Published in Proc Natl Acad Sci U S A on May 14, 2012
The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes. Microbiol Mol Biol Rev (2015) 1.51
PLAZA 3.0: an access point for plant comparative genomics. Nucleic Acids Res (2014) 1.44
Comparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies. Genome Biol (2013) 1.18
Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean. BMC Genomics (2014) 1.11
Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. Philos Trans R Soc Lond B Biol Sci (2014) 1.11
Population genomics of the facultatively mutualistic bacteria Sinorhizobium meliloti and S. medicae. PLoS Genet (2012) 0.97
Commonalities and differences of T3SSs in rhizobia and plant pathogenic bacteria. Front Plant Sci (2014) 0.92
High-resolution transcriptomic analyses of Sinorhizobium sp. NGR234 bacteroids in determinate nodules of Vigna unguiculata and indeterminate nodules of Leucaena leucocephala. PLoS One (2013) 0.90
Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti. Genome Biol Evol (2013) 0.89
Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria. Sci Rep (2015) 0.88
Robust markers reflecting phylogeny and taxonomy of rhizobia. PLoS One (2012) 0.85
The tRNAarg gene and engA are essential genes on the 1.7-Mb pSymB megaplasmid of Sinorhizobium meliloti and were translocated together from the chromosome in an ancestral strain. J Bacteriol (2012) 0.84
Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness. BMC Genomics (2014) 0.84
Phylogenetic analysis of erythritol catabolic loci within the Rhizobiales and proteobacteria. BMC Microbiol (2013) 0.82
Short and long-term genome stability analysis of prokaryotic genomes. BMC Genomics (2013) 0.82
Insights into the history of a bacterial group II intron remnant from the genomes of the nitrogen-fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae. Heredity (Edinb) (2014) 0.82
Genetic divergence of bradyrhizobium strains nodulating soybeans as revealed by multilocus sequence analysis of genes inside and outside the symbiosis island. Appl Environ Microbiol (2014) 0.79
Replicon-dependent differentiation of symbiosis-related genes in Sinorhizobium strains nodulating Glycine max. Appl Environ Microbiol (2013) 0.77
Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria. Front Microbiol (2015) 0.77
Microevolution Analysis of Bacillus coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation. Front Microbiol (2016) 0.76
Improvement in nitrogen fixation capacity could be part of the domestication process in soybean. Heredity (Edinb) (2016) 0.76
Unraveling adaptation of Pontibacter korlensis to radiation and infertility in desert through complete genome and comparative transcriptomic analysis. Sci Rep (2015) 0.76
Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics. Front Microbiol (2016) 0.76
Genetic diversity and evolution of Bradyrhizobium populations nodulating Erythrophleum fordii, an evergreen tree indigenous to the southern subtropical region of China. Appl Environ Microbiol (2014) 0.75
Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts. BMC Genomics (2017) 0.75
Genetic Analysis Reveals the Essential Role of Nitrogen Phosphotransferase System Components in Sinorhizobium fredii CCBAU 45436 Symbioses with Soybean and Pigeonpea Plants. Appl Environ Microbiol (2015) 0.75
Genomic characterization of Sinorhizobium meliloti AK21, a wild isolate from the Aral Sea Region. Springerplus (2015) 0.75
Nodulation Characterization and Proteomic Profiling of Bradyrhizobium liaoningense CCBAU05525 in Response to Water-Soluble Humic Materials. Sci Rep (2015) 0.75
Adaptive evolution of extreme acidophile Sulfobacillus thermosulfidooxidans potentially driven by horizontal gene transfer and gene loss. Appl Environ Microbiol (2017) 0.75
High-quality permanent draft genome sequence of the Bradyrhizobium elkanii type strain USDA 76(T), isolated from Glycine max (L.) Merr. Stand Genomic Sci (2017) 0.75
Two Major Clades of Bradyrhizobia Dominate Symbiotic Interactions with Pigeonpea in Fields of Côte d'Ivoire. Front Microbiol (2016) 0.75
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol (2011) 220.97
MODELTEST: testing the model of DNA substitution. Bioinformatics (1998) 101.19
Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (2007) 47.63
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol (2000) 35.86
The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res (1987) 26.51
progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One (2010) 24.31
Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A (2009) 17.13
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol (2006) 12.96
Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics (2006) 10.83
Inference of bacterial microevolution using multilocus sequence data. Genetics (2006) 7.93
A simple and robust statistical test for detecting the presence of recombination. Genetics (2006) 6.71
Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol (2006) 5.94
Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc Natl Acad Sci U S A (1998) 4.44
Recombination and the nature of bacterial speciation. Science (2007) 3.98
Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci U S A (2004) 3.89
Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science (2007) 3.42
Phylogenetic analysis using PHYLIP. Methods Mol Biol (2000) 3.27
The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol (2006) 2.93
Biology's next revolution. Nature (2007) 2.46
Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes? Trends Microbiol (2009) 1.98
Evolving ideas of legume evolution and diversity: a taxonomic perspective on the occurrence of nodulation. New Phytol (2007) 1.78
Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res (2008) 1.71
Horizontal gene transfer in evolution: facts and challenges. Proc Biol Sci (2009) 1.65
Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor Appl Genet (2008) 1.62
The Apicomplexan whole-genome phylogeny: an analysis of incongruence among gene trees. Mol Biol Evol (2008) 1.48
Molecular characterization of the bet genes encoding glycine betaine synthesis in Sinorhizobium meliloti 102F34. Microbiology (1997) 1.32
The glutamine synthetases of rhizobia: phylogenetics and evolutionary implications. Mol Biol Evol (2000) 1.32
HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. Nucleic Acids Res (2007) 1.30
Burkholderia species are ancient symbionts of legumes. Mol Ecol (2009) 1.29
Experimental evolution of a plant pathogen into a legume symbiont. PLoS Biol (2010) 1.20
Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent. Appl Environ Microbiol (2008) 1.18
Biodiversity and biogeography of rhizobia associated with soybean plants grown in the North China Plain. Appl Environ Microbiol (2011) 1.07
The Sinorhizobium medicae WSM419 lpiA gene is transcriptionally activated by FsrR and required to enhance survival in lethal acid conditions. Microbiology (2006) 1.01
Genetic diversity of fast-growing rhizobia that nodulate soybean ( Glycine max L. Merr). Arch Microbiol (2003) 1.01
Population mixing of Rhizobium leguminosarum bv. viciae nodulating Vicia faba: the role of recombination and lateral gene transfer. FEMS Microbiol Ecol (2010) 0.93
Diversity and biogeography of rhizobia isolated from root nodules of Glycine max grown in Hebei Province, China. Microb Ecol (2011) 0.93
Diversity analyses of Aeschynomene symbionts in Tropical Africa and Central America reveal that nod-independent stem nodulation is not restricted to photosynthetic bradyrhizobia. Environ Microbiol (2009) 0.89
NodMutDB: a database for genes and mutants involved in symbiosis. Bioinformatics (2005) 0.87
Soils of the Chinese Hubei province show a very high diversity of Sinorhizobium fredii strains. Syst Appl Microbiol (2002) 0.85
Trees from trees: construction of phylogenetic supertrees using clann. Methods Mol Biol (2009) 0.84
The pha2 gene cluster involved in Na+ resistance and adaption to alkaline pH in Sinorhizobium fredii RT19 encodes a monovalent cation/proton antiporter. FEMS Microbiol Lett (2006) 0.81
Ensifer sojae sp. nov., isolated from root nodules of Glycine max grown in saline-alkaline soils. Int J Syst Evol Microbiol (2010) 0.81
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Enterotypes of the human gut microbiome. Nature (2011) 24.36
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res (2008) 7.45
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med (2011) 7.11
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
Aberrant excitatory neuronal activity and compensatory remodeling of inhibitory hippocampal circuits in mouse models of Alzheimer's disease. Neuron (2007) 6.60
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62
Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58
Building the sequence map of the human pan-genome. Nat Biotechnol (2009) 5.53
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20
Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Hippo pathway inhibits Wnt signaling to restrain cardiomyocyte proliferation and heart size. Science (2011) 4.76
Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ (2011) 4.50
Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26
The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol (2010) 4.25
Regression of castrate-recurrent prostate cancer by a small-molecule inhibitor of the amino-terminus domain of the androgen receptor. Cancer Cell (2010) 4.16
KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics (2006) 4.15
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Dynamic T cell migration program provides resident memory within intestinal epithelium. J Exp Med (2010) 4.09
Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet (2012) 4.07
Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet (2010) 4.06
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell (2012) 4.03
Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature (2010) 3.95
Urinary neutrophil gelatinase-associated lipocalin and acute kidney injury after cardiac surgery. Am J Kidney Dis (2008) 3.95
Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation. Nat Genet (2013) 3.87
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nat Biotechnol (2012) 3.83
Comparative population genomics of maize domestication and improvement. Nat Genet (2012) 3.78
Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. Science (2006) 3.77
Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet (2012) 3.74
Sclerostin mediates bone response to mechanical unloading through antagonizing Wnt/beta-catenin signaling. J Bone Miner Res (2009) 3.69
Epidemiological evidence for the link between sleep duration and high blood pressure: a systematic review and meta-analysis. Sleep Med (2013) 3.68
Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet (2011) 3.66
TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. Brain (2010) 3.66
Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11,105 pregnancies with mixed risk factors. Prenat Diagn (2012) 3.54
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat Biotechnol (2011) 3.51
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat Biotechnol (2013) 3.41
Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature (2013) 3.40
Neuronal SIRT1 activation as a novel mechanism underlying the prevention of Alzheimer disease amyloid neuropathology by calorie restriction. J Biol Chem (2006) 3.40
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome. Genome Res (2010) 3.34
Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature (2011) 3.19
The draft genome of a diploid cotton Gossypium raimondii. Nat Genet (2012) 3.18
BioMart Central Portal: an open database network for the biological community. Database (Oxford) (2011) 3.03
Snap: an integrated SNP annotation platform. Nucleic Acids Res (2006) 2.99
Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res (2004) 2.95
Whole-genome sequence of Schistosoma haematobium. Nat Genet (2012) 2.91
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol (2011) 2.87
Draft genome of the wheat A-genome progenitor Triticum urartu. Nature (2013) 2.86
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat Biotechnol (2012) 2.82
Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science (2010) 2.78
Constrained motion control of flexible robot manipulators based on recurrent neural networks. IEEE Trans Syst Man Cybern B Cybern (2004) 2.75
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics. Nucleic Acids Res (2004) 2.69
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (2009) 2.68
An intraoral fixation method of endotracheal tube using the surgical suture in pediatric patients. Paediatr Anaesth (2008) 2.66
Urinary biomarkers in the early detection of acute kidney injury after cardiac surgery. Clin J Am Soc Nephrol (2009) 2.57
Diet-induced insulin resistance promotes amyloidosis in a transgenic mouse model of Alzheimer's disease. FASEB J (2004) 2.56
Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells. Nat Cell Biol (2012) 2.56
The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res (2012) 2.55
Exome sequencing identifies ZNF644 mutations in high myopia. PLoS Genet (2011) 2.52
Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods (2013) 2.51
SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res (2005) 2.50
Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr Biol (2012) 2.50
Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing. Am J Hum Genet (2013) 2.47
A glimpse of streptococcal toxic shock syndrome from comparative genomics of S. suis 2 Chinese isolates. PLoS One (2007) 2.47
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol (2012) 2.45
Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nat Biotechnol (2011) 2.45
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology. Nucleic Acids Res (2009) 2.45
Prenatal airborne polycyclic aromatic hydrocarbon exposure and child IQ at age 5 years. Pediatrics (2009) 2.43