Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots

Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

(2018) Mahmoud W. Yaish et al.   BMC GENOMICS

Dynamics and function of DNA methylation in plants

(2018) Huiming Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

UTR-Dependent Control of Gene Expression in Plants

(2018) Ashish Kumar Srivastava et al.   TRENDS IN PLANT SCIENCE

De novo assembly of a Chinese soybean genome

(2018) Yanting Shen et al.   Science China-Life Sciences

Genome-wide analysis of long non-coding RNAs at the mature stage of sea buckthorn ( Hippophae rhamnoides Linn) fruit

(2017) Guoyun Zhang et al.   GENE

The Long Intergenic Noncoding RNA (LincRNA) Landscape of the Soybean Genome

(2017) Agnieszka A. Golicz et al.   PLANT PHYSIOLOGY

Corrigendum: Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

(2017) Shuxia Li et al.   Scientific Reports

Editorial: Epigenetic Modifications Associated with Abiotic and Biotic Stresses in Plants: An Implication for Understanding Plant Evolution

(2017) Mahmoud W. Yaish   Frontiers in Plant Science

Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

(2016) Stanford Kwenda et al.   BMC GENOMICS

Genome-wide identification and functional prediction of novel and fungi-responsive lincRNAs in Triticum aestivum

(2016) Hong Zhang et al.   BMC GENOMICS

No longer a nuisance: long non-coding RNAs join CENP-A in epigenetic centromere regulation

(2016) Silvana Rošić et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Long noncoding RNA (lincRNA), a new paradigm in gene expression control

(2016) Emre Deniz et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Genome-wide identification and characterization of novel lncRNAs in Populus under nitrogen deficiency

(2016) Min Chen et al.   MOLECULAR GENETICS AND GENOMICS

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)

(2016) Xuke Lu et al.   PLoS One

Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development

(2016) Niraj Khemka et al.   Scientific Reports

Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development

(2015) Chunying Kang et al.   BMC GENOMICS

Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae

(2015) Setareh Mohammadin et al.   BMC PLANT BIOLOGY

Long Noncoding RNA in Hematopoiesis and Immunity

(2015) Ansuman T. Satpathy et al.   IMMUNITY

GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes

(2015) Patricia P. Chan et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNA transcriptome of plants

(2015) Jun Liu et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-Wide Identification, Characterization and Evolutionary Analysis of Long Intergenic Noncoding RNAs in Cucumber

(2015) Zhiqiang Hao et al.   PLoS One

Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

(2015) Jinyan Wang et al.   Scientific Reports

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

(2015) Rohini Garg et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Long Noncoding RNAs in Cell-Fate Programming and Reprogramming

(2014) Ryan A. Flynn et al.   Cell Stem Cell

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Induced and Constitutive DNA Methylation in a Salinity-Tolerant Wheat Introgression Line

(2014) Meng Wang et al.   PLANT AND CELL PHYSIOLOGY

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

Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light

(2014) Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Lin Li et al.   GENOME BIOLOGY

Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa

(2013) Xiang Yu et al.   BMC PLANT BIOLOGY

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

(2013) Hume Stroud et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

A Rice cis-Natural Antisense RNA Acts as a Translational Enhancer for Its Cognate mRNA and Contributes to Phosphate Homeostasis and Plant Fitness

(2013) M. Jabnoune et al.   PLANT CELL

Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing

(2013) Xin Qi et al.   PLANT MOLECULAR BIOLOGY

Arabidopsis thaliana RESISTANCE TO FUSARIUM OXYSPORUM 2 Implicates Tyrosine-Sulfated Peptide Signaling in Susceptibility and Resistance to Root Infection

(2013) Yunping Shen et al.   PLoS Genetics

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

(2012) J. Liu et al.   PLANT CELL

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

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

SoyTEdb: a comprehensive database of transposable elements in the soybean genome

(2010) Jianchang Du et al.   BMC GENOMICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes

(2008) Andrzej T. Wierzbicki et al.   CELL