Gene expression atlas of pigeonpea and its application to gain insights into genes associated with pollen fertility implicated in seed formation

Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan)

(2016) Lekha T. Pazhamala et al.   PLoS One

Quantitative visualization of alternative exon expression from RNA-seq data

(2015) Yarden Katz et al.   BIOINFORMATICS

The Arabidopsis epitranscriptome

(2015) Rupert G Fray et al.   CURRENT OPINION IN PLANT BIOLOGY

Next-generation sequencing for identification of candidate genes forFusariumwilt and sterility mosaic disease in pigeonpea (Cajanus cajan)

(2015) Vikas K. Singh et al.   PLANT BIOTECHNOLOGY JOURNAL

Full-lengthde novoassembly of RNA-seq data in pea (Pisum sativumL.) provides a gene expression atlas and gives insights into root nodulation in this species

(2015) Susete Alves-Carvalho et al.   PLANT JOURNAL

Evaluation and Validation of Housekeeping Genes as Reference for Gene Expression Studies in Pigeonpea (Cajanus cajan) Under Drought Stress Conditions

(2015) Pallavi Sinha et al.   PLoS One

NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

(2015) Mohan A. V. S. K. Katta et al.   PLoS One

An RNA-Seq based gene expression atlas of the common bean

(2014) Jamie A O’Rourke et al.   BMC GENOMICS

Gene expression regulation mediated through reversible m6A RNA methylation

(2014) Ye Fu et al.   NATURE REVIEWS GENETICS

FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions

(2014) Alberto Gatto et al.   NUCLEIC ACIDS RESEARCH

Floral Transcriptomes in Woodland Strawberry Uncover Developing Receptacle and Anther Gene Networks

(2014) C. A. Hollender et al.   PLANT PHYSIOLOGY

Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics

(2013) Rajeev K. Varshney et al.   BIOTECHNOLOGY ADVANCES

Establishment of theLotus japonicusGene Expression Atlas (LjGEA) and its use to explore legume seed maturation

(2013) Jerome Verdier et al.   PLANT JOURNAL

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Transcriptome Profiling Analysis Reveals That Flavonoid and Ascorbate-Glutathione Cycle Are Important during Anther Development in Upland Cotton

(2012) Jianhui Ma et al.   PLoS One

The birth of the Epitranscriptome: deciphering the function of RNA modifications

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes

(2011) Kevin L. Childs et al.   PLoS One

Cytoscape Web: an interactive web-based network browser

(2010) Christian T. Lopes et al.   BIOINFORMATICS

RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome

(2010) Andrew J Severin et al.   BMC PLANT BIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Male-sterility systems in pigeonpea and their role in enhancing yield

(2010) K. B. Saxena et al.   PLANT BREEDING

Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm

(2009) M. Mutwil et al.   PLANT PHYSIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

MTA Is an Arabidopsis Messenger RNA Adenosine Methylase and Interacts with a Homolog of a Sex-Specific Splicing Factor

(2008) S. Zhong et al.   PLANT CELL

A gene expression atlas of the model legumeMedicago truncatula

(2008) Vagner A. Benedito et al.   PLANT JOURNAL