| scholarly article | Q13442814 |
| P356 | DOI | 10.1002/9783527645480.CH15 |
| P50 | author | Javier Tamames | Q84336868 |
| Victor de Lorenzo | Q30513692 | ||
| Rafael Silva-Rocha | Q42137373 | ||
| P2860 | cites work | Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles | Q21145898 |
| A protocol for generating a high-quality genome-scale metabolic reconstruction | Q24603373 | ||
| Nature, nurture, or chance: stochastic gene expression and its consequences | Q24610764 | ||
| The incoherent feed-forward loop can generate non-monotonic input functions for genes | Q24644242 | ||
| Diverse two-dimensional input functions control bacterial sugar genes | Q24647458 | ||
| Synthetic biology: new engineering rules for an emerging discipline | Q24672399 | ||
| Structure and function of the feed-forward loop network motif | Q24683513 | ||
| Spatial analysis of expression patterns predicts genetic interactions at the mid-hindbrain boundary | Q27335171 | ||
| Transcriptional regulatory code of a eukaryotic genome | Q27933887 | ||
| Genome-wide location and function of DNA binding proteins | Q28131765 | ||
| Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures. | Q54513931 | ||
| Genetic evidence of separate repressor and activator activities of the XylR regulator of the TOL plasmid, pWW0, of Pseudomonas putida. | Q54569809 | ||
| Exact stochastic simulation of coupled chemical reactions | Q56536017 | ||
| The XylS-dependent Pm promoter is transcribed in vivo by RNA polymerase with sigma32 or sigma38 depending on the growth phase | Q57340438 | ||
| Transcription regulation and environmental adaptation in bacteria | Q57936057 | ||
| Identification of genome-scale metabolic network models using experimentally measured flux profiles | Q28469016 | ||
| Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology | Q28473829 | ||
| The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes | Q28474349 | ||
| Anaerobic catabolism of aromatic compounds: a genetic and genomic view. | Q28755251 | ||
| A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory | Q28756812 | ||
| Current approaches to gene regulatory network modelling | Q28756983 | ||
| Network motifs in the transcriptional regulation network of Escherichia coli | Q29547342 | ||
| Using Bayesian networks to analyze expression data | Q29617295 | ||
| The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation | Q29617813 | ||
| Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data | Q29618517 | ||
| Plasticity of the cis-regulatory input function of a gene | Q33239285 | ||
| Accelerating the reconstruction of genome-scale metabolic networks | Q33246681 | ||
| Toward the automated generation of genome-scale metabolic networks in the SEED. | Q33282913 | ||
| Orthologous transcription factors in bacteria have different functions and regulate different genes | Q33298403 | ||
| It's a noisy business! Genetic regulation at the nanomolar scale | Q33546905 | ||
| On schemes of combinatorial transcription logic | Q33711386 | ||
| Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. | Q33841134 | ||
| Active recruitment of sigma54-RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and alphaCTD. | Q33889426 | ||
| Logic functions of the genomic cis-regulatory code | Q33935921 | ||
| Integration host factor suppresses promiscuous activation of the sigma 54-dependent promoter Pu of Pseudomonas putida | Q34042512 | ||
| Genetic flexibility of regulatory networks | Q34059313 | ||
| Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics | Q34075113 | ||
| Develop reusable and combinable designs for transcriptional logic gates | Q34078874 | ||
| Bacterial adaptation through distributed sensing of metabolic fluxes | Q34102801 | ||
| The Coherent Feedforward Loop Serves as a Sign-sensitive Delay Element in Transcription Networks | Q34275513 | ||
| Modeling and simulation of genetic regulatory systems: a literature review | Q34575847 | ||
| Mining logic gates in prokaryotic transcriptional regulation networks | Q34750229 | ||
| Engineered gene circuits. | Q34997456 | ||
| Concatenated logic gates using four coupled biocatalysts operating in series | Q35126817 | ||
| Integrated regulation in response to aromatic compounds: from signal sensing to attractive behaviour | Q35594592 | ||
| The evolution of genetic regulatory systems in bacteria | Q35670177 | ||
| Systems approach to refining genome annotation | Q35768707 | ||
| Simulating complex intracellular processes using object-oriented computational modelling. | Q35859327 | ||
| Bacterial transcriptional regulators for degradation pathways of aromatic compounds | Q35880920 | ||
| Trends between gene content and genome size in prokaryotic species with larger genomes | Q36854338 | ||
| The regulatory genome and the computer | Q36932798 | ||
| Metabolic diversity in bacterial degradation of aromatic compounds | Q36947080 | ||
| New surveyor tools for charting microbial metabolic maps. | Q37008197 | ||
| Modelling and analysis of gene regulatory networks | Q37271452 | ||
| Enzyme-based logic systems and their applications for novel multi-signal-responsive materials | Q37288602 | ||
| Systems biology approaches to bioremediation | Q37322826 | ||
| Bacteria as computers making computers | Q37328409 | ||
| Designing and encoding models for synthetic biology | Q37443420 | ||
| Computational design tools for synthetic biology | Q37598457 | ||
| Logic-based models for the analysis of cell signaling networks | Q37708260 | ||
| Carbon catabolite repression in Pseudomonas : optimizing metabolic versatility and interactions with the environment. | Q37735901 | ||
| Enzyme-based logic systems for information processing | Q37737110 | ||
| Engineering input/output nodes in prokaryotic regulatory circuits | Q37771431 | ||
| Synthetic gene networks in mammalian cells | Q37778460 | ||
| Noise and robustness in prokaryotic regulatory networks | Q37786338 | ||
| In vivo and in vitro effects of (p)ppGpp on the sigma(54) promoter Pu of the TOL plasmid of Pseudomonas putida. | Q39587573 | ||
| Computational design of digital and memory biological devices. | Q39862211 | ||
| Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators | Q41620651 | ||
| Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0. | Q42482351 | ||
| The IIANtr (PtsN) protein of Pseudomonas putida mediates the C source inhibition of the sigma54-dependent Pu promoter of the TOL plasmid | Q42602104 | ||
| Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways. | Q42637200 | ||
| RNA polymerase holoenzymes can share a single transcription start site for the Pm promoter. Critical nucleotides in the -7 to -18 region are needed to select between RNA polymerase with sigma38 or sigma32. | Q42670941 | ||
| Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida | Q42692935 | ||
| The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid. | Q43018524 | ||
| Linking data to models: data regression | Q43919550 | ||
| Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene | Q44100060 | ||
| Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. | Q45160570 | ||
| Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma54-promoter Pu to the response regulator PprA. | Q46166665 | ||
| Inferring the genetic network of m-xylene metabolism through expression profiling of the xyl genes of Pseudomonas putida mt-2. | Q46680771 | ||
| DESHARKY: automatic design of metabolic pathways for optimal cell growth | Q48322620 | ||
| Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. | Q48605631 | ||
| Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks | Q48647911 | ||
| Implementing an OR–NOT (ORN) logic gate with components of the SOS regulatory network of Escherichia coli | Q48668624 | ||
| The xylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproduction leading to constitutive expression of meta cleavage operon | Q50201339 | ||
| Comparing different ODE modelling approaches for gene regulatory networks. | Q51803503 | ||
| Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach | Q53801017 | ||
| Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida. | Q54369433 | ||
| P921 | main subject | decision making | Q1331926 |
| P304 | page(s) | 279-302 | |
| P577 | publication date | 2012-12-21 | |
| P1476 | title | The Logic of Decision Making in Environmental Bacteria |
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