Temperature expression patterns of genes and their coexpression with LncRNAs revealed by RNA-Seq in non-heading Chinese cabbage

Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing

(2014) Coline Billerey et al.   BMC GENOMICS

ABA-dependent and ABA-independent signaling in response to osmotic stress in plants

(2014) Takuya Yoshida et al.   CURRENT OPINION IN PLANT BIOLOGY

Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs

(2014) S. Ounzain et al.   EUROPEAN HEART JOURNAL

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat

(2014) Kazuo Nakashima et al.   Frontiers in Plant Science

Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing

(2014) Meng-Yao Li et al.   Horticulture Research

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

Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress

(2013) Yanjie Xu et al.   BMC GENOMICS

Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing

(2013) Rosemarie Weikard et al.   BMC GENOMICS

De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud)

(2013) Touming Liu et al.   BMC GENOMICS

Differential expression of CPKs and cytosolic Ca2+ variation in resistant and susceptible apple cultivars (Malus x domestica) in response to the pathogen Erwinia amylovora and mechanical wounding

(2013) Chidananda Nagamangala Kanchiswamy et al.   BMC GENOMICS

Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis)

(2013) Xiaoming Song et al.   BMC GENOMICS

De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism

(2013) Yan Wang et al.   BMC GENOMICS

Transcriptome analysis of heat stress response in switchgrass (Panicum virgatum L.)

(2013) Yong-Fang Li et al.   BMC PLANT BIOLOGY

Differential physiological responses of different rice (Oryza sativa) cultivars to elevated night temperature during vegetative growth

(2013) Ulrike Glaubitz et al.   FUNCTIONAL PLANT BIOLOGY

Predicting long non-coding RNAs using RNA sequencing

(2013) Nicholas E. Ilott et al.   METHODS

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

(2013) Liang Sun et al.   NUCLEIC ACIDS RESEARCH

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

Cross-talk between abscisic acid-dependent and abscisic acid-independent pathways during abiotic stress

(2013) Aryadeep Roychoudhury et al.   PLANT CELL REPORTS

Roles of CAMTA transcription factors and salicylic acid in configuring the low-temperature transcriptome and freezing tolerance of Arabidopsis

(2013) YongSig Kim et al.   PLANT JOURNAL

Simultaneous Application of Heat, Drought, and Virus to Arabidopsis Plants Reveals Significant Shifts in Signaling Networks

(2013) C. M. Prasch et al.   PLANT PHYSIOLOGY

Identification and Characterization of Long Non-Coding RNAs Related to Mouse Embryonic Brain Development from Available Transcriptomic Data

(2013) Jie Lv et al.   PLoS One

De Novo Assembly and Characterization of the Transcriptome, and Development of SSR Markers in Wax Gourd (Benicasa hispida)

(2013) Biao Jiang et al.   PLoS One

Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks

(2012) J. Krasensky et al.   JOURNAL OF EXPERIMENTAL BOTANY

Rfam 11.0: 10 years of RNA families

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

Pivotal role of the AREB/ABF-SnRK2 pathway in ABRE-mediated transcription in response to osmotic stress in plants

(2012) Yasunari Fujita et al.   PHYSIOLOGIA PLANTARUM

Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays

(2012) Susan Boerner et al.   PLoS One

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

BRAD, the genetics and genomics database for Brassica plants

(2011) Feng Cheng et al.   BMC PLANT BIOLOGY

Non-coding RNAs as regulators of gene expression and epigenetics

(2011) M. U. Kaikkonen et al.   CARDIOVASCULAR RESEARCH

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

ABA-mediated transcriptional regulation in response to osmotic stress in plants

(2011) Yasunari Fujita et al.   JOURNAL OF PLANT RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

Plant responses to cold: transcriptome analysis of wheat

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

ABA perception and signalling

(2010) Agepati S. Raghavendra et al.   TRENDS IN PLANT SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Roles for Arabidopsis CAMTA Transcription Factors in Cold-Regulated Gene Expression and Freezing Tolerance

(2009) C. J. Doherty et al.   PLANT CELL

AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent ABA signaling involved in drought stress tolerance and require ABA for full activation

(2009) Takuya Yoshida et al.   PLANT JOURNAL

Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses

(2009) K. Nakashima et al.   PLANT PHYSIOLOGY

Cytochrome P450 Monooxygenases as Reporters for Circadian-Regulated Pathways

(2009) Y. Pan et al.   PLANT PHYSIOLOGY

Metabolic Pathways Involved in Cold Acclimation Identified by Integrated Analysis of Metabolites and Transcripts Regulated by DREB1A and DREB2A

(2009) K. Maruyama et al.   PLANT PHYSIOLOGY

Transcription factors and regulation of photosynthetic and related metabolism under environmental stresses

(2008) Nelson J. M. Saibo et al.   ANNALS OF BOTANY

Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature

(2008) Stephen J Robinson et al.   BMC GENOMICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH