Published in BMC Genomics on April 15, 2013
Fit for consumption: zebrafish as a model for tuberculosis. Dis Model Mech (2014) 0.86
COPASutils: an R package for reading, processing, and visualizing data from COPAS large-particle flow cytometers. PLoS One (2014) 0.84
Evaluation of zebrafish as a model to study the pathogenesis of the opportunistic pathogen Cronobacter turicensis. Emerg Microbes Infect (2015) 0.82
Common and specific downstream signaling targets controlled by Tlr2 and Tlr5 innate immune signaling in zebrafish. BMC Genomics (2015) 0.82
Establishment and optimization of a high throughput setup to study Staphylococcus epidermidis and Mycobacterium marinum infection as a model for drug discovery. J Vis Exp (2014) 0.79
Unusual fluorescent granulomas and myonecrosis in Danio rerio infected by the microsporidian pathogen Pseudoloma neurophilia. Zebrafish (2014) 0.78
The level of residual dispersion variation and the power of differential expression tests for RNA-Seq data. PLoS One (2015) 0.78
Parallel deep transcriptome and proteome analysis of zebrafish larvae. BMC Res Notes (2013) 0.78
The Zebrafish as a Tool to Cancer Drug Discovery. Austin J Pharmacol Ther (2015) 0.78
Establishment of three Francisella infections in zebrafish embryos at different temperatures. Infect Immun (2014) 0.78
Disparate developmental patterns of immune responses to bacterial and viral infections in fish. Sci Rep (2015) 0.77
Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics. Immunogenetics (2014) 0.77
Identification and functional characterization of nonmammalian Toll-like receptor 20. Immunogenetics (2013) 0.77
Circadian variations in the liver metabolites of medaka (Oryzias latipes). Sci Rep (2016) 0.77
Zebrafish (Danio rerio) as a Vertebrate Model Host To Study Colonization, Pathogenesis, and Transmission of Foodborne Escherichia coli O157. mSphere (2017) 0.75
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res (2008) 54.83
Foreign body reaction to biomaterials. Semin Immunol (2007) 8.32
WikiPathways: pathway editing for the people. PLoS Biol (2008) 8.13
Guidelines for the management of intravascular catheter-related infections. Clin Infect Dis (2001) 4.94
A transgenic zebrafish model of neutrophilic inflammation. Blood (2006) 3.93
Real-time visualization of mycobacterium-macrophage interactions leading to initiation of granuloma formation in zebrafish embryos. Immunity (2002) 3.48
Staphylococcus epidermidis infections. Microbes Infect (2002) 3.45
Characterization of the importance of polysaccharide intercellular adhesin/hemagglutinin of Staphylococcus epidermidis in the pathogenesis of biomaterial-based infection in a mouse foreign body infection model. Infect Immun (1999) 2.92
mpeg1 promoter transgenes direct macrophage-lineage expression in zebrafish. Blood (2010) 2.82
Alternative sigma factors and their roles in bacterial virulence. Microbiol Mol Biol Rev (2005) 2.15
Techniques for analysis, sorting, and dispensing of C. elegans on the COPAS flow-sorting system. Methods Mol Biol (2006) 2.12
Characterization of the importance of Staphylococcus epidermidis autolysin and polysaccharide intercellular adhesin in the pathogenesis of intravascular catheter-associated infection in a rat model. J Infect Dis (2001) 2.10
Zebrafish embryos as a model host for the real time analysis of Salmonella typhimurium infections. Cell Microbiol (2003) 1.98
How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes? BMC Genomics (2012) 1.84
Host-pathogen interactions made transparent with the zebrafish model. Curr Drug Targets (2011) 1.60
Molecular basis of Staphylococcus epidermidis infections. Semin Immunopathol (2011) 1.56
A high-throughput screen for tuberculosis progression. PLoS One (2011) 1.48
Zebrafish development and regeneration: new tools for biomedical research. Int J Dev Biol (2009) 1.46
A novel vertebrate model of Staphylococcus aureus infection reveals phagocyte-dependent resistance of zebrafish to non-host specialized pathogens. Cell Microbiol (2008) 1.45
Biomaterial-associated infection: locating the finish line in the race for the surface. Sci Transl Med (2012) 1.44
MyD88 innate immune function in a zebrafish embryo infection model. Infect Immun (2006) 1.35
Specificity of the zebrafish host transcriptome response to acute and chronic mycobacterial infection and the role of innate and adaptive immune components. Mol Immunol (2009) 1.35
Macrophage-specific gene functions in Spi1-directed innate immunity. Blood (2010) 1.30
The spectrum of infections in catheter-dependent hemodialysis patients. Clin J Am Soc Nephrol (2011) 1.29
Burkholderia cenocepacia creates an intramacrophage replication niche in zebrafish embryos, followed by bacterial dissemination and establishment of systemic infection. Infect Immun (2010) 1.25
RNA-seq and microarray complement each other in transcriptome profiling. BMC Genomics (2012) 1.22
Surfactant protein A (SP-A)-mediated clearance of Staphylococcus aureus involves binding of SP-A to the staphylococcal adhesin eap and the macrophage receptors SP-A receptor 210 and scavenger receptor class A. J Biol Chem (2010) 1.14
Biomaterial-associated persistence of Staphylococcus epidermidis in pericatheter macrophages. J Infect Dis (2000) 1.12
Comparison of static immersion and intravenous injection systems for exposure of zebrafish embryos to the natural pathogen Edwardsiella tarda. BMC Immunol (2011) 1.12
Pathogenesis of implant-associated infection: the role of the host. Semin Immunopathol (2011) 1.09
Colonization, pathogenicity, host susceptibility, and therapeutics for Staphylococcus aureus: what is the clinical relevance? Semin Immunopathol (2011) 1.06
Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection. Fish Shellfish Immunol (2010) 1.03
Infectious disease modeling and innate immune function in zebrafish embryos. Methods Cell Biol (2011) 0.98
Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos. Mol Immunol (2010) 0.96
Microfibril-associated protein 4 binds to surfactant protein A (SP-A) and colocalizes with SP-A in the extracellular matrix of the lung. Scand J Immunol (2006) 0.95
Tissue around catheters is a niche for bacteria associated with medical device infection. Crit Care Med (2008) 0.87
Host tissue as a niche for biomaterial-associated infection. Future Microbiol (2010) 0.84
The influence of antibodies on Staphylococcus epidermidis adherence to polyvinylpyrrolidone-coated silicone elastomer in experimental biomaterial-associated infection in mice. Biomaterials (2009) 0.83
Stimulation of the intracellular bacterial sensor NOD2 programs dendritic cells to promote interleukin-17 production in human memory T cells. Immunity (2007) 4.70
Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol Immunol (2009) 2.42
Single-molecule imaging of the H-ras membrane-anchor reveals domains in the cytoplasmic leaflet of the cell membrane. Biophys J (2004) 1.95
Neutrophil-mediated experimental metastasis is enhanced by VEGFR inhibition in a zebrafish xenograft model. J Pathol (2012) 1.93
Medical-grade honey kills antibiotic-resistant bacteria in vitro and eradicates skin colonization. Clin Infect Dis (2008) 1.75
Expression analysis of the Toll-like receptor and TIR domain adaptor families of zebrafish. Mol Immunol (2004) 1.73
How honey kills bacteria. FASEB J (2010) 1.71
The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proc Natl Acad Sci U S A (2013) 1.68
Transcriptome profiling and functional analyses of the zebrafish embryonic innate immune response to Salmonella infection. J Immunol (2009) 1.65
Host-pathogen interactions made transparent with the zebrafish model. Curr Drug Targets (2011) 1.60
Identification and real-time imaging of a myc-expressing neutrophil population involved in inflammation and mycobacterial granuloma formation in zebrafish. Dev Comp Immunol (2007) 1.58
A high-throughput screen for tuberculosis progression. PLoS One (2011) 1.48
Model systems for infectious disease and cancer in zebrafish: a report on an EMBO workshop held at the Lorentz Center, Leiden, The Netherlands, July 16-18, 2007. Zebrafish (2007) 1.47
Zebrafish development and regeneration: new tools for biomedical research. Int J Dev Biol (2009) 1.46
The procambium specification gene Oshox1 promotes polar auxin transport capacity and reduces its sensitivity toward inhibition. Plant Physiol (2002) 1.45
Biomaterial-associated infection: locating the finish line in the race for the surface. Sci Transl Med (2012) 1.44
The RADICLELESS1 gene is required for vascular pattern formation in rice. Development (2003) 1.39
Serum stabilities of short tryptophan- and arginine-rich antimicrobial peptide analogs. PLoS One (2010) 1.38
Infection of zebrafish embryos with intracellular bacterial pathogens. J Vis Exp (2012) 1.36
MyD88 innate immune function in a zebrafish embryo infection model. Infect Immun (2006) 1.35
Specificity of the zebrafish host transcriptome response to acute and chronic mycobacterial infection and the role of innate and adaptive immune components. Mol Immunol (2009) 1.35
Single-molecule diffusion measurements of H-Ras at the plasma membrane of live cells reveal microdomain localization upon activation. J Cell Sci (2005) 1.34
Zebrafish embryos and larvae: a new generation of disease models and drug screens. Birth Defects Res C Embryo Today (2011) 1.32
Gene expression profiling of the long-term adaptive response to hypoxia in the gills of adult zebrafish. Am J Physiol Regul Integr Comp Physiol (2005) 1.30
Macrophage-specific gene functions in Spi1-directed innate immunity. Blood (2010) 1.30
Auxin distribution in Lotus japonicus during root nodule development. Plant Mol Biol (2003) 1.27
Burkholderia cenocepacia creates an intramacrophage replication niche in zebrafish embryos, followed by bacterial dissemination and establishment of systemic infection. Infect Immun (2010) 1.25
Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection. Mol Immunol (2005) 1.23
Primitive duplicate Hox clusters in the European eel's genome. PLoS One (2012) 1.21
A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members. Plant Mol Biol (2007) 1.20
Has2 is required upstream of Rac1 to govern dorsal migration of lateral cells during zebrafish gastrulation. Development (2004) 1.19
Two major medicinal honeys have different mechanisms of bactericidal activity. PLoS One (2011) 1.17
Gene expression and digit homology in the chicken embryo wing. Evol Dev (2005) 1.14
Comparison of static immersion and intravenous injection systems for exposure of zebrafish embryos to the natural pathogen Edwardsiella tarda. BMC Immunol (2011) 1.12
Discovery of a functional glucocorticoid receptor beta-isoform in zebrafish. Endocrinology (2007) 1.12
Distinct functions for ERK1 and ERK2 in cell migration processes during zebrafish gastrulation. Dev Biol (2008) 1.11
Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts. J Comp Physiol B (2007) 1.09
Candidates for membrane progestin receptors--past approaches and future challenges. Comp Biochem Physiol C Toxicol Pharmacol (2008) 1.09
Single-molecule diffusion reveals similar mobility for the Lck, H-ras, and K-ras membrane anchors. Biophys J (2006) 1.08
EU-OSTID: a collection of transposon insertional mutants for functional genomics in rice. Plant Mol Biol (2005) 1.08
Functional analysis of a zebrafish myd88 mutant identifies key transcriptional components of the innate immune system. Dis Model Mech (2013) 1.07
Pathogen recognition and activation of the innate immune response in zebrafish. Adv Hematol (2012) 1.07
Functions of the MAPK family in vertebrate-development. FEBS Lett (2006) 1.07
ZebraFISH: fluorescent in situ hybridization protocol and three-dimensional imaging of gene expression patterns. Zebrafish (2006) 1.06
Genetic analysis of a pH-regulated operon from Rhizobium tropici CIAT899 involved in acid tolerance and nodulation competitiveness. Mol Plant Microbe Interact (2003) 1.05
Exploring the zebrafish embryo as an alternative model for the evaluation of liver toxicity by histopathology and expression profiling. Arch Toxicol (2013) 1.05
Automated whole animal bio-imaging assay for human cancer dissemination. PLoS One (2012) 1.05
Magnetic resonance microscopy of the adult zebrafish. Zebrafish (2006) 1.04
Antibacterial components of honey. IUBMB Life (2011) 1.03
Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection. Fish Shellfish Immunol (2010) 1.03
Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine. Genome Biol (2009) 1.03
Genomic annotation and expression analysis of the zebrafish Rho small GTPase family during development and bacterial infection. Genomics (2005) 1.01
Time-lapse tracking of barley androgenesis reveals position-determined cell death within pro-embryos. Planta (2004) 1.00
Isoform-specific differences in rapid nucleocytoplasmic shuttling cause distinct subcellular distributions of 14-3-3 sigma and 14-3-3 zeta. J Cell Sci (2004) 1.00
First draft genome sequence of the Japanese eel, Anguilla japonica. Gene (2012) 1.00
Robotic injection of zebrafish embryos for high-throughput screening in disease models. Methods (2013) 0.99
Deep RNA sequencing of the skeletal muscle transcriptome in swimming fish. PLoS One (2013) 0.98
Infectious disease modeling and innate immune function in zebrafish embryos. Methods Cell Biol (2011) 0.98
Establishing zebrafish as a novel exercise model: swimming economy, swimming-enhanced growth and muscle growth marker gene expression. PLoS One (2010) 0.97
Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos. Mol Immunol (2010) 0.96
Single-molecule microscopy reveals membrane microdomain organization of cells in a living vertebrate. Biophys J (2009) 0.96
Characterization and expression patterns of the MAPK family in zebrafish. Gene Expr Patterns (2006) 0.96
In vitro antibacterial activity of porous TiO2-Ag composite layers against methicillin-resistant Staphylococcus aureus. Acta Biomater (2009) 0.96
Langerhans cells favor skin flora tolerance through limited presentation of bacterial antigens and induction of regulatory T cells. J Invest Dermatol (2013) 0.95
ERK1 and ERK2 MAPK are key regulators of distinct gene sets in zebrafish embryogenesis. BMC Genomics (2008) 0.95
A spatially restricted increase in receptor mobility is involved in directional sensing during Dictyostelium discoideum chemotaxis. J Cell Sci (2008) 0.94
Comparison of the exomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio). Zebrafish (2012) 0.94
Genetic and transcriptome characterization of model zebrafish cell lines. Zebrafish (2006) 0.94