Published in Syst Synth Biol on January 22, 2010
Modeling formalisms in Systems Biology. AMB Express (2011) 1.61
Functional Information: Towards Synthesis of Biosemiotics and Cybernetics. Entropy (Basel) (2010) 0.94
The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology. Bioinformatics (2011) 0.80
Evolving robust gene regulatory networks. PLoS One (2015) 0.77
Evolving modular genetic regulatory networks with a recursive, top-down approach. Syst Synth Biol (2015) 0.75
Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol (1961) 65.10
From molecular to modular cell biology. Nature (1999) 23.51
Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet (2005) 14.39
Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A (2003) 12.50
Stochastic simulation of chemical kinetics. Annu Rev Phys Chem (2007) 7.59
A synthetic multicellular system for programmed pattern formation. Nature (2005) 6.93
Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell (2003) 6.03
Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol (2006) 5.92
Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci U S A (2002) 5.29
Generating realistic in silico gene networks for performance assessment of reverse engineering methods. J Comput Biol (2009) 5.14
Synthetic biology. Nat Rev Genet (2005) 4.67
Executable cell biology. Nat Biotechnol (2007) 4.64
From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays (1998) 4.42
Spatiotemporal control of gene expression with pulse-generating networks. Proc Natl Acad Sci U S A (2004) 3.61
Towards a reliable objective function for multiple sequence alignments. J Mol Biol (2001) 3.07
Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics (2003) 2.57
Modeling regulatory networks with weight matrices. Pac Symp Biocomput (1999) 2.52
Modular modeling of cellular systems with ProMoT/Diva. Bioinformatics (2003) 1.79
Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J R Soc Interface (2009) 1.69
Representation and simulation of biochemical processes using the pi-calculus process algebra. Pac Symp Biocomput (2001) 1.62
The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics (2006) 1.61
Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations. Pac Symp Biocomput (2003) 1.34
Model Selection Based on Minimum Description Length. J Math Psychol (2000) 1.30
Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study. BMC Syst Biol (2010) 1.25
Computational methodologies for modelling, analysis and simulation of signalling networks. Brief Bioinform (2006) 1.22
Genetdes: automatic design of transcriptional networks. Bioinformatics (2007) 1.18
Bifurcation discovery tool. Bioinformatics (2005) 1.15
The imitation game--a computational chemical approach to recognizing life. Nat Biotechnol (2006) 1.14
A Turing-like test for biological modeling. Nat Biotechnol (2005) 1.01
Toward verified biological models. IEEE/ACM Trans Comput Biol Bioinform (2008) 1.00
A model of the quorum sensing system in Vibrio fischeri using P systems. Artif Life (2008) 0.96
Quorum sensing. Curr Biol (2007) 0.93
Asmparts: assembly of biological model parts. Syst Synth Biol (2008) 0.92
Evolving complex dynamics in electronic models of genetic networks. Chaos (2004) 0.91
Computational design of digital and memory biological devices. Syst Synth Biol (2008) 0.84
A formal language for computational systems biology. OMICS (2004) 0.83
Modelling gene expression control using P systems: The Lac Operon, a case study. Biosystems (2007) 0.82
P systems applications to systems biology. Biosystems (2007) 0.77
Retracted Cell-cell signaling in Xanthomonas campestris involves an HD-GYP domain protein that functions in cyclic di-GMP turnover. Proc Natl Acad Sci U S A (2006) 4.92
Look who's talking: communication and quorum sensing in the bacterial world. Philos Trans R Soc Lond B Biol Sci (2007) 4.24
miR-214 targets ATF4 to inhibit bone formation. Nat Med (2012) 3.01
N-acylhomoserine lactones undergo lactonolysis in a pH-, temperature-, and acyl chain length-dependent manner during growth of Yersinia pseudotuberculosis and Pseudomonas aeruginosa. Infect Immun (2002) 3.00
The Pseudomonas aeruginosa quinolone signal molecule overcomes the cell density-dependency of the quorum sensing hierarchy, regulates rhl-dependent genes at the onset of stationary phase and can be produced in the absence of LasR. Mol Microbiol (2003) 2.74
Quorum sensing and environmental adaptation in Pseudomonas aeruginosa: a tale of regulatory networks and multifunctional signal molecules. Curr Opin Microbiol (2009) 2.64
Advancing the quorum in Pseudomonas aeruginosa: MvaT and the regulation of N-acylhomoserine lactone production and virulence gene expression. J Bacteriol (2002) 2.34
Positive control of swarming, rhamnolipid synthesis, and lipase production by the posttranscriptional RsmA/RsmZ system in Pseudomonas aeruginosa PAO1. J Bacteriol (2004) 2.25
The Pseudomonas aeruginosa 4-quinolone signal molecules HHQ and PQS play multifunctional roles in quorum sensing and iron entrapment. Chem Biol (2007) 2.05
Functional genetic analysis reveals a 2-Alkyl-4-quinolone signaling system in the human pathogen Burkholderia pseudomallei and related bacteria. Chem Biol (2006) 2.03
The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal. Mol Microbiol (2011) 2.00
EnrichNet: network-based gene set enrichment analysis. Bioinformatics (2012) 1.92
Characterization of N-acylhomoserine lactone-degrading bacteria associated with the Zingiber officinale (ginger) rhizosphere: co-existence of quorum quenching and quorum sensing in Acinetobacter and Burkholderia. BMC Microbiol (2011) 1.82
Quorum quenching by an N-acyl-homoserine lactone acylase from Pseudomonas aeruginosa PAO1. Infect Immun (2006) 1.77
Quinolones: from antibiotics to autoinducers. FEMS Microbiol Rev (2011) 1.75
Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains. J Bacteriol (2009) 1.73
4-quinolone signalling in Pseudomonas aeruginosa: old molecules, new perspectives. Int J Med Microbiol (2006) 1.65
Direct detection of N-acylhomoserine lactones in cystic fibrosis sputum. FEMS Microbiol Lett (2002) 1.65
The galactophilic lectin, LecA, contributes to biofilm development in Pseudomonas aeruginosa. Environ Microbiol (2006) 1.56
RsmY, a small regulatory RNA, is required in concert with RsmZ for GacA-dependent expression of biocontrol traits in Pseudomonas fluorescens CHA0. Mol Microbiol (2003) 1.55
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. BMC Bioinformatics (2009) 1.50
GacS sensor domains pertinent to the regulation of exoproduct formation and to the biocontrol potential of Pseudomonas fluorescens CHA0. Mol Plant Microbe Interact (2003) 1.50
Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions. Proc Natl Acad Sci U S A (2011) 1.49
The Pseudomonas aeruginosa sensor RetS switches type III and type VI secretion via c-di-GMP signalling. Environ Microbiol (2011) 1.48
Simultaneous quantitative profiling of N-acyl-L-homoserine lactone and 2-alkyl-4(1H)-quinolone families of quorum-sensing signaling molecules using LC-MS/MS. Anal Bioanal Chem (2010) 1.45
Cell-to-cell communication across the prokaryote-eukaryote boundary. Science (2002) 1.45
A thermodynamic switch modulates abscisic acid receptor sensitivity. EMBO J (2011) 1.44
The MexGHI-OpmD multidrug efflux pump controls growth, antibiotic susceptibility and virulence in Pseudomonas aeruginosa via 4-quinolone-dependent cell-to-cell communication. Microbiology (2005) 1.43
LuxS-dependent quorum sensing in Porphyromonas gingivalis modulates protease and haemagglutinin activities but is not essential for virulence. Microbiology (2002) 1.43
VanT, a homologue of Vibrio harveyi LuxR, regulates serine, metalloprotease, pigment, and biofilm production in Vibrio anguillarum. J Bacteriol (2002) 1.43
N-Acylhomoserine lactone quorum-sensing molecules are modified and degraded by Rhodococcus erythropolis W2 by both amidolytic and novel oxidoreductase activities. Microbiology (2005) 1.35
N-acylhomoserine lactones antagonize virulence gene expression and quorum sensing in Staphylococcus aureus. Infect Immun (2006) 1.35
Inhibition and dispersion of Pseudomonas aeruginosa biofilms by glycopeptide dendrimers targeting the fucose-specific lectin LecB. Chem Biol (2008) 1.34
Biofilm formation in Pseudomonas aeruginosa: fimbrial cup gene clusters are controlled by the transcriptional regulator MvaT. J Bacteriol (2004) 1.32
Extracellular protease of Pseudomonas fluorescens CHA0, a biocontrol factor with activity against the root-knot nematode Meloidogyne incognita. Appl Environ Microbiol (2005) 1.28
Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study. BMC Syst Biol (2010) 1.25
TopoGSA: network topological gene set analysis. Bioinformatics (2010) 1.24
Transcriptional dynamics of two seed compartments with opposing roles in Arabidopsis seed germination. Plant Physiol (2013) 1.23
Real-coded memetic algorithms with crossover hill-climbing. Evol Comput (2004) 1.20
Comprehensive profiling of N-acylhomoserine lactones produced by Yersinia pseudotuberculosis using liquid chromatography coupled to hybrid quadrupole-linear ion trap mass spectrometry. Anal Bioanal Chem (2006) 1.18
Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas species. BMC Genomics (2008) 1.17
Quorum sensing in Yersinia enterocolitica controls swimming and swarming motility. J Bacteriol (2006) 1.16
Transcriptomic analysis reveals a global alkyl-quinolone-independent regulatory role for PqsE in facilitating the environmental adaptation of Pseudomonas aeruginosa to plant and animal hosts. Environ Microbiol (2010) 1.14
The imitation game--a computational chemical approach to recognizing life. Nat Biotechnol (2006) 1.14
A LuxRI-family regulatory system controls excision and transfer of the Mesorhizobium loti strain R7A symbiosis island by activating expression of two conserved hypothetical genes. Mol Microbiol (2009) 1.13
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. BMC Bioinformatics (2010) 1.12
A distinctive dual-channel quorum-sensing system operates in Vibrio anguillarum. Mol Microbiol (2004) 1.10
Disruption of quorum sensing in seawater abolishes attraction of zoospores of the green alga Ulva to bacterial biofilms. Environ Microbiol (2005) 1.08
Quorum quenching activity in Anabaena sp. PCC 7120: identification of AiiC, a novel AHL-acylase. FEMS Microbiol Lett (2008) 1.07
Quorum sensing regulates dpsA and the oxidative stress response in Burkholderia pseudomallei. Microbiology (2006) 1.07
A dual biosensor for 2-alkyl-4-quinolone quorum-sensing signal molecules. Environ Microbiol (2007) 1.05
ProCKSI: a decision support system for Protein (structure) Comparison, Knowledge, Similarity and Information. BMC Bioinformatics (2007) 1.04
Acylhomoserine lactone production and degradation by the fish pathogen Tenacibaculum maritimum, a member of the Cytophaga-Flavobacterium-Bacteroides (CFB) group. FEMS Microbiol Lett (2010) 1.03
Functional analysis of the post-transcriptional regulator RsmA reveals a novel RNA-binding site. J Mol Biol (2005) 1.03
Phenotypic and genome-wide analysis of an antibiotic-resistant small colony variant (SCV) of Pseudomonas aeruginosa. PLoS One (2011) 1.03
Quorum sensing in Vibrio cholerae. Nat Genet (2002) 1.03
Biosensor-based assays for PQS, HHQ and related 2-alkyl-4-quinolone quorum sensing signal molecules. Nat Protoc (2007) 1.02
Using rule-based machine learning for candidate disease gene prioritization and sample classification of cancer gene expression data. PLoS One (2012) 1.00
Turnover of quorum sensing signal molecules modulates cross-kingdom signalling. Environ Microbiol (2009) 1.00
Garlic as an inhibitor of Pseudomonas aeruginosa quorum sensing in cystic fibrosis--a pilot randomized controlled trial. Pediatr Pulmonol (2010) 1.00
Significant immunomodulatory effects of Pseudomonas aeruginosa quorum-sensing signal molecules: possible link in human sepsis. Clin Sci (Lond) (2008) 0.98
Goethe's dream. Challenges and opportunities for synthetic biology. EMBO Rep (2009) 0.97
Photoperiodic control of carbon distribution during the floral transition in Arabidopsis. Plant Cell (2014) 0.96
CKIP-1 inhibits cardiac hypertrophy by regulating class II histone deacetylase phosphorylation through recruiting PP2A. Circulation (2012) 0.96
Emergence of secretion-defective sublines of Pseudomonas aeruginosa PAO1 resulting from spontaneous mutations in the vfr global regulatory gene. Appl Environ Microbiol (2008) 0.96
Structural basis for native agonist and synthetic inhibitor recognition by the Pseudomonas aeruginosa quorum sensing regulator PqsR (MvfR). PLoS Pathog (2013) 0.95
Bursting the bubble on bacterial biofilms: a flow cell methodology. Biofouling (2012) 0.95
The Gac/Rsm and cyclic-di-GMP signalling networks coordinately regulate iron uptake in Pseudomonas aeruginosa. Environ Microbiol (2013) 0.94
Quorum sensing. Curr Biol (2007) 0.93
A glycopeptide dendrimer inhibitor of the galactose-specific lectin LecA and of Pseudomonas aeruginosa biofilms. Angew Chem Int Ed Engl (2011) 0.93
Functional interplay between the Yersinia pseudotuberculosis YpsRI and YtbRI quorum sensing systems modulates swimming motility by controlling expression of flhDC and fliA. Mol Microbiol (2008) 0.93
Transgenic tomato plants alter quorum sensing in plant growth-promoting rhizobacteria. Plant Biotechnol J (2008) 0.92
The Pseudomonas aeruginosa global regulator MvaT specifically binds to the ptxS upstream region and enhances ptxS expression. Microbiology (2004) 0.92
Automated alphabet reduction for protein datasets. BMC Bioinformatics (2009) 0.92
The ten grand challenges of synthetic life. Syst Synth Biol (2011) 0.91
Bacteria clustering by polymers induces the expression of quorum-sensing-controlled phenotypes. Nat Chem (2013) 0.91
Structural rearrangement in an RsmA/CsrA ortholog of Pseudomonas aeruginosa creates a dimeric RNA-binding protein, RsmN. Structure (2013) 0.91
RERG (Ras-like, oestrogen-regulated, growth-inhibitor) expression in breast cancer: a marker of ER-positive luminal-like subtype. Breast Cancer Res Treat (2010) 0.91
JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks. Bioinformatics (2013) 0.90
Novel approaches to the treatment of Pseudomonas aeruginosa infections in cystic fibrosis. Eur Respir J (2012) 0.89
N-acyl homoserine lactones are degraded via an amidolytic activity in Comamonas sp. strain D1. Arch Microbiol (2006) 0.89
Prediction of recursive convex hull class assignments for protein residues. Bioinformatics (2008) 0.88
Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features. Bioinformatics (2012) 0.88
Dioxygenase-mediated quenching of quinolone-dependent quorum sensing in Pseudomonas aeruginosa. Chem Biol (2009) 0.88
Characterisation of two quorum sensing systems in the endophytic Serratia plymuthica strain G3: differential control of motility and biofilm formation according to life-style. BMC Microbiol (2011) 0.86
Biofilm development on Caenorhabditis elegans by Yersinia is facilitated by quorum sensing-dependent repression of type III secretion. PLoS Pathog (2011) 0.85
The PA4204 gene encodes a periplasmic gluconolactonase (PpgL) which is important for fitness of Pseudomonas aeruginosa. Microbiology (2008) 0.85
Controlled polymer synthesis--from biomimicry towards synthetic biology. Chem Soc Rev (2009) 0.85
Quorum sensing and the lifestyle of Yersinia. Curr Issues Mol Biol (2006) 0.84
The Pseudomonas aeruginosa quinolone quorum sensing signal alters the multicellular behaviour of Pseudomonas putida KT2440. Res Microbiol (2011) 0.82
Interference with the germination and growth of Ulva zoospores by quorum-sensing molecules from Ulva-associated epiphytic bacteria. Environ Microbiol (2013) 0.81
A novel virulence strategy for Pseudomonas aeruginosa mediated by an autotransporter with arginine-specific aminopeptidase activity. PLoS Pathog (2012) 0.80