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

Bridger: a new framework for de novo transcriptome assembly using RNA-seq data

(2015) Zheng Chang et al.   GENOME BIOLOGY

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

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

Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea

(2014) Jorge Duarte et al.   BMC GENOMICS

An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing

(2014) Brice Roux et al.   PLANT JOURNAL

Patterns of divergence of a large family of nodule cysteine-rich peptides in accessions ofMedicago truncatula

(2014) Sumitha Nallu et al.   PLANT JOURNAL

A Paradigm for Endosymbiotic Life: Cell Differentiation ofRhizobiumBacteria Provoked by Host Plant Factors

(2013) Eva Kondorosi et al.   Annual Review of Microbiology

Transport and Metabolism in Legume-Rhizobia Symbioses

(2013) Michael Udvardi et al.   Annual Review of Plant Biology

Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)

(2013) Peng Zhou et al.   BMC BIOINFORMATICS

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Speak, friend and enter: signalling systems that promote beneficial symbiotic associations in plants

(2013) Giles E. D. Oldroyd   NATURE REVIEWS MICROBIOLOGY

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

(2013) MARC LOHSE et al.   PLANT CELL AND ENVIRONMENT

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

(2013) Jerome Verdier et al.   PLANT JOURNAL

Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatumL.)

(2013) Ji-Yi Zhang et al.   PLANT JOURNAL

Cell- and Tissue-Specific Transcriptome Analyses of Medicago truncatula Root Nodules

(2013) Erik Limpens et al.   PLoS One

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

(2012) Nicole Gruenheit et al.   BMC GENOMICS

Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers

(2012) Sukhjiwan Kaur et al.   BMC GENOMICS

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

The Rules of Engagement in the Legume-Rhizobial Symbiosis

(2011) Giles E.D. Oldroyd et al.   Annual Review of Genetics

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

(2011) Susanne U Franssen et al.   BMC GENOMICS

Regulation of signal transduction and bacterial infection during root nodule symbiosis

(2011) Claudia Popp et al.   CURRENT OPINION IN PLANT BIOLOGY

IPD3 Controls the Formation of Nitrogen-Fixing Symbiosomes in Pea andMedicagoSpp.

(2011) Evgenia Ovchinnikova et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The ROOT DETERMINED NODULATION1 Gene Regulates Nodule Number in Roots of Medicago truncatula and Defines a Highly Conserved, Uncharacterized Plant Gene Family

(2011) Elise L. Schnabel et al.   PLANT PHYSIOLOGY

Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development

(2011) R. Garg et al.   PLANT PHYSIOLOGY

Translational Genomics in Legumes Allowed Placing In Silico 5460 Unigenes on the Pea Functional Map and Identified Candidate Genes in Pisum sativum L.

(2011) Amandine Bordat et al.   G3-Genes Genomes Genetics

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

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

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

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

The Clavata2 genes of pea and Lotus japonicus affect autoregulation of nodulation

(2010) Lene Krusell et al.   PLANT JOURNAL

Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq

(2010) S. Zenoni et al.   PLANT PHYSIOLOGY

The molecular network governing nodule organogenesis and infection in the model legume Lotus japonicus

(2010) Lene H. Madsen et al.   Nature Communications

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The unbearable naivety of legumes in symbiosis

(2009) Griet Den Herder et al.   CURRENT OPINION IN PLANT BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

A gene expression atlas of the model legumeMedicago truncatula

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

UTILLdb, a Pisum sativum in silico forward and reverse genetics tool

(2008) Marion Dalmais et al.   GENOME BIOLOGY