Published in BMC Genomics on April 27, 2014
Classification and characterization of species within the genus lens using genotyping-by-sequencing (GBS). PLoS One (2015) 1.46
The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome. Genome Biol (2014) 0.96
ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biol (2015) 0.95
Structural Studies of Medicago truncatula Histidinol Phosphate Phosphatase from Inositol Monophosphatase Superfamily Reveal Details of Penultimate Step of Histidine Biosynthesis in Plants. J Biol Chem (2016) 0.90
Loss of the nodule-specific cysteine rich peptide, NCR169, abolishes symbiotic nitrogen fixation in the Medicago truncatula dnf7 mutant. Proc Natl Acad Sci U S A (2015) 0.90
Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. BMC Genomics (2015) 0.89
ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data. BMC Bioinformatics (2015) 0.88
Diversification of the C-TERMINALLY ENCODED PEPTIDE (CEP) gene family in angiosperms, and evolution of plant-family specific CEP genes. BMC Genomics (2014) 0.86
De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome. Int J Genomics (2015) 0.85
Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. Nucleic Acids Res (2015) 0.85
The bHLH Transcription Factors TSAR1 and TSAR2 Regulate Triterpene Saponin Biosynthesis in Medicago truncatula. Plant Physiol (2015) 0.83
A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti. Nat Biotechnol (2016) 0.81
Mining the Cicer arietinum genome for the mildew locus O (Mlo) gene family and comparative evolutionary analysis of the Mlo genes from Medicago truncatula and some other plant species. J Plant Res (2016) 0.80
Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing. PLoS One (2015) 0.79
Genome-wide identification and expression profiling analysis of the Aux/IAA gene family in Medicago truncatula during the early phase of Sinorhizobium meliloti infection. PLoS One (2014) 0.79
Optical mapping in plant comparative genomics. Gigascience (2015) 0.78
Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits. PLoS One (2017) 0.78
Naturally occurring diversity helps to reveal genes of adaptive importance in legumes. Front Plant Sci (2015) 0.77
Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing. BMC Genomics (2016) 0.77
Plant Carbonic Anhydrases: Structures, Locations, Evolution, and Physiological Roles. Mol Plant (2016) 0.77
Field Guide to Plant Model Systems. Cell (2016) 0.77
De Novo Transcriptional Analysis of Alfalfa in Response to Saline-Alkaline Stress. Front Plant Sci (2016) 0.77
Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials. BMC Genomics (2015) 0.77
Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform. Plant Physiol (2017) 0.75
A community resource for exploring and utilizing genetic diversity in the USDA pea single plant plus collection. Hortic Res (2017) 0.75
Six Medicago truncatula Dicer-like protein genes are expressed in plant cells and upregulated in nodules. Plant Cell Rep (2016) 0.75
Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula. Front Plant Sci (2016) 0.75
Pre-announcement of symbiotic guests: transcriptional reprogramming by mycorrhizal lipochitooligosaccharides shows a strict co-dependency on the GRAS transcription factors NSP1 and RAM1. BMC Genomics (2015) 0.75
No evidence for adaptation to local rhizobial mutualists in the legume Medicago lupulina. Ecol Evol (2017) 0.75
Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.). BMC Plant Biol (2017) 0.75
Validating Genome-Wide Association candidates through quantitative variation in nodulation. Plant Physiol (2017) 0.75
Genetic Mapping of a Major Resistance Gene to Pea Aphid (Acyrthosipon pisum) in the Model Legume Medicago truncatula. Int J Mol Sci (2016) 0.75
Nod Factor Effects on Root Hair-Specific Transcriptome of Medicago truncatula: Focus on Plasma Membrane Transport Systems and Reactive Oxygen Species Networks. Front Plant Sci (2016) 0.75
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes. BMC Genomics (2017) 0.75
Interplay of Pathogen-Induced Defense Responses and Symbiotic Establishment in Medicago truncatula. Front Microbiol (2017) 0.75
An Insight into T-DNA Integration Events in Medicago sativa. Int J Mol Sci (2017) 0.75
Saturation mapping of regions determining resistance to Ascochyta blight and broomrape in faba bean using transcriptome-based SNP genotyping. Theor Appl Genet (2017) 0.75
Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics (2017) 0.75
How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes. Front Plant Sci (2017) 0.75
Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula. BMC Genomics (2017) 0.75
Receptor-mediated chitin perception in legume roots is functionally separable from Nod factor perception. Proc Natl Acad Sci U S A (2017) 0.75
Medicago truncatula Oleanolic-Derived Saponins Are Correlated with Caterpillar Deterrence. J Chem Ecol (2017) 0.75
Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation. Front Plant Sci (2017) 0.75
Nitrate transporters: an overview in legumes. Planta (2017) 0.75
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res (1997) 142.55
EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet (2000) 69.26
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics (2011) 25.76
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82
A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One (2011) 15.19
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics (2007) 12.21
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (2011) 8.19
JBrowse: a next-generation genome browser. Genome Res (2009) 6.77
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res (2007) 6.48
Pack-MULE transposable elements mediate gene evolution in plants. Nature (2004) 5.13
Adaptive seeds tame genomic sequence comparison. Genome Res (2011) 4.96
Hierarchical scaffolding with Bambus. Genome Res (2004) 4.95
The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature (2011) 4.94
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) (2013) 4.27
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol (2008) 3.73
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol (2011) 3.51
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol (2013) 3.41
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc (2012) 3.17
Gene movement by Helitron transposons contributes to the haplotype variability of maize. Proc Natl Acad Sci U S A (2005) 3.13
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A (2006) 2.61
High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A (2010) 2.47
Validation of rice genome sequence by optical mapping. BMC Genomics (2007) 2.44
A single molecule scaffold for the maize genome. PLoS Genet (2009) 2.33
Alignment of optical maps. J Comput Biol (2006) 1.88
A nodule-specific protein secretory pathway required for nitrogen-fixing symbiosis. Science (2010) 1.46
Nuclear DNA amounts in angiosperms: targets, trends and tomorrow. Ann Bot (2011) 1.37
RNA-Seq improves annotation of protein-coding genes in the cucumber genome. BMC Genomics (2011) 1.27
TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences. Nucleic Acids Res (2005) 1.22
Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics (2011) 1.11
Identification of quantitative trait loci influencing aerial morphogenesis in the model legume Medicago truncatula. Theor Appl Genet (2007) 0.96
Natural diversity in the model legume Medicago truncatula allows identifying distinct genetic mechanisms conferring partial resistance to Verticillium wilt. J Exp Bot (2012) 0.96
Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application). BMC Bioinformatics (2013) 0.95
The Medicago truncatula reference accession A17 has an aberrant chromosomal configuration. New Phytol (2007) 0.94
Guidelines for genetic nomenclature and community governance for the model legume Medicago truncatula. Mol Plant Microbe Interact (2001) 0.94
A proteogenomic survey of the Medicago truncatula genome. Mol Cell Proteomics (2012) 0.87
EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome. BMC Genomics (2007) 0.82
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
The B73 maize genome: complexity, diversity, and dynamics. Science (2009) 18.73
The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20
The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62
The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science (2004) 9.97
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
The genome of the kinetoplastid parasite, Leishmania major. Science (2005) 8.64
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2007) 8.12
A standard variation file format for human genome sequences. Genome Biol (2010) 7.83
A physical, genetic and functional sequence assembly of the barley genome. Nature (2012) 7.25
Genome sequence of Yersinia pestis KIM. J Bacteriol (2002) 7.14
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res (2007) 6.48
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature (2009) 6.44
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature (2010) 5.79
Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature (2012) 5.67
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature (2008) 5.54
Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol (2003) 5.45
Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol (2009) 5.45
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics (2011) 5.35
The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature (2011) 4.94
Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A (2009) 4.65
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet (2011) 4.65
Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell (2004) 4.59
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (N Y) (2013) 4.27
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome. Nucleic Acids Res (2002) 4.05
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science (2009) 4.05
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature (2012) 4.00
Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet (2011) 3.43
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature (2013) 3.40
Self-assembling protein microarrays. Science (2004) 3.37
Sequence composition and genome organization of maize. Proc Natl Acad Sci U S A (2004) 3.22
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science (2010) 3.18
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17
Genome-wide atlas of transcription during maize development. Plant J (2011) 3.07
Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell (2011) 3.03
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res (2012) 3.02
The Celera Discovery System. Nucleic Acids Res (2002) 2.95
Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet (2012) 2.92
Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol (2008) 2.91
The challenges of sequencing by synthesis. Nat Biotechnol (2009) 2.89
The African coelacanth genome provides insights into tetrapod evolution. Nature (2013) 2.78
Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci U S A (2010) 2.76
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci U S A (2006) 2.61
A microfluidic system for large DNA molecule arrays. Anal Chem (2004) 2.57
A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nat Genet (2010) 2.57
A single-molecule barcoding system using nanoslits for DNA analysis. Proc Natl Acad Sci U S A (2007) 2.53
Structure and architecture of the maize genome. Plant Physiol (2005) 2.52
Analysis of recombinant yeast decapping enzyme. RNA (2003) 2.50
High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A (2010) 2.47
Validation of rice genome sequence by optical mapping. BMC Genomics (2007) 2.44
Exon discovery by genomic sequence alignment. Bioinformatics (2002) 2.38
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol (2010) 2.36
A single molecule scaffold for the maize genome. PLoS Genet (2009) 2.33
The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion. PLoS Genet (2009) 2.29
Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera. Nucleic Acids Res (2010) 2.15
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet (2013) 2.07
Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J (2013) 2.02
Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci U S A (2005) 2.01
Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell (2011) 1.98
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucleic Acids Res (2004) 1.97
Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol (2004) 1.96
Uneven chromosome contraction and expansion in the maize genome. Genome Res (2006) 1.96
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol (2014) 1.95
Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci U S A (2011) 1.94
Community annotation: procedures, protocols, and supporting tools. Genome Res (2006) 1.91