Published in Microbiologyopen on February 18, 2015
The RAST Server: rapid annotations using subsystems technology. BMC Genomics (2008) 175.18
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
Clustal W and Clustal X version 2.0. Bioinformatics (2007) 126.47
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol (2013) 112.81
SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol (2012) 62.36
Artemis: sequence visualization and annotation. Bioinformatics (2000) 46.68
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res (2005) 29.61
PHAST: a fast phage search tool. Nucleic Acids Res (2011) 19.09
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res (2007) 15.56
HMMER web server: interactive sequence similarity searching. Nucleic Acids Res (2011) 13.00
A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol (2005) 11.82
Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics (2009) 6.97
CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One (2013) 4.62
Easyfig: a genome comparison visualizer. Bioinformatics (2011) 4.23
The single-stranded DNA-binding protein of Escherichia coli. Microbiol Rev (1990) 3.21
Characterization of a prokaryotic SMC protein involved in chromosome partitioning. Genes Dev (1998) 3.13
The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell (2006) 2.19
Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics (2014) 2.07
Bacterial cysteine desulfurases: their function and mechanisms. Appl Microbiol Biotechnol (2002) 1.73
Identification of the genes encoding Mn2+-dependent RNase HII and Mg2+-dependent RNase HIII from Bacillus subtilis: classification of RNases H into three families. Biochemistry (1999) 1.71
Peptide methionine sulfoxide reductase (MsrA) is a virulence determinant in Mycoplasma genitalium. J Bacteriol (2001) 1.67
KtrAB, a new type of bacterial K(+)-uptake system from Vibrio alginolyticus. J Bacteriol (1998) 1.63
Alterations in topoisomerase IV and DNA gyrase in quinolone-resistant mutants of Mycoplasma hominis obtained in vitro. Antimicrob Agents Chemother (1998) 1.61
Structure and specific activity of macrophage-stimulating lipopeptides from Mycoplasma hyorhinis. Infect Immun (1998) 1.38
Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet (2013) 1.32
Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family. RNA (2006) 1.28
Mechanisms of attachment of Mycoplasma arthritidis to host cells in vitro. Infect Immun (1993) 1.27
Structure and function of the bacterial mechanosensitive channel of large conductance. Protein Sci (1999) 1.19
DNA repair in Mycoplasma gallisepticum. BMC Genomics (2013) 1.12
The adherence-associated lipoprotein P100, encoded by an opp operon structure, functions as the oligopeptide-binding domain OppA of a putative oligopeptide transport system in Mycoplasma hominis. J Bacteriol (1999) 1.08
The hsd loci of Mycoplasma pulmonis: organization, rearrangements and expression of genes. Mol Microbiol (1997) 1.07
Structural and mechanistic insights into prokaryotic energy-coupling factor transporters. Nat Rev Microbiol (2013) 1.05
DNA repair in reduced genome: the Mycoplasma model. Gene (2005) 1.02
Cloning and sequence analysis of the rpsL and rpsG genes of Mycobacterium smegmatis and characterization of mutations causing resistance to streptomycin. J Bacteriol (1994) 1.02
Composition and conservation of the mRNA-degrading machinery in bacteria. J Biomed Sci (2011) 1.02
Analysis of the immunoproteome of Mycoplasma mycoides subsp. mycoides small colony type reveals immunogenic homologues to other known virulence traits in related Mycoplasma species. Vet Immunol Immunopathol (2009) 1.01
Structural and biochemical characterization of HP0315 from Helicobacter pylori as a VapD protein with an endoribonuclease activity. Nucleic Acids Res (2012) 0.99
Suppression of a sensor kinase-dependent phenotype in Pseudomonas syringae by ribosomal proteins L35 and L20. J Bacteriol (1996) 0.97
Finegoldia magna: a forgotten pathogen in prosthetic joint infection rediscovered by molecular biology. Clin Infect Dis (2009) 0.97
Evidence for type III restriction and modification systems in Mycoplasma pulmonis. J Bacteriol (2007) 0.96
Amino acid changes in elongation factor Tu of Mycoplasma pneumoniae and Mycoplasma genitalium influence fibronectin binding. Infect Immun (2009) 0.96
Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae. RNA (2011) 0.94
The SsrA-SmpB ribosome rescue system is important for growth of Bacillus subtilis at low and high temperatures. J Bacteriol (2007) 0.94
The acylation state of surface lipoproteins of mollicute Acholeplasma laidlawii. J Biol Chem (2011) 0.94
Molecular characterization of Mycoplasma arthritidis membrane lipoprotein MAA1. Infect Immun (2000) 0.94
Critical role of dispensable genes in Mycoplasma agalactiae interaction with mammalian cells. Infect Immun (2010) 0.93
Ffh and FtsY in a Mycoplasma mycoides signal-recognition particle pathway: SRP RNA and M domain of Ffh are not required for stimulation of GTPase activity in vitro. Mol Microbiol (1997) 0.93
OppA, the ecto-ATPase of Mycoplasma hominis induces ATP release and cell death in HeLa cells. BMC Microbiol (2008) 0.93
Transcriptional heat shock response in the smallest known self-replicating cell, Mycoplasma genitalium. J Bacteriol (2006) 0.91
The Mycoplasma fermentans prophage phiMFV1: genome organization, mobility and variable expression of an encoded surface protein. Mol Microbiol (2004) 0.90
Progression of Mycoplasma hyosynoviae infection in three pig herds. Development of tonsillar carrier state, arthritis and antibodies in serum and synovial fluid in pigs from birth to slaughter. Zentralbl Veterinarmed A (1999) 0.90
Effect of mycoplasmas on apoptosis of 32D cells is species-dependent. Curr Microbiol (2007) 0.85
Phylogenomics of "Candidatus Hepatoplasma crinochetorum," a lineage of mollicutes associated with noninsect arthropods. Genome Biol Evol (2014) 0.84
The isolation of Mycoplasm hyosynoviae and exposure of pigs to experimental infection. Aust Vet J (1975) 0.83
A mollicute (mycoplasma) DNA repair enzyme: purification and characterization of uracil-DNA glycosylase. J Bacteriol (1990) 0.83
Decoding in Candidatus Riesia pediculicola, close to a minimal tRNA modification set? Trends Cell Mol Biol (2012) 0.82
Induction of arthritis with Mycoplasma hyosynoviae in pigs: clinical response and re-isolation of the organism from body fluids and organs. Zentralbl Veterinarmed A (1999) 0.82
Nucleoside diphosphate kinase-like activity in adenylate kinase of Mycobacterium tuberculosis. Biotechnol Appl Biochem (2003) 0.80
Crystal structure of a novel single-stranded DNA binding protein from Mycoplasma pneumoniae. Proteins (2007) 0.79
Biochemical and antigenic characterisation of Mycoplasma gallisepticum membrane proteins P52 and P67 (pMGA). Arch Microbiol (2001) 0.78
Characterization of Mycoplasma hyosynoviae strains by amplified fragment length polymorphism analysis, pulsed-field gel electrophoresis and 16S ribosomal DNA sequencing. J Vet Med B Infect Dis Vet Public Health (2002) 0.77
Effects of biotin, folic acid, and pantothenic acid on the growth of Mycoplasma meleagridis, a turkey pathogen. Poult Sci (1978) 0.76
Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol (2008) 15.90
The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet (2010) 8.07
Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods (2005) 6.23
Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet (2008) 5.80
Cellular transcriptional profiling in influenza A virus-infected lung epithelial cells: the role of the nonstructural NS1 protein in the evasion of the host innate defense and its potential contribution to pandemic influenza. Proc Natl Acad Sci U S A (2002) 4.26
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nat Biotechnol (2008) 3.43
Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics (2005) 3.21
Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)-T-cell lines. J Virol (2003) 2.46
Clustering gene-expression data with repeated measurements. Genome Biol (2003) 2.37
On the persistence of supplementary resources in biomedical publications. BMC Bioinformatics (2006) 2.27
Donuts, scratches and blanks: robust model-based segmentation of microarray images. Bioinformatics (2005) 1.90
Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation. PLoS Biol (2012) 1.82
Multifunctionality of PAI-1 in fibrogenesis: evidence from obstructive nephropathy in PAI-1-overexpressing mice. Kidney Int (2005) 1.74
Identification of high and low responders to lipopolysaccharide in normal subjects: an unbiased approach to identify modulators of innate immunity. J Immunol (2005) 1.66
Bayesian robust inference for differential gene expression in microarrays with multiple samples. Biometrics (2006) 1.57
Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein. J Virol (2003) 1.56
Multiclass classification of microarray data with repeated measurements: application to cancer. Genome Biol (2003) 1.55
Sample size for detecting differentially expressed genes in microarray experiments. BMC Genomics (2004) 1.45
Identification of novel tumor markers in hepatitis C virus-associated hepatocellular carcinoma. Cancer Res (2003) 1.40
From co-expression to co-regulation: how many microarray experiments do we need? Genome Biol (2004) 1.40
MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis. Genome Biol (2008) 1.34
Construction of regulatory networks using expression time-series data of a genotyped population. Proc Natl Acad Sci U S A (2011) 1.31
Genome sequence of Aggregatibacter actinomycetemcomitans serotype c strain D11S-1. J Bacteriol (2009) 1.28
Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS (2006) 1.26
The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data. Blood (2009) 1.23
Chlamydia trachomatis infection alters host cell transcription in diverse cellular pathways. J Infect Dis (2003) 1.21
Mycoplasma ovipneumoniae can predispose bighorn sheep to fatal Mannheimia haemolytica pneumonia. Vet Microbiol (2010) 1.16
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. BMC Syst Biol (2012) 1.16
Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis. PLoS One (2011) 1.12
Mannheimia haemolytica serotype A1 exhibits differential pathogenicity in two related species, Ovis canadensis and Ovis aries. Vet Microbiol (2008) 1.08
A three-way comparative genomic analysis of Mannheimia haemolytica isolates. BMC Genomics (2010) 1.07
Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases and their relationship to isoflavone reductases. J Biol Chem (2003) 1.05
The role of two f-box proteins, SLEEPY1 and SNEEZY, in Arabidopsis gibberellin signaling. Plant Physiol (2010) 1.04
Attenuation of the type I interferon response in cells infected with human rhinovirus. Virology (2008) 1.04
cDNA microarray analysis reveals fundamental differences in the expression profiles of primary human monocytes, monocyte-derived macrophages, and alveolar macrophages. J Leukoc Biol (2006) 1.02
Genome sequence of naturally competent Aggregatibacter actinomycetemcomitans serotype a strain D7S-1. J Bacteriol (2010) 0.99
Genome sequence of a novel species, Propionibacterium humerusii. J Bacteriol (2011) 0.99
Genome sequences of Mannheimia haemolytica serotype A2: ovine and bovine isolates. J Bacteriol (2009) 0.98
Retracted Human rhinovirus attenuates the type I interferon response by disrupting activation of interferon regulatory factor 3. J Virol (2006) 0.97
Hierarchical gene expression profiles of HUVEC stimulated by different lipid A structures obtained from Porphyromonas gingivalis and Escherichia coli. Cell Microbiol (2006) 0.96
Independent and cooperative antiviral actions of beta interferon and gamma interferon against herpes simplex virus replication in primary human fibroblasts. J Virol (2007) 0.96
What is the best reference RNA? And other questions regarding the design and analysis of two-color microarray experiments. OMICS (2007) 0.95
Relationships between deficits in tissue mass and transcriptional programs after partial hepatectomy in mice. Am J Pathol (2009) 0.93
Protinfo PPC: a web server for atomic level prediction of protein complexes. Nucleic Acids Res (2009) 0.93
Chlamydia trachomatis variant with nonfusing inclusions: growth dynamic and host-cell transcriptional response. J Infect Dis (2005) 0.91
Concerted action of two avirulent spore effectors activates Reaction to Puccinia graminis 1 (Rpg1)-mediated cereal stem rust resistance. Proc Natl Acad Sci U S A (2011) 0.91
Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data. BMC Bioinformatics (2009) 0.89
RNA amplification, fidelity and reproducibility of expression profiling. C R Biol (2004) 0.89
Human rhinovirus attenuates the type I interferon response by disrupting activation of interferon regulatory factor 3. J Virol (2007) 0.81
Genome sequence of a serotype b non-JP2 aggregatibacter actinomycetemcomitans strain, ANH9381, from a periodontally healthy individual. J Bacteriol (2012) 0.80
Metagenomic analysis of subgingival microbiota following non-surgical periodontal therapy: a pilot study. Open Dent J (2012) 0.79
Genomic Stability of Aggregatibacter actinomycetemcomitans during Persistent Oral Infection in Human. PLoS One (2013) 0.79
Characterization of the effects of an rpoC mutation that confers resistance to the Fst peptide toxin-antitoxin system toxin. J Bacteriol (2012) 0.79
Comparative genomics of susceptibility to mammary carcinogenesis among inbred rat strains: role of reduced prolactin signaling in resistance of the Copenhagen strain. Carcinogenesis (2007) 0.78
Resistance detected by pyrosequencing following zidovudine monotherapy for prevention of HIV-1 mother-to-child-transmission. AIDS (2015) 0.77
Genome Sequence of a Presumptive Mannheimia haemolytica Strain with an A1/A6-Cross-Reactive Serotype from a White-Tailed Deer (Odocoileus virginianus). Genome Announc (2014) 0.75
A virion-associated protein kinase induces apoptosis. J Virol (2011) 0.75
Co-expression of ovine LPS receptor CD14 with Mannheimia haemolytica leukotoxin receptor LFA-1 or Mac-1 does not enhance leukotoxin-induced cytotoxicity. Vet Immunol Immunopathol (2011) 0.75