Published in BMC Bioinformatics on September 11, 2012
Investigation of possible molecular mechanisms underlying the regulation of adhesion in Vibrio alginolyticus with comparative transcriptome analysis. Antonie Van Leeuwenhoek (2015) 0.90
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Genome-Wide Detection of Predicted Non-coding RNAs Related to the Adhesion Process in Vibrio alginolyticus Using High-Throughput Sequencing. Front Microbiol (2016) 0.78
Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512. Front Microbiol (2017) 0.77
A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae. RNA (2016) 0.75
In vitro transcriptome analysis of two Chinese isolates of Streptococcus suis serotype 2. Genomics Proteomics Bioinformatics (2014) 0.75
A Transcriptome Map of Actinobacillus pleuropneumoniae at Single-Nucleotide Resolution Using Deep RNA-Seq. PLoS One (2016) 0.75
Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. Bioinform Biol Insights (2015) 0.75
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Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
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The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell (2004) 8.89
The primary transcriptome of the major human pathogen Helicobacter pylori. Nature (2010) 7.70
Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol (2001) 7.56
Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res (2010) 6.58
Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology (2002) 5.17
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol (2007) 4.27
Tag-based approaches for transcriptome research and genome annotation. Nat Methods (2005) 3.52
DOOR: a database for prokaryotic operons. Nucleic Acids Res (2008) 3.50
A single-base resolution map of an archaeal transcriptome. Genome Res (2009) 3.42
Identification of tandem duplicate regulatory small RNAs in Pseudomonas aeruginosa involved in iron homeostasis. Proc Natl Acad Sci U S A (2004) 3.31
Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet (2009) 3.24
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Systems biology. Life's complexity pyramid. Science (2002) 2.98
A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet (2009) 2.87
The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol (2009) 2.85
What is a hidden Markov model? Nat Biotechnol (2004) 2.56
CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae. Mol Microbiol (2005) 2.56
Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. Proc Natl Acad Sci U S A (2005) 2.55
Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence. BMC Genomics (2007) 2.31
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res (2009) 2.25
A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res (2009) 2.19
The role of RNAs in the regulation of virulence-gene expression. Curr Opin Microbiol (2006) 2.09
RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression. Cell Host Microbe (2011) 2.05
Genome-wide detection of novel regulatory RNAs in E. coli. Genome Res (2011) 1.82
A re-annotation of the Saccharomyces cerevisiae genome. Comp Funct Genomics (2001) 1.75
Small regulatory non-coding RNAs in bacteria: physiology and mechanistic aspects. Biol Cell (2009) 1.66
Economic impact associated with respiratory disease in beef cattle. Vet Clin North Am Food Anim Pract (1997) 1.57
6S RNA: a small RNA regulator of transcription. Curr Opin Microbiol (2007) 1.57
Demonstration of Type IV pilus expression and a twitching phenotype by Haemophilus influenzae. Infect Immun (2005) 1.55
The genome sequence of Mannheimia haemolytica A1: insights into virulence, natural competence, and Pasteurellaceae phylogeny. J Bacteriol (2006) 1.55
Neuraminidase activity of Pasteurella haemolytica isolates. Infect Immun (1981) 1.28
Role of adhesin release for mucosal colonization by a bacterial pathogen. J Exp Med (2003) 1.26
Molecular genetic analysis of virulence in Mannheimia (pasteurella) haemolytica. Front Biosci (2001) 1.10
Analysis of the capsule biosynthetic locus of Mannheimia (Pasteurella) haemolytica A1 and proposal of a nomenclature system. Infect Immun (2001) 1.02
Reannotation of hypothetical ORFs in plant pathogen Erwinia carotovora subsp. atroseptica SCRI1043. FEBS J (2007) 0.92
RNA-seq based transcriptional map of bovine respiratory disease pathogen "Histophilus somni 2336". PLoS One (2012) 0.90
Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics. Environ Microbiol (2011) 0.89
Comparison of antemortem antimicrobial treatment regimens to antimicrobial susceptibility patterns of postmortem lung isolates from feedlot cattle with bronchopneumonia. J Vet Diagn Invest (2011) 0.83
Prior exposure to Mannheimia haemolytica leukotoxin or LPS enhances beta(2)-integrin expression by bovine neutrophils and augments LKT cytotoxicity. Microb Pathog (2003) 0.82
Gene re-annotation in genome of the extremophile Pyrobaculum aerophilum by using bioinformatics methods. J Biomol Struct Dyn (2011) 0.79
Structural bioinformatics of Neisseria meningitidis LD-carboxypeptidase: implications for substrate binding and specificity. Protein J (2011) 0.78
TAAPP: Tiling Array Analysis Pipeline for Prokaryotes. Genomics Proteomics Bioinformatics (2011) 0.78
AgBase: a unified resource for functional analysis in agriculture. Nucleic Acids Res (2006) 2.92
AgBase: a functional genomics resource for agriculture. BMC Genomics (2006) 2.53
No-boundary thinking in bioinformatics research. BioData Min (2013) 1.76
Study of water supply & sanitation practices in India using geographic information systems: some design & other considerations in a village setting. Indian J Med Res (2009) 1.60
Gene Ontology annotation quality analysis in model eukaryotes. Nucleic Acids Res (2008) 1.50
Water handling, sanitation and defecation practices in rural southern India: a knowledge, attitudes and practices study. Trans R Soc Trop Med Hyg (2007) 1.50
AgBase: supporting functional modeling in agricultural organisms. Nucleic Acids Res (2010) 1.48
Complete Genome Sequence of a Channel Catfish Epidemic Isolate, Aeromonas hydrophila Strain ML09-119. Genome Announc (2013) 1.42
Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biol (2015) 1.40
Chaperoning a cellular upheaval in malaria: heat shock proteins in Plasmodium falciparum. Mol Biochem Parasitol (2007) 1.39
Prediction of peptides observable by mass spectrometry applied at the experimental set level. BMC Bioinformatics (2007) 1.39
Systems analysis of chaperone networks in the malarial parasite Plasmodium falciparum. PLoS Comput Biol (2007) 1.34
Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol (2012) 1.33
HPIDB--a unified resource for host-pathogen interactions. BMC Bioinformatics (2010) 1.31
Contributions of pneumolysin, pneumococcal surface protein A (PspA), and PspC to pathogenicity of Streptococcus pneumoniae D39 in a mouse model. Infect Immun (2007) 1.25
Contribution of choline-binding proteins to cell surface properties of Streptococcus pneumoniae. Infect Immun (2002) 1.23
Modeling a whole organ using proteomics: the avian bursa of Fabricius. Proteomics (2006) 1.22
Development of bioluminescent Edwardsiella ictaluri for noninvasive disease monitoring. FEMS Microbiol Lett (2006) 1.22
Pneumococcal carriage results in ganglioside-mediated olfactory tissue infection. Proc Natl Acad Sci U S A (2003) 1.19
Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility. BMC Syst Biol (2008) 1.19
The Chicken Gene Nomenclature Committee report. BMC Genomics (2009) 1.15
Genome sequence of the fish pathogen Flavobacterium columnare ATCC 49512. J Bacteriol (2012) 1.14
Differential detergent fractionation for non-electrophoretic eukaryote cell proteomics. J Proteome Res (2005) 1.14
Characterization of virulent and avirulent Listeria monocytogenes strains by PCR amplification of putative transcriptional regulator and internalin genes. J Med Microbiol (2003) 1.13
Identification of novel non-coding small RNAs from Streptococcus pneumoniae TIGR4 using high-resolution genome tiling arrays. BMC Genomics (2010) 1.12
ProtQuant: a tool for the label-free quantification of MudPIT proteomics data. BMC Bioinformatics (2007) 1.09
Effect of developmental exposure to chlorpyrifos on the expression of neurotrophin growth factors and cell-specific markers in neonatal rat brain. Toxicol Sci (2006) 1.08
Listeria monocytogenes subgroups IIIA, IIIB, and IIIC delineate genetically distinct populations with varied pathogenic potential. J Clin Microbiol (2006) 1.07
An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biol (2010) 1.06
Prediction of cell penetrating peptides by support vector machines. PLoS Comput Biol (2011) 1.03
Altered microbiota associated with abnormal humoral immune responses to commensal organisms in enthesitis-related arthritis. Arthritis Res Ther (2014) 1.02
Dielectrophoretic characterization of erythrocytes: positive ABO blood types. Electrophoresis (2008) 1.01
The proteogenomic mapping tool. BMC Bioinformatics (2011) 1.01
Effects of subminimum inhibitory concentrations of antibiotics on the Pasteurella multocida proteome. J Proteome Res (2006) 1.01
Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T. J Bacteriol (2008) 1.01
High-throughput bioluminescence-based mutant screening strategy for identification of bacterial virulence genes. Appl Environ Microbiol (2009) 0.99
Listeria monocytogenes serotype 4b strains belonging to lineages I and III possess distinct molecular features. J Clin Microbiol (2006) 0.99
A multiplex PCR for species- and virulence-specific determination of Listeria monocytogenes. J Microbiol Methods (2007) 0.99
Association of Actinobacillus pleuropneumoniae capsular polysaccharide with virulence in pigs. Infect Immun (2003) 0.98
Proteomic analysis using an unfinished bacterial genome: the effects of subminimum inhibitory concentrations of antibiotics on Mannheimia haemolytica virulence factor expression. Proteomics (2005) 0.98
Modeling the proteome of a Marek's disease transformed cell line: a natural animal model for CD30 overexpressing lymphomas. Proteomics (2007) 0.98
Broad host range fluorescence and bioluminescence expression vectors for Gram-negative bacteria. Plasmid (2007) 0.98
Polyamine biosynthesis and transport mechanisms are crucial for fitness and pathogenesis of Streptococcus pneumoniae. Microbiology (2010) 0.97
Use of PCR primers derived from a putative transcriptional regulator gene for species-specific determination of Listeria monocytogenes. Int J Food Microbiol (2004) 0.97
Proteome analysis of Edwardsiella ictaluri. Proteomics (2009) 0.96
Diet-related modification of cuticular hydrocarbon profiles of the Argentine ant, Linepithema humile, diminishes intercolony aggression. J Chem Ecol (2005) 0.95
Alteration of DNA adenine methylase (Dam) activity in Pasteurella multocida causes increased spontaneous mutation frequency and attenuation in mice. Microbiology (2003) 0.93
The silent codon change I507-ATC->ATT contributes to the severity of the ΔF508 CFTR channel dysfunction. FASEB J (2013) 0.93
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays. BMC Bioinformatics (2009) 0.92
Complete Genome Sequence of Channel Catfish Gastrointestinal Septicemia Isolate Edwardsiella tarda C07-087. Genome Announc (2013) 0.92
Comparative assessment of acid, alkali and salt tolerance in Listeria monocytogenes virulent and avirulent strains. FEMS Microbiol Lett (2005) 0.92
Genome sequence of the solvent-producing bacterium Clostridium carboxidivorans strain P7T. J Bacteriol (2010) 0.92
Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome. BMC Genomics (2007) 0.92
Genome sequence of lineage III Listeria monocytogenes strain HCC23. J Bacteriol (2011) 0.92
Rapid identification of Streptococcus pyogenes with PCR primers from a putative transcriptional regulator gene. Res Microbiol (2005) 0.91
Cyclic strain regulates pro-inflammatory protein expression in porcine aortic valve endothelial cells. J Heart Valve Dis (2008) 0.91
GOModeler--a tool for hypothesis-testing of functional genomics datasets. BMC Bioinformatics (2010) 0.91
Differential immediate-early gene responses to elevated pressure in porcine aortic valve interstitial cells. J Heart Valve Dis (2006) 0.90
RNA-seq based transcriptional map of bovine respiratory disease pathogen "Histophilus somni 2336". PLoS One (2012) 0.90
Complete genome and comparative analysis of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5. BMC Genomics (2010) 0.90
Topical application of Escherichia coli-vectored vaccine as a simple method for eliciting protective immunity. Infect Immun (2006) 0.89
Transcriptome-based differentiation of closely-related Miscanthus lines. PLoS One (2012) 0.89
Development of bioluminescent Salmonella strains for use in food safety. BMC Microbiol (2008) 0.89
Quantitative analysis of Streptococcus pneumoniae TIGR4 response to in vitro iron restriction by 2-D LC ESI MS/MS. Proteomics (2008) 0.88
Re-annotation is an essential step in systems biology modeling of functional genomics data. PLoS One (2010) 0.88
Expression of CD134 and CXCR4 mRNA in term placentas from FIV-infected and control cats. Vet Immunol Immunopathol (2008) 0.88
Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res (2015) 0.88
Experimental annotation of channel catfish virus by probabilistic proteogenomic mapping. Proteomics (2009) 0.88
PCR amplification of a species-specific putative transcriptional regulator gene reveals the identity of Enterococcus faecalis. Res Microbiol (2005) 0.87
The transcriptional response of Pasteurella multocida to three classes of antibiotics. BMC Genomics (2009) 0.87
Alcohol abuse and Streptococcus pneumoniae infections: consideration of virulence factors and impaired immune responses. Alcohol (2011) 0.87
Bovine viral diarrhea virus infection affects the expression of proteins related to professional antigen presentation in bovine monocytes. Biochim Biophys Acta (2008) 0.86
Gene model detection using mass spectrometry. Methods Mol Biol (2010) 0.86
Ultrasonic incisions produce less inflammatory mediator response during early healing than electrosurgical incisions. PLoS One (2013) 0.86
Accelerating string set matching in FPGA hardware for bioinformatics research. BMC Bioinformatics (2008) 0.86
Facilitating functional annotation of chicken microarray data. BMC Bioinformatics (2009) 0.86