERIMENTAL BOTANY

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs

(2014) Reina Komiya et al.   PLANT JOURNAL

Long non-coding RNAs

(2014) Xiaoxia Ma et al.   RNA Biology

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

(2014) R. Johnson et al.   RNA

Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs

(2014) Ricardo A. Chávez Montes et al.   Nature Communications

Genome-wide discovery and characterization of maize long non-coding RNAs

(2014) Lin Li et al.   GENOME BIOLOGY

A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

(2013) Kenneth M. Olsen et al.   Annual Review of Plant Biology

The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads

(2013) Lucia Natali et al.   BMC GENOMICS

Comparative expression profiling of miRNA during anther development in genetic male sterile and wild type cotton

(2013) Mingming Wei et al.   BMC PLANT BIOLOGY

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Long non-coding genes implicated in response to stripe rust pathogen stress in wheat (Triticum aestivum L.)

(2013) Hong Zhang et al.   MOLECULAR BIOLOGY REPORTS

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Widespread Long Noncoding RNAs as Endogenous Target Mimics for MicroRNAs in Plants

(2013) H.-J. Wu et al.   PLANT PHYSIOLOGY

The dynamics of histone H3 modifications is species-specific in plant meiosis

(2013) Cecilia Oliver et al.   PLANTA

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Characterization of a set of novel meiotically-active promoters in Arabidopsis

(2012) Junhua Li et al.   BMC PLANT BIOLOGY

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Posttranscriptional Gene Regulation by Long Noncoding RNA

(2012) Je-Hyun Yoon et al.   JOURNAL OF MOLECULAR BIOLOGY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MIPS PlantsDB: a database framework for comparative plant genome research

(2012) Thomas Nussbaumer et al.   NUCLEIC ACIDS RESEARCH

A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice

(2012) J. Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reshaping of the maize transcriptome by domestication

(2012) R. Swanson-Wagner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Meiosis-Specific Noncoding RNA Mediates Robust Pairing of Homologous Chromosomes in Meiosis

(2012) D.-Q. Ding et al.   SCIENCE

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

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

(2011) Changbin Chen et al.   BMC PLANT BIOLOGY

Global transcriptome analysis of two ameiotic1 alleles in maize anthers: defining steps in meiotic entry and progression through prophase I

(2011) Guo-Ling Nan et al.   BMC PLANT BIOLOGY

MicroRNA activity in the Arabidopsis male germline

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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

BRCA2 is a mediator of RAD51- and DMC1-facilitated homologous recombination in Arabidopsis thaliana

(2011) Katharina Seeliger et al.   NEW PHYTOLOGIST

Pathways to meiotic recombination in Arabidopsis thaliana

(2011) Kim Osman et al.   NEW PHYTOLOGIST

PlantNATsDB: a comprehensive database of plant natural antisense transcripts

(2011) D. Chen et al.   NUCLEIC ACIDS RESEARCH

Small RNAs in angiosperms: sequence characteristics, distribution and generation

(2010) Dijun Chen et al.   BIOINFORMATICS

Control of female gamete formation by a small RNA pathway in Arabidopsis

(2010) Vianey Olmedo-Monfil et al.   NATURE

The transcriptome landscape of Arabidopsis male meiocytes from high-throughput sequencing: the complexity and evolution of the meiotic process

(2010) Hongxing Yang et al.   PLANT JOURNAL

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

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

Small RNA Diversity in Plants and its Impact in Development

(2009) Christine Lelandais-Briere et al.   CURRENT GENOMICS

RNA-mediated chromatin-based silencing in plants

(2009) Marjori Matzke et al.   CURRENT OPINION IN CELL BIOLOGY

Maize AMEIOTIC1 is essential for multiple early meiotic processes and likely required for the initiation of meiosis

(2009) W. P. Pawlowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

(2008) Shijun Mi et al.   CELL

Zm401, a short-open reading-frame mRNA or noncoding RNA, is essential for tapetum and microspore development and can regulate the floret formation in maize

(2008) Jinxia Ma et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Defining diversity, specialization, and gene specificity in transcriptomes through information theory

(2008) O. Martinez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Eukaryotic Genome as an RNA Machine

(2008) P. P. Amaral et al.   SCIENCE

Plant ARGONAUTES

(2008) Hervé Vaucheret   TRENDS IN PLANT SCIENCE