Genome‐wide lncRNAs identification and association analysis for cold‐responsive genes at the booting stage in rice ( Oryza sativa L.)

Genes, pathways and transcription factors involved in seedling stage chilling stress tolerance in indica rice through RNA-Seq analysis

(2019) Sharat Kumar Pradhan et al.   BMC PLANT BIOLOGY

Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress

(2018) Liang Chen et al.   BMC GENOMICS

Integrative analysis of long non-coding RNA acting as ceRNAs involved in chilling injury in tomato fruit

(2018) Yunxiang Wang et al.   GENE

Identification of a cold-tolerant locus in rice (Oryza sativa L.) using bulked segregant analysis with a next-generation sequencing strategy

(2018) Jian Sun et al.   Rice

Long Non-Coding RNAs Responsive to Salt and Boron Stress in the Hyper-Arid Lluteño Maize from Atacama Desert

(2018) Wilson Huanca-Mamani et al.   Genes

Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants

(2018) Priyanka Borah et al.   Genes

Transcriptome profiling of rice seedlings under cold stress

(2017) Luciano C. da Maia et al.   FUNCTIONAL PLANT BIOLOGY

Association analysis of the glutelin synthesis genes GluA and GluB1 in a Japonica rice collection

(2017) Wentao Zhang et al.   MOLECULAR BREEDING

Updating the elite rice variety Kongyu 131 by improving the Gn1a locus

(2017) Xiaomin Feng et al.   Rice

Quantitative trait loci identification and meta-analysis for rice panicle-related traits

(2016) Yahui Wu et al.   MOLECULAR GENETICS AND GENOMICS

Rice-cold tolerance across reproductive stages

(2016) J. H. Mitchell et al.   Crop & Pasture Science

Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing

(2015) Tian-Zuo Wang et al.   BMC PLANT BIOLOGY

Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress

(2015) Bin Bai et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Enhancing blast disease resistance by overexpression of the calcium-dependent protein kinaseOsCPK4in rice

(2015) Mireia Bundó et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-wide screening for novel, drought stress-responsive long non-coding RNAs in drought-stressed leaf transcriptome of drought-tolerant and -susceptible banana (Musa spp) cultivars using Illumina high-throughput sequencing

(2015) M. Muthusamy et al.   Plant Biotechnology Reports

Comparative Transcriptome Analysis of Shoots and Roots of TNG67 and TCN1 Rice Seedlings under Cold Stress and Following Subsequent Recovery: Insights into Metabolic Pathways, Phytohormones, and Transcription Factors

(2015) Yun-Wei Yang et al.   PLoS One

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

(2014) Jianwei Li et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Comparative transcriptome analysis of RNA-seq data for cold-tolerant and cold-sensitive rice genotypes under cold stress

(2014) Chunxiu Shen et al.   JOURNAL OF PLANT BIOLOGY

Overexpression of a Calcium-Dependent Protein Kinase Confers Salt and Drought Tolerance in Rice by Preventing Membrane Lipid Peroxidation

(2014) S. Campo et al.   PLANT PHYSIOLOGY

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

(2014) R. Johnson et al.   RNA

The genetic architecture of zinc and iron content in maize grains as revealed by QTL mapping and meta-analysis

(2013) Tiantian Jin et al.   BREEDING SCIENCE

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

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer 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

Avoiding damage and achieving cold tolerance in rice plants

(2013) Renata Pereira da Cruz et al.   Food and Energy Security

BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms

(2012) O. Sosnowski et al.   BIOINFORMATICS

Genome-wide analysis of long noncoding RNA stability

(2012) M. B. Clark et al.   GENOME RESEARCH

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

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

(2012) J. Liu et al.   PLANT CELL

Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

(2011) Mingming Xin et al.   BMC PLANT BIOLOGY

A meta-analysis of seed protein concentration QTL in soybean

(2011) Qi Zhao-ming et al.   CANADIAN JOURNAL OF PLANT SCIENCE

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Erratum: Corrigendum: Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Meta-analysis: Its strengths and limitations

(2009) E. WALKER et al.   CLEVELAND CLINIC JOURNAL OF MEDICINE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Diamonds in the rough: mRNA-like non-coding RNAs

(2008) Linda A. Rymarquis et al.   TRENDS IN PLANT SCIENCE