Published in Bioinformatics on February 19, 2007
Integration of biological networks and gene expression data using Cytoscape. Nat Protoc (2007) 27.10
Human Protein Reference Database--2009 update. Nucleic Acids Res (2008) 21.25
InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol (2008) 4.61
Visualization of omics data for systems biology. Nat Methods (2010) 4.59
The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog (2008) 3.11
InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Res (2012) 2.66
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data. Bioinformatics (2013) 1.82
Primary biliary cirrhosis is associated with altered hepatic microRNA expression. J Autoimmun (2009) 1.41
Grouping annotations on the subcellular layered interactome demonstrates enhanced autophagy activity in a recurrent experimental autoimmune uveitis T cell line. PLoS One (2014) 1.39
AutoSOME: a clustering method for identifying gene expression modules without prior knowledge of cluster number. BMC Bioinformatics (2010) 1.37
Curating the innate immunity interactome. BMC Syst Biol (2010) 1.30
NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration. Nucleic Acids Res (2014) 1.29
Nuclear import of the glucocorticoid receptor-hsp90 complex through the nuclear pore complex is mediated by its interaction with Nup62 and importin beta. Mol Cell Biol (2009) 1.24
Integrated cellular network of transcription regulations and protein-protein interactions. BMC Syst Biol (2010) 1.20
Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nat Commun (2012) 1.09
Identification of a human neonatal immune-metabolic network associated with bacterial infection. Nat Commun (2014) 1.08
The glomerular transcriptome and a predicted protein-protein interaction network. J Am Soc Nephrol (2007) 1.07
xiNET: cross-link network maps with residue resolution. Mol Cell Proteomics (2015) 1.03
RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. BMC Bioinformatics (2012) 1.03
The Pseudomonas aeruginosa autoinducer 3O-C12 homoserine lactone provokes hyperinflammatory responses from cystic fibrosis airway epithelial cells. PLoS One (2011) 1.00
ROCK1 is a potential combinatorial drug target for BRAF mutant melanoma. Mol Syst Biol (2014) 0.97
A systems biology approach to understanding atherosclerosis. EMBO Mol Med (2010) 0.97
ReactionFlow: an interactive visualization tool for causality analysis in biological pathways. BMC Proc (2015) 0.97
Using biological networks to integrate, visualize and analyze genomics data. Genet Sel Evol (2016) 0.96
Immunoinformatics: an integrated scenario. Immunology (2010) 0.94
Early-life environmental variation affects intestinal microbiota and immune development in new-born piglets. PLoS One (2014) 0.91
Layered functional network analysis of gene expression in human heart failure. PLoS One (2009) 0.89
ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis. Nucleic Acids Res (2014) 0.89
Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease. BMC Genomics (2014) 0.88
Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation. BioData Min (2011) 0.88
Systems-level analysis of innate immunity. Annu Rev Immunol (2014) 0.88
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. BMC Bioinformatics (2012) 0.87
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. BMC Genomics (2012) 0.85
Network based analyses of gene expression profile of LCN2 overexpression in esophageal squamous cell carcinoma. Sci Rep (2014) 0.84
Lectin-Glycan Interaction Network-Based Identification of Host Receptors of Microbial Pathogenic Adhesins. MBio (2016) 0.84
Novel modeling of cancer cell signaling pathways enables systematic drug repositioning for distinct breast cancer metastases. Cancer Res (2013) 0.84
The Hsp90 co-chaperone p23 of Toxoplasma gondii: Identification, functional analysis and dynamic interactome determination. Mol Biochem Parasitol (2010) 0.84
Reconstruction of regulatory networks through temporal enrichment profiling and its application to H1N1 influenza viral infection. BMC Bioinformatics (2013) 0.82
The involvement of cholesterol in sepsis and tolerance to lipopolysaccharide highlighted by the transcriptome analysis of zebrafish (Danio rerio). Zebrafish (2014) 0.81
Integrin-mediated signaling induced by simian virus 40 leads to transient uncoupling of cortical actin and the plasma membrane. PLoS One (2013) 0.81
Visualizing time-related data in biology, a review. Brief Bioinform (2013) 0.81
Layered signaling regulatory networks analysis of gene expression involved in malignant tumorigenesis of non-resolving ulcerative colitis via integration of cross-study microarray profiles. PLoS One (2013) 0.80
The protein architecture of human secretory vesicles reveals differential regulation of signaling molecule secretion by protein kinases. PLoS One (2012) 0.80
PPI network analysis of mRNA expression profile of ezrin knockdown in esophageal squamous cell carcinoma. Biomed Res Int (2014) 0.80
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization. Database (Oxford) (2015) 0.79
A systems biology approach to the analysis of subset-specific responses to lipopolysaccharide in dendritic cells. PLoS One (2014) 0.79
Reconstructed cell fate-regulatory programs in stem cells reveal hierarchies and key factors of neurogenesis. Genome Res (2016) 0.78
Methods for visual mining of genomic and proteomic data atlases. BMC Bioinformatics (2012) 0.78
LucidDraw: efficiently visualizing complex biochemical networks within MATLAB. BMC Bioinformatics (2010) 0.78
SLDR: a computational technique to identify novel genetic regulatory relationships. BMC Bioinformatics (2014) 0.78
Essential functional modules for pathogenic and defensive mechanisms in Candida albicans infections. Biomed Res Int (2014) 0.78
BirdsEyeView (BEV): graphical overviews of experimental data. BMC Bioinformatics (2012) 0.77
Exploring potential new floral organ morphogenesis genes of Arabidopsis thaliana using systems biology approach. Front Plant Sci (2015) 0.77
Transcriptome profiling identifies p53 as a key player during calreticulin deficiency: Implications in lipid accumulation. Cell Cycle (2015) 0.77
A network-based approach on elucidating the multi-faceted nature of chronological aging in S. cerevisiae. PLoS One (2011) 0.77
An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information. BMC Bioinformatics (2010) 0.77
Dynamic protein-protein interaction subnetworks of lung cancer in cases with smoking history. Chin J Cancer (2012) 0.77
CellWhere: graphical display of interaction networks organized on subcellular localizations. Nucleic Acids Res (2015) 0.75
Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps. PLoS One (2012) 0.75
Antiviral innate immunity through the lens of systems biology. Virus Res (2015) 0.75
Taming data. Cell Host Microbe (2008) 0.75
A systematic analysis of human lipocalin family and its expression in esophageal carcinoma. Sci Rep (2015) 0.75
Reconstruction of gene regulatory networks reveals chromatin remodelers and key transcription factors in tumorigenesis. Genome Med (2016) 0.75
CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components. BMC Bioinformatics (2017) 0.75
Network analyses elucidate the role of SMYD3 in esophageal squamous cell carcinoma. FEBS Open Bio (2017) 0.75
Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat Protoc (2008) 7.92
Peptide antimicrobial agents. Clin Microbiol Rev (2006) 6.04
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res (2010) 5.23
PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Methods (2011) 5.01
Pseudomonas aeruginosa anaerobic respiration in biofilms: relationships to cystic fibrosis pathogenesis. Dev Cell (2002) 4.94
InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol (2008) 4.61
Designing antimicrobial peptides: form follows function. Nat Rev Drug Discov (2011) 4.16
Association between the 2008-09 seasonal influenza vaccine and pandemic H1N1 illness during Spring-Summer 2009: four observational studies from Canada. PLoS Med (2010) 3.85
Pseudomonas aeruginosa: all roads lead to resistance. Trends Microbiol (2011) 3.49
Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nat Methods (2012) 3.17
Cationic antimicrobial peptides activate a two-component regulatory system, PmrA-PmrB, that regulates resistance to polymyxin B and cationic antimicrobial peptides in Pseudomonas aeruginosa. Mol Microbiol (2003) 3.06
Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res (2008) 3.03
Recognition of host immune activation by Pseudomonas aeruginosa. Science (2005) 2.84
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res (2008) 2.71
Cationic host defense (antimicrobial) peptides. Curr Opin Immunol (2005) 2.71
InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Res (2012) 2.66
Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res (2005) 2.61
The human antimicrobial peptide LL-37 is a multifunctional modulator of innate immune responses. J Immunol (2002) 2.57
Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin. Chem Biol (2004) 2.51
The relationship between peptide structure and antibacterial activity. Peptides (2003) 2.51
Multidrug efflux systems play an important role in the invasiveness of Pseudomonas aeruginosa. J Exp Med (2002) 2.40
Mode of action of the new antibiotic for Gram-positive pathogens daptomycin: comparison with cationic antimicrobial peptides and lipopeptides. Biochim Biophys Acta (2006) 2.35
Modulation of the TLR-mediated inflammatory response by the endogenous human host defense peptide LL-37. J Immunol (2006) 2.32
Pseudomonas aeruginosa: new insights into pathogenesis and host defenses. Pathog Dis (2013) 2.32
Rational design of alpha-helical antimicrobial peptides with enhanced activities and specificity/therapeutic index. J Biol Chem (2005) 2.28
Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: a tool for identifying differentially regulated genes. Genome Res (2005) 2.22
Inhibition of LpxC protects mice from resistant Acinetobacter baumannii by modulating inflammation and enhancing phagocytosis. MBio (2012) 2.15
Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion. Nat Protoc (2007) 2.08
Alternative mechanisms of action of cationic antimicrobial peptides on bacteria. Expert Rev Anti Infect Ther (2007) 2.06
PSORTdb: a protein subcellular localization database for bacteria. Nucleic Acids Res (2005) 2.05
ArrayPipe: a flexible processing pipeline for microarray data. Nucleic Acids Res (2004) 2.03
High-throughput generation of small antibacterial peptides with improved activity. Nat Biotechnol (2005) 2.01
Impact of LL-37 on anti-infective immunity. J Leukoc Biol (2004) 2.01
Multifunctional cationic host defence peptides and their clinical applications. Cell Mol Life Sci (2011) 1.99
Swarming of Pseudomonas aeruginosa is a complex adaptation leading to increased production of virulence factors and antibiotic resistance. J Bacteriol (2008) 1.98
An anti-infective peptide that selectively modulates the innate immune response. Nat Biotechnol (2007) 1.97
Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet (2013) 1.93
The roles of cathelicidin LL-37 in immune defences and novel clinical applications. Curr Opin Hematol (2009) 1.92
Regulation of virulence and antibiotic resistance by two-component regulatory systems in Pseudomonas aeruginosa. FEMS Microbiol Rev (2009) 1.91
Human host defense peptide LL-37 prevents bacterial biofilm formation. Infect Immun (2008) 1.91
Can innate immunity be enhanced to treat microbial infections? Nat Rev Microbiol (2004) 1.90
Sequence requirements and an optimization strategy for short antimicrobial peptides. Chem Biol (2006) 1.84
Ciprofloxacin induction of a susceptibility determinant in Pseudomonas aeruginosa. Antimicrob Agents Chemother (2005) 1.82
The cationic antimicrobial peptide LL-37 modulates dendritic cell differentiation and dendritic cell-induced T cell polarization. J Immunol (2004) 1.78
The pmrCAB operon mediates polymyxin resistance in Acinetobacter baumannii ATCC 17978 and clinical isolates through phosphoethanolamine modification of lipid A. Antimicrob Agents Chemother (2011) 1.78
A re-evaluation of the role of host defence peptides in mammalian immunity. Curr Protein Pept Sci (2005) 1.78
Genome-wide identification of Pseudomonas aeruginosa exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen. Genome Res (2005) 1.77
Adaptive resistance to the "last hope" antibiotics polymyxin B and colistin in Pseudomonas aeruginosa is mediated by the novel two-component regulatory system ParR-ParS. Antimicrob Agents Chemother (2010) 1.74
Adaptive and mutational resistance: role of porins and efflux pumps in drug resistance. Clin Microbiol Rev (2012) 1.74
Using microarray gene signatures to elucidate mechanisms of antibiotic action and resistance. Drug Discov Today (2005) 1.74
Immune modulation by multifaceted cationic host defense (antimicrobial) peptides. Nat Chem Biol (2013) 1.73
Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast. Genome Res (2002) 1.72
Sublethal concentrations of pleurocidin-derived antimicrobial peptides inhibit macromolecular synthesis in Escherichia coli. Antimicrob Agents Chemother (2002) 1.69
Immunomodulatory activities of small host defense peptides. Antimicrob Agents Chemother (2005) 1.67
Complex ciprofloxacin resistome revealed by screening a Pseudomonas aeruginosa mutant library for altered susceptibility. Antimicrob Agents Chemother (2008) 1.67
Endotoxin tolerance represents a distinctive state of alternative polarization (M2) in human mononuclear cells. J Immunol (2011) 1.65
Bacterial biofilm development as a multicellular adaptation: antibiotic resistance and new therapeutic strategies. Curr Opin Microbiol (2013) 1.63
Inhibition of bacterial biofilm formation and swarming motility by a small synthetic cationic peptide. Antimicrob Agents Chemother (2012) 1.63
Systems-level comparison of host-responses elicited by avian H5N1 and seasonal H1N1 influenza viruses in primary human macrophages. PLoS One (2009) 1.61
Aminoglycoside efflux in Pseudomonas aeruginosa: involvement of novel outer membrane proteins. Antimicrob Agents Chemother (2003) 1.59
AMPer: a database and an automated discovery tool for antimicrobial peptides. Bioinformatics (2007) 1.59
Potential of immunomodulatory host defense peptides as novel anti-infectives. Trends Biotechnol (2009) 1.58
A sentinel platform to evaluate influenza vaccine effectiveness and new variant circulation, Canada 2010-2011 season. Clin Infect Dis (2012) 1.58
Identification of genes involved in swarming motility using a Pseudomonas aeruginosa PAO1 mini-Tn5-lux mutant library. J Bacteriol (2006) 1.54
Effects of net charge and the number of positively charged residues on the biological activity of amphipathic alpha-helical cationic antimicrobial peptides. Biopolymers (2008) 1.51
Characterization of a proteolytically stable multifunctional host defense peptidomimetic. Chem Biol (2013) 1.49
Antibody responses in adult and neonatal BALB/c mice to immunization with novel Bordetella pertussis vaccine formulations. Vaccine (2011) 1.48
INMEX--a web-based tool for integrative meta-analysis of expression data. Nucleic Acids Res (2013) 1.48
Cross-reactive and vaccine-induced antibody to an emerging swine-origin variant of influenza A virus subtype H3N2 (H3N2v). J Infect Dis (2012) 1.47
Cerebral: visualizing multiple experimental conditions on a graph with biological context. IEEE Trans Vis Comput Graph (2008) 1.45
Antimicrobial peptide therapeutics for cystic fibrosis. Antimicrob Agents Chemother (2005) 1.44
The human cationic peptide LL-37 induces activation of the extracellular signal-regulated kinase and p38 kinase pathways in primary human monocytes. J Immunol (2004) 1.41
MizBee: a multiscale synteny browser. IEEE Trans Vis Comput Graph (2009) 1.41
Intracellular receptor for human host defense peptide LL-37 in monocytes. J Immunol (2009) 1.38
Enhanced inflammatory responses of chronic granulomatous disease leukocytes involve ROS-independent activation of NF-kappa B. Eur J Immunol (2007) 1.37
Host defense peptide LL-37, in synergy with inflammatory mediator IL-1beta, augments immune responses by multiple pathways. J Immunol (2007) 1.37
The commensal Streptococcus salivarius K12 downregulates the innate immune responses of human epithelial cells and promotes host-microbe homeostasis. Infect Immun (2008) 1.36
Genetic determinants involved in the susceptibility of Pseudomonas aeruginosa to beta-lactam antibiotics. Antimicrob Agents Chemother (2010) 1.35
Cationic peptides: distribution and mechanisms of resistance. Curr Pharm Des (2002) 1.35
Enabling a systems biology approach to immunology: focus on innate immunity. Trends Immunol (2009) 1.35
Secondary acylation of Klebsiella pneumoniae lipopolysaccharide contributes to sensitivity to antibacterial peptides. J Biol Chem (2007) 1.33
Use of artificial intelligence in the design of small peptide antibiotics effective against a broad spectrum of highly antibiotic-resistant superbugs. ACS Chem Biol (2009) 1.33
Synthetic cationic peptide IDR-1002 provides protection against bacterial infections through chemokine induction and enhanced leukocyte recruitment. J Immunol (2010) 1.32
Curating the innate immunity interactome. BMC Syst Biol (2010) 1.30
Permeabilization of fungal hyphae by the plant defensin NaD1 occurs through a cell wall-dependent process. J Biol Chem (2010) 1.28
Systems-level comparison of host responses induced by pandemic and seasonal influenza A H1N1 viruses in primary human type I-like alveolar epithelial cells in vitro. Respir Res (2010) 1.26
Fluorescent probes alter miscibility phase boundaries in ternary vesicles. J Phys Chem B (2007) 1.26
The human cationic host defense peptide LL-37 mediates contrasting effects on apoptotic pathways in different primary cells of the innate immune system. J Leukoc Biol (2006) 1.25
Interaction and cellular localization of the human host defense peptide LL-37 with lung epithelial cells. Infect Immun (2005) 1.24
Antimicrobial properties of lactoferrin. Biochimie (2008) 1.24
Structural studies of a peptide with immune modulating and direct antimicrobial activity. Chem Biol (2010) 1.24
Creeping baselines and adaptive resistance to antibiotics. Drug Resist Updat (2011) 1.24
Novel genetic determinants of low-level aminoglycoside resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother (2008) 1.24
Identification of novel antibacterial peptides by chemoinformatics and machine learning. J Med Chem (2009) 1.23