De Novo Assembly and Transcriptome Analysis of Bulb Onion (Allium cepa L.) during Cold Acclimation Using Contrasting Genotypes

Molecular and Functional Characterization of FLOWERING LOCUS T Homologs in Allium cepa

(2016) Ranjith Manoharan et al.   MOLECULES

Genome-wide analysis of the distribution of AP2/ERF transcription factors reveals duplication and CBFs genes elucidate their potential function in Brassica oleracea

(2014) Senthil Thamilarasan et al.   BMC GENOMICS

De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification

(2014) Steven A Yates et al.   BMC GENOMICS

Drought stress responses in crops

(2014) Arun K. Shanker et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Transcriptome analysis of newly classified bZIP transcription factors of Brassica rapa in cold stress response

(2014) Indeok Hwang et al.   GENOMICS

De novo sequencing and transcriptome analysis of the desert shrub, Ammopiptanthus mongolicus, during cold acclimation using Illumina/Solexa

(2013) Tao Pang et al.   BMC GENOMICS

De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress

(2013) Dan-Qing Tian et al.   BMC GENOMICS

Molecular Characterization of Chenopodium album Chloroplast Small Heat Shock Protein and Its Expression in Response to Different Abiotic Stresses

(2013) Noor Ul Haq et al.   PLANT MOLECULAR BIOLOGY REPORTER

Global Analysis of Transcriptome Responses and Gene Expression Profiles to Cold Stress of Jatropha curcas L.

(2013) Haibo Wang et al.   PLoS One

Transcriptome sequencing to produce SNP-based genetic maps of onion

(2013) J. Duangjit et al.   THEORETICAL AND APPLIED GENETICS

Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq

(2012) Chao Feng et al.   BMC GENOMICS

De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.)

(2012) Dejun Li et al.   BMC GENOMICS

Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.)

(2012) Yongli Zhao et al.   BMC PLANT BIOLOGY

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

(2011) S Samuel Yang et al.   BMC GENOMICS

Engineering Cold Stress Tolerance in Crop Plants

(2011) Gulzar S. Sanghera et al.   CURRENT GENOMICS

A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana

(2011) Marcela A. Carvallo et al.   JOURNAL OF EXPERIMENTAL BOTANY

Molecular characterization of 60 isolated wheat MYB genes and analysis of their expression during abiotic stress

(2011) Lichao Zhang 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

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Profiling of Dehydration Stress in the Chinese Cabbage (Brassica rapa L. ssp. pekinensis) by Tag Sequencing

(2011) Shuancang Yu et al.   PLANT MOLECULAR BIOLOGY REPORTER

CBF-dependent signaling pathway: A key responder to low temperature stress in plants

(2010) M.Q. Zhou et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing

(2010) Cinzia Cantacessi et al.   NUCLEIC ACIDS RESEARCH

Plant responses to cold: transcriptome analysis of wheat

(2010) Mark O. Winfield et al.   PLANT BIOTECHNOLOGY JOURNAL

Molecular Basis of Plant Cold Acclimation: Insights Gained from Studying the CBF Cold Response Pathway

(2010) M. F. Thomashow   PLANT PHYSIOLOGY

The CBFs: Three arabidopsis transcription factors to cold acclimate

(2010) Joaquín Medina et al.   PLANT SCIENCE

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

(2009) Zoltán Hegedűs et al.   MOLECULAR IMMUNOLOGY

Functions and mechanisms of the CBL–CIPK signaling system in plant response to abiotic stress

(2009) Ruifen Li et al.   Progress in Natural Science-Materials International

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Role of fructose in the adaptation of plants to cold-induced oxidative stress

(2008) J. Bogdanović et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array

(2008) A. Matsui et al.   PLANT AND CELL PHYSIOLOGY

iPath: interactive exploration of biochemical pathways and networks

(2008) Ivica Letunic et al.   TRENDS IN BIOCHEMICAL SCIENCES

msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design

(2007) BRANT C. FAIRCLOTH   Molecular Ecology Resources