A reference genome for pea provides insight into legume genome evolution

Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.)

(2019) Krishna Kishore Gali et al.   Frontiers in Plant Science

Reducing food’s environmental impacts through producers and consumers

(2018) J. Poore et al.   SCIENCE

Domestication of Pea (Pisum sativum L.): The Case of the Abyssinian Pea

(2018) Norman F. Weeden   Frontiers in Plant Science

Genome Size Diversity and Its Impact on the Evolution of Land Plants

(2018) et al.   Genes

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

(2017) Hélène Badouin et al.   NATURE

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Legumes as Functional Ingredients in Gluten-Free Bakery and Pasta Products

(2017) Martina Foschia et al.   Annual Review of Food Science and Technology

Patterns of Genetic Structure and Linkage Disequilibrium in a Large Collection of Pea Germplasm

(2017) Mathieu Siol et al.   G3-Genes Genomes Genetics

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

(2017) Shu-Fen Li et al.   Genes

Genomic diversity and macroecology of the crop wild relatives of domesticated pea

(2017) Petr Smýkal et al.   Scientific Reports

MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data

(2016) Mohammed-Amin Madoui et al.   BMC BIOINFORMATICS

Reconstruction of a composite comparative map composed of ten legume genomes

(2016) Chaeyoung Lee et al.   Genes & Genomics

A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution

(2016) James K. Hane et al.   PLANT BIOTECHNOLOGY JOURNAL

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map

(2015) Nadim Tayeh et al.   PLANT 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

High-resolution skim genotyping by sequencing reveals the distribution of crossovers and gene conversions in Cicer arietinum and Brassica napus

(2015) Philipp E. Bayer et al.   THEORETICAL AND APPLIED GENETICS

Draft genome sequence of adzuki bean, Vigna angularis

(2015) Yang Jae Kang et al.   Scientific Reports

Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement

(2015) Jose J. De Vega et al.   Scientific Reports

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae

(2015) Jiří Macas et al.   PLoS One

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

An improved genome release (version Mt4.0) for the model legume Medicago truncatula

(2014) Haibao Tang et al.   BMC GENOMICS

Reciprocal compatibility within the genus Pisum L. as studied in F1 hybrids: 1. Crosses involving P. sativum L. subsp. sativum

(2014) O. E. Kosterin et al.   GENETIC RESOURCES AND CROP EVOLUTION

Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

(2014) Steven B. Cannon et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Genome sequence of mungbean and insights into evolution within Vigna species

(2014) Yang Jae Kang et al.   Nature Communications

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

(2013) P. Novak et al.   BIOINFORMATICS

Characterization of pea (Pisum sativum) seed protein fractions

(2013) Luis A Rubio et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

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

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

(2013) Peter J.A. Cock et al.   PeerJ

Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool

(2012) Luca Pagani et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

(2012) R. J. P. Bonnal et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Review of the health benefits of peas (Pisum sativum L.)

(2012) Wendy J. Dahl et al.   BRITISH JOURNAL OF NUTRITION

Inference of Genome Duplications from Age Distributions Revisited

(2012) Kevin Vanneste et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

(2012) Pavel Neumann et al.   PLoS Genetics

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Sequence-based physical mapping of complex genomes by whole genome profiling

(2011) J. van Oeveren et al.   GENOME RESEARCH

The first draft of the pigeonpea genome sequence

(2011) Nagendra K. Singh et al.   JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY

The Medicago genome provides insight into the evolution of rhizobial symbioses

(2011) Nevin D. Young et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

A PQL (protein quantity loci) analysis of mature pea seed proteins identifies loci determining seed protein composition

(2011) Michael Bourgeois et al.   PROTEOMICS

Mendel, 150 years on

(2011) T.H. Noel Ellis et al.   TRENDS IN PLANT SCIENCE

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data

(2010) Petr Novák et al.   BMC BIOINFORMATICS

A TRANSLOCATION TESTER SET IN PISUM

(2010) R. LAMM et al.   HEREDITAS

PARALLELISM OF CHROMOSOME RING FORMATION, STERILITY AND LINKAGE IN PISUM

(2010) C. HAMMARLUND et al.   HEREDITAS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Genome-Wide Medicago truncatula Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules

(2009) C. Lelandais-Briere et al.   PLANT CELL

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

(2008) Sylvain Foissac et al.   Current Bioinformatics

Genome Structure of the Legume, Lotus japonicus

(2008) S. Sato et al.   DNA RESEARCH

Environmental impacts of introducing grain legumes into European crop rotations

(2008) Thomas Nemecek et al.   EUROPEAN JOURNAL OF AGRONOMY

Dissecting the proteome of pea mature seeds reveals the phenotypic plasticity of seed protein composition

(2008) Michael Bourgeois et al.   PROTEOMICS

Variation in seed protein digestion of different pea (Pisum sativum L.) genotypes by cecectomized broiler chickens: 1. Endogenous amino acid losses, true digestibility and in vitro hydrolysis of proteins

(2007) I. Gabriel et al.   Livestock Science