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"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling approaches using published data sets and data emerging from our own work. We construct increasingly elaborate models of the system at different levels of detail, which are used to generate new hypotheses and influence further experimental design.
Programme: SysMO
FAIRDOMHub ID: https://seek.sysmo-db.org/projects/3
Public web page: http://www.sysmo.net/index.php?index=55
Organisms: Escherichia coli, Escherichia coli k-12
FAIRDOM PALs: Sebastian Henkel, Afsaneh Maleki-Dizaji, Maikel Verouden, David Knies
Related items
- People (29)
- Institutions (5)
- Investigations (7)
- Studies (7)
- Assays (23)
- Strains (23)
- Data files (30+13)
- Models (9+4)
- SOPs (15+2)
- Publications (17)
- Presentations (3+1)
Institutions: University of Amsterdam
Disciplines: Not specified
Roles: Postdoc
Expertise: HPLC, Escherichia coli, Molecular Biology, Biochemistry, Microbiology
Tools: Chromatography, Fermentation, Molecular Biology, Biochemistry
Martijn Bekker (1979) was born in Amstelveen (The Netherlands). He started his studies in biology in 1997 at the University of Amsterdam, and graduated in 2003 with specializations in molecular microbiology and in immunology. The internships during his undergraduate studies were carried out in the labs of Prof. dr. B. Oudega (VU, Amsterdam, The Netherlands) and Prof. dr. F. Heffron (OHSU, Portland, Oregon, USA).
He continued with his graduate studies in 2003 in the Laboratory for Molecular Microbial
...
Projects: SUMO
Institutions: University of Sheffield
Disciplines: Not specified
Roles: Postdoc
Expertise: Microarray Data Analysis, Agent-based modelling, Bioinformatics
Tools: Bioconductor Packages in R, Taverna, Java, Copasi
I am a research associate in the department of computer science at the University of Sheffield since January 2008. My research is primarily involved with using agent-based modelling techniques and mathematical modelling techniques to model Escherichia coli K-12 Respiratory Adaptation. My research interests also include, development of workflows to analyze Microarray Data.
Projects: SUMO
Institutions: University of Amsterdam
Disciplines: Not specified
Roles: Not specified
Expertise: stress responses, Escherichia coli, Bacillus subtilis, Transcriptomics
Tools: Chemostats, HPLC, phage transduction
Projects: SUMO
Institutions: University of Stuttgart
Disciplines: Modeller
Roles: Postdoc
Expertise: reduced-order modeling, Mathemical Modeling (in particular: Thermodynamic-Kinetic Modeling), model reduction
Tools: trac (wiki for data management), R, Matlab, Mathematica
I'm interested in the application and development of methods of systems theory in biology (systems biology). In particulary I work on the following topics:
Thermodynamic constraints on biochemical network; Model reduction; Modeling and Analysis of metabolic regulation.
Projects: SUMO
Institutions: Max Planck Institute for Dynamics of Complex Technical Systems
Disciplines: Not specified
Roles: Not specified
Expertise: Regulatory Networks, Molecular Biology, Genetics, Microbiology
I am interested in the coupling of global regulation and metabolism in E. coli. To analyze this I construct and analyze defined mutant strains. These strains are characterized in bioreactor experiments of different types (batch, conti, pulse ...) and measurements on the level of metabolites, mRNA, and protein are applied. For all projects there are cooperation partners that use the data in modeling approaches either from the MPI Magdeburg or from the SUMO consortium.
Projects: SUMO
Institutions: University of Stuttgart
Disciplines: Modeller
Roles: Not specified
Expertise: Systems Biology, parameter estimation, Data Management, Mathematical modelling
Tools: Matlab, Mathematica, SBML, ODE
Former:
PhD student as research associate at the Institute for System Dynamics (ISYS), Universität Stuttgart, Germany. Engineering background→modelling, identification and analyses. Detailed kinetic modelling, identification and analysis of the TCA cycle (tricarboxylic acid cycle, citric acid cycle) and the ETC (electron transport chains, respiratory chains) of Escherichia coli. One of the SysMO-DB pals for SUMO.
Now:
Industrial affiliation
Projects: SUMO
Institutions: University of Edinburgh
Disciplines: Not specified
Roles: Not specified
Expertise: Not specified
Tools: Not specified
Cultures grown under standard SUMO conditions were analyzed with respect to heterogeneity in gene expression. To this end GFP reporter strains were constructed and GFP expression at single cell level was monitored by flow cytometry.
Snapshots: No snapshots
Studies: No Studies
Assays: No Assays
The electron transport chain of E. coli is branched. Different NAD Dehydrogenases and terminal oxidases are known to be expressed at different oxygen availabilities. By deleting multiple genes mutant strains were constructed that posses a linear electron transport chain. These mutants were investigated in continous bioreactor experiments with limiting glucose and varying oxygen supply.
Snapshots: No snapshots
Studies: Analysis of Escherichia coli strains with linear respiratory chain
Assays: Determination of by-product formation and glucose uptake of mutants with..., Deternination of ArcA phosphroylation level in mutants with linear ETC a..., Gene expression analysis of mutants with linear electron transport chain...
A further investigation of the variation of FNR number in E.coli Cyo/Cyd mutants is carrying out at different oxygen supply levels. The agent-based FNR and ArcBA model is going to be used for this prediction. The number of Cyo or Cyd and other unrelated agents would be set as ‘0’ at the initial XML file with which the model starts. According to the restrictions of supercomputer ‘Iceberg’ (serviced provided by the University of Sheffield), certain parameters, such as memory per node, would be
...
Snapshots: No snapshots
Studies: No Studies
Assays: No Assays
In Escherichia coli several systems are known to transport glucose into the cytoplasm. A series of mutant strains were constructed, which lack one or more of these uptake systems. These were analyzed in aerobic and anaerobic batch cultures, as well as glucose limited continuous cultivations.
Snapshots: No snapshots
Studies: Characterization of mutant strains with defects in sugar transport systems
Assays: Aerobic and anaerobic characterization of MG1655 and mutant strains with..., Aerobic and anaerobic characterization of MG1655 and mutant strains with..., Characterization of MG1655 and mutant strains under conditions of glucos..., TFinfer2
Changing the oxygen availability leads to an adaptation of Escherichia coli at different biological levels. After pertubation of oxygen in chemostat experiments the microorganism(s) will come back to another steady state. This investigation deals with these stationary responses of Escherichia coli within the aerobiosis scale. The change for different biological variables, in different areas of the organism like the electron transport chain, the TCA cycle or globally is investigated by wildtype
...
Snapshots: No snapshots
Studies: Basic regulatory principles of Escherichia coli’s electron transport cha..., Determination of the impact of specific enzyme reactions and regulatory ..., Quantitative analysis of catabolic carbon and electron fluxes in E. coli..., The Escherichia coli steady state response to oxygen: from molecular int...
Assays: Analysis of by-product formation rates in MG1655, Analysis of gene expression rates at different aerobiosis levels via RT-PCR, ArcA phosphorylation at different aerobiosis levels (steady states), Characterization of E. coli MG1655 and ∆sdhC and ∆frdA isogenic mutant s..., Determination of intracellular metabolite concentrations, Determination of intracellular redox state by means of NAD/NADH ratio, Determination of intracellular redox state by means of ubiquinones (oxd/..., FNR activity at different aerobiosis levels (steady state), Kinetic modelling of Escherichia coli's electron transport chain, Kinetic modelling of Escherichia coli's electron transport chain coupled..., Literature Data from Alexeeva et al., J. Bacteriol., 2000, 2002, 2003, Measurement of cytochrome numbers, Physiological measurements from Sheffield chemostat, Steady State Oxygen Response of E. coli WT and two Electron Transport Ch..., Transcriptional profiling of steady states at different aerobiosis levels
Changing the oxygen availability leads to an adaptation of Escherichia coli at different biological levels. After pertubation of oxygen in chemostat experiments there are very quick responses. This investigation deals with this dynamical behaviour (transitions) of Escherichia coli within the aerobiosis scale. The change for different biological variables, in different areas of the organism like the electron transport chain, the TCA cycle or globally is investigated by wildtype and mutants experiments
...
Snapshots: No snapshots
A set of isogenic mutant strains was constructed which lack NADH Dehydrogenase I as well as two terminal oxidases, resulting in strains with linear respiratory chain. The different strains hence differ in the terminal oxidase and express either cytochrome bo, cytochrome bdI or cytochrome bdII.
The different strains were cultivated in glucose-limited chemostats with defined low levels of oxygen supply. Biomass and by-product formation, gene expression and the phosphorylation state of the important
...
Person responsible: Katja Bettenbrock
Snapshots: No snapshots
Investigation: Analysis of Escherichia coli with linear electr...
Assays: Determination of by-product formation and glucose uptake of mutants with..., Deternination of ArcA phosphroylation level in mutants with linear ETC a..., Gene expression analysis of mutants with linear electron transport chain...
Mutant strains in which one or more of the potential glucose uptake systems was deleted have been analyzed in aerobic and anaerobic batch cultures, as well as aerobic chemostat cultures.
Person responsible: Sonja Steinsiek
Snapshots: No snapshots
Investigation: Analysis of the glucose transport in Escherichi...
Assays: Aerobic and anaerobic characterization of MG1655 and mutant strains with..., Aerobic and anaerobic characterization of MG1655 and mutant strains with..., Characterization of MG1655 and mutant strains under conditions of glucos..., TFinfer2
Person responsible: Michael Ederer
Snapshots: No snapshots
Investigation: Steady state studies for different oxygen avail...
Assays: No Assays
Person responsible: Michael Ederer
Snapshots: No snapshots
Investigation: Steady state studies for different oxygen avail...
Assays: ArcA phosphorylation at different aerobiosis levels (steady states), Determination of intracellular redox state by means of NAD/NADH ratio, Determination of intracellular redox state by means of ubiquinones (oxd/..., FNR activity at different aerobiosis levels (steady state), Literature Data from Alexeeva et al., J. Bacteriol., 2000, 2002, 2003, Measurement of cytochrome numbers, Physiological measurements from Sheffield chemostat, Steady State Oxygen Response of E. coli WT and two Electron Transport Ch..., Transcriptional profiling of steady states at different aerobiosis levels
Goals:
1. Understanding the regulatory principles of Escherichia coli’s electron transport chain (ETC) for varying oxygen conditions in glucose-limited continuous cultures (especially regulatory loops via the transcription factors FNR and ArcA).
2. Explaining the observed phenomena in the measurement data.
3. Predicting unmeasured variables especially of the gene expression regulatory loops.
Means:
1. Experiments (chemostat experiments within the aerobiosis scale).
2. Kinetic modelling (especially
...
Person responsible: Sebastian Henkel
Snapshots: No snapshots
Mutant strains which carry deletions of important metabolic enzymes, as well as mutant strains with altered regulation, need to adapt by changing fluxes or gene expression to compensate with the absence/differed concentration of these key enzymes. This may give new insights in the regulation of these pathways/enzymes.
Person responsible: Sonja Steinsiek
Snapshots: No snapshots
Investigation: Steady state studies for different oxygen avail...
Assays: Analysis of by-product formation rates in MG1655, Analysis of gene expression rates at different aerobiosis levels via RT-PCR, Characterization of E. coli MG1655 and ∆sdhC and ∆frdA isogenic mutant s..., Determination of intracellular metabolite concentrations
Mutants with a linear respiratory chain consisting of NADH Dehydrogenase II and one of the terminal oxidases cytochrom bo, cytochrome bd I or cytochrome bd II were growth in chemostats with defined oxygen supply. The amounts of biomass formed and of acetate and formate produced were determined.
Contributor: Katja Bettenbrock
Assay type: Experimental Assay Type
Technology type: Chemostat Measurement
Snapshots: No snapshots
Investigation: Analysis of Escherichia coli with linear electr...
Study: Analysis of Escherichia coli strains with linea...
Organisms: No organisms
SOPs: Measurement of extracellular metabolites, SUMO chemostat conditions
Data files: ETCmutants_metabolites
Mutant strains with linear electron transport chain were grown in chemostat cultures at different defined aerobiosis levels. Expression of selected genes was determined by Real Time RT-PCR
Contributor: Katja Bettenbrock
Assay type: Experimental Assay Type
Technology type: qRT-PCR
Snapshots: No snapshots
Investigation: Analysis of Escherichia coli with linear electr...
Study: Analysis of Escherichia coli strains with linea...
Organisms: No organisms
SOPs: Evans Medium, SUMO chemostat conditions, SUMO mRNA isolation Epicentre
Data files: ETCmutants_mRNA, Gene expression levels in mutants with linear r...
Mutants with linear respiratory chains were grown under SUMO chemostat conditions at different defined aerobiosis levels. The ArcA phoshorylation state as determined.
Contributor: Katja Bettenbrock
Assay type: Experimental Assay Type
Technology type: Gel Electrophoresis
Snapshots: No snapshots
Investigation: Analysis of Escherichia coli with linear electr...
Study: Analysis of Escherichia coli strains with linea...
Organisms: No organisms
SOPs: No SOPs
Data files: ETC_mutants_ArcA
Contributor: Michael Ederer
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Steady state studies for different oxygen avail...
Study: The Escherichia coli steady state response to o...
Organisms: No organisms
SOPs: No SOPs
Data files: Numeric Data from Alexeeva et al., J. Bacteriol...
ArcA phosphorylation in chemostat cultures grown at different aerobiosis levels was quantitated by Phos-tag SDS-PAGE gel analysis and subsequent immunodetection of ArcA.
Contributor: Matthew Rolfe
Assay type: Experimental Assay Type
Technology type: SDS-PAGE
Snapshots: No snapshots
Investigation: Steady state studies for different oxygen avail...
Study: The Escherichia coli steady state response to o...
Organisms: Escherichia coli : MG1655 (del LAM;del rph-1 / pyrimidine starvation ) (chemostat)
SOPs: Determination of protein phosphorylation levels..., Evans Medium, SUMO chemostat conditions
Data files: No Data files
E. coli MG1655 and ∆sdhC and ∆frdA isogenic mutant strains were characterized in batch growth curves aerobic and anaerobically. Optical density, glucose consumption and by-product accumulation were measured during growth.
Contributor: Sonja Steinsiek
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Steady state studies for different oxygen avail...
Study: Determination of the impact of specific enzyme ...
Organisms: Escherichia coli : K-12/MG1655 (wild-type / wild-type) (batch)
SOPs: Evans Medium, Measurement of extracellular metabolites
Data files: 2 hidden items
Glucose transporter mutants were analyzed under aerobic and aerobic conditions in batch cultures with glucose as substrate. Acetate formation rates and glucose consumption rates were measured, as well as extracellular cAMP concentrations.
Contributor: Sonja Steinsiek
Assay type: Extracellular Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Analysis of the glucose transport in Escherichi...
Study: Characterization of mutant strains with defects...
Organisms: Escherichia coli : MG1655 (del LAM;del rph-1 / pyrimidine starvation ) (batch)
SOPs: Measurement of extracellular metabolites and 1 hidden item
Data files: Growth, by-product formation and glucose consum..., Growth, yield and cAMP excretion under anaerobi...
Contributor: Katja Bettenbrock
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Escherichia coli k-12
Genotypes: del ptsG;del manXYZ
Phenotypes: wild-type
Comment: Not specified
Contributor: Katja Bettenbrock
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Escherichia coli k-12
Genotypes: del ptsG;del malEFG
Phenotypes: wild-type
Comment: Not specified
Contributor: Katja Bettenbrock
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Escherichia coli k-12
Genotypes: del ptsG;del mglBAC;del galP
Phenotypes: wild-type
Comment: Not specified
Contributor: Katja Bettenbrock
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Escherichia coli k-12
Genotypes: del ptsG;del mglBAC
Phenotypes: wild-type
Comment: Not specified
Contributor: Katja Bettenbrock
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Escherichia coli k-12
Genotypes: del ptsG
Phenotypes: slow growth with glucose
Comment: Not specified
Contributor: Katja Bettenbrock
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Escherichia coli k-12
Genotypes: del manXYZ
Phenotypes: wild-type
Comment: Not specified
Contributor: Katja Bettenbrock
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Escherichia coli k-12
Genotypes: del malEFG
Phenotypes: wild-type
Comment: Not specified
The file contains simulated data of the electron transport chain model (EcoliETC1) for varying parameter values, i.e. a local sensitivity analysis.
Creator: Sebastian Henkel
Contributor: JERM
This data file shows results from the different chemostat experiments.Gene expression rates are presented.
Creators: Katja Bettenbrock, Sonja Steinsiek
Contributor: Katja Bettenbrock
Mutants with defects in glucose transport systems were analyzed in a bioreactor and the transcription of certain uptake systems analyzed. Transcription profiles between batch and chemostat conditions were compared
Creator: Sonja Steinsiek
Contributor: Sonja Steinsiek
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
by-product formation rates and glucose uptake rates of mutants with linear electron transport chain at different aerobiosis levels
Creator: Katja Bettenbrock
Contributor: Katja Bettenbrock
The ArcA phosphorylation state was determined for mutants with linear respiratory chain at defined aerobiosis levels.
Creator: Katja Bettenbrock
Contributor: Katja Bettenbrock
Gene expression levels in mutants with linear ETC were determined by RealTime RT-PCR
Creator: Katja Bettenbrock
Contributor: Katja Bettenbrock
The model describes the catabolism of Escherichia coli and its regulation. The metabolic reactions are modeled by the thermokinetic model formalism. The model is simplified by assuming rapid equilibrium of many reactions. Regulation is modeled by phenomenological laws describing the activation or repression of enzymes and genes in dependence of metabolic signals. The model is intended to describe the behavior of E. coli in a chemostat culture in depedence on the oxygen supply.
The model is described
...
Creators: Michael Ederer, David Knies
Contributor: Michael Ederer
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Escherichia coli
Investigations: Steady state studies for different oxygen avail...
Studies: The Escherichia coli steady state response to o...
Modelling analyses: Steady State Oxygen Response of E. coli WT and ...
This ordinary-differential equation model is a spatially lumped model showing the behaviour of oxygen in the three compartments medium, membrane and cytoplasm and its impact on FNR inactivation, hereby showing the effects of different oxygen concentrations, diffusion coefficients and reaction rates. The model was created with the Matlab SimBiology toolbox.
Creator: Samantha Nolan
Contributor: David Knies
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Escherichia coli
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
This partial-differential equations model focuses on the oxygen gradients in consideration of the three-dimensional cell and environment.
Creator: Samantha Nolan
Contributor: David Knies
Model type: Partial differential equations (PDE)
Model format: Mathematica
Environment: Not specified
Organism: Escherichia coli
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Code for joint probabilistic inference of transcription factor behaviour and gene-transcription factor as well as metabolite-transcription factor interaction based on genome and metabolite data.
Creators: Botond Cseke, Guido Sanguinetti
Contributor: Botond Cseke
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Escherichia coli
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
The model presents the response of E.coli to different levels of oxygen supply, in which the oxidases, Cyo and Cyd, and their regulators, FNR and ArcBA systems, are included. The initial file 0.xml and supporting documents are for the model with FNR only. Four 0.xml files provided are at AAU level 31, 85, 115 and 217 respectively. The ArcBA system can be activated by revising the number of agents, ArcB, ArcA dimer, ArcA monomer, ArcA tetramer and ArcA octamer, in the initial file. The model needs
...
Creator: Hao Bai
Contributor: Hao Bai
Model type: Agent based modelling
Model format: Not specified
Environment: FLAME
Organism: Escherichia coli
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
Bayesian model for inference of the activity of transcription factors from targets' mRNA levels. A standalone C sharp package (runs on linux and mac under MONO).
Creator: Guido Sanguinetti
Contributor: Guido Sanguinetti
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Not specified
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
The model describes the electron transport chain (ETC) of Escherichia coli by ordinary differential equations. Also a simplified growth model based on an abstract reducing potential describing the balance of electron donor (glucose) and electron acceptors is coupled to the ETC. The model should reproduce and predict the regulation of the described system for different oxygen availability within the aerobiosis scale (glucose limited continuous culture<=>chemostat). Therefore oxygen is changed
...
Creator: Sebastian Henkel
Contributor: Sebastian Henkel
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Escherichia coli
Investigations: Steady state studies for different oxygen avail...
Studies: Basic regulatory principles of Escherichia coli...
Modelling analyses: Kinetic modelling of Escherichia coli's electro...
This assay uses a dual-wavelength spectrophotometer to quantify cytochromes present in the E. coli respiratory chain.
Creators: Alison Graham, Robert Poole, Jeff Green
Contributor: Alison Graham
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This is a well-established, classical genetic method of constructing chromosomal monolysogenic fusions to a promoterless lacZ gene.
Creators: Alison Graham, Jeff Green, Robert Poole
Contributor: Alison Graham
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The phosphorylation level of a particular protein can be determined using a procedure based upon western immunoblotting, with Phos-tag™ reagent present in the SDS-PAGE gel. The Phos-tag™ reagent, supplied in the form of Phos-tag™ acrylamide (Wako Pure Chemical Industries, AAL-107), causes proteins to be resolved both on the basis of size and phosphorylation state. This means that phosphorylated and de-phosphorylated forms of the same protein can be distinguished.
Creator: Matthew Rolfe
Contributor: Matthew Rolfe
The Gene-doctoring method of lambda-red deletion (Lee et al., 2009) was modified slightly to create chromosomal mutations of fnr.
Creator: Matthew Rolfe
Contributor: Matthew Rolfe
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This method describes how one can quench metabolism of Escherichia coli and extract metabolites from many kinds of metabolite classes like: nucleotides, sugar-phosphates, organic acids ....
Creator: Stefan Stagge
Contributor: Stefan Stagge
This protocol describes the transcriptional profiling of E. coli cultures using microarrays. The protocol utilises RNA isolated as described in another SOP (SUMO RNA isolation from E. coli) and with hybridisation to Ocimum Ocichip E. coli K-12 microarrays.
Creator: Matthew Rolfe
Contributor: Matthew Rolfe
Investigations: Dynamical studies for different oxygen availabi..., Steady state studies for different oxygen avail...
Studies: The Escherichia coli dynamical response to oxyg..., The Escherichia coli steady state response to o...
Assays: Transcriptional profiling of E. coli during ana..., Transcriptional profiling of steady states at d...
This SOP describes the preparation of E. coli RNA
Creator: Matthew Rolfe
Contributor: Matthew Rolfe
Investigations: Dynamical studies for different oxygen availabi..., Steady state studies for different oxygen avail...
Studies: The Escherichia coli dynamical response to oxyg..., The Escherichia coli steady state response to o...
Assays: Transcriptional profiling of E. coli during ana..., Transcriptional profiling of steady states at d...
Abstract (Expand)
Authors: Hao Bai, Matthew Rolfe, Wenjing Jia, Robert Poole, Jeff Green, Michael Holcombe, Coakley S.
Date Published: 24th Apr 2014
Journal: PLoS Comput Biol
PubMed ID: 24763195
Citation:
Abstract (Expand)
Authors: None
Date Published: 27th Mar 2014
Journal: Front Microbiol
PubMed ID: 24723921
Citation:
Abstract (Expand)
Authors: None
Date Published: 30th Sep 2014
Journal: PLoS One
PubMed ID: 25268772
Citation:
Abstract (Expand)
Authors: Katja Bettenbrock, Hao Bai, Michael Ederer, Jeff Green, Klaas Hellingwerf, Michael Holcombe, Matthew Rolfe, Guido Sanguinetti, Oliver Sawodny, Poonam Sharma, Sonja Steinsiek, Robert Poole, Kunz S.
Date Published: 7th May 2014
Journal: Adv Microb Physiol
PubMed ID: 24797925
Citation:
Abstract (Expand)
Author: Sharma P.,Stagge S.,Bekker M.,Bettenbrock K.,Hellingwerf K. J.
Date Published: 7th Oct 2013
Journal: PLoS One
PubMed ID: 24116043
Citation:
Abstract (Expand)
Authors: None
Date Published: 27th Jan 2014
Journal: PLoS One
PubMed ID: 24475268
Citation:
Abstract (Expand)
Authors: Poonam Sharma, Joost Teixeira De Mattos, Martijn Bekker, Hellingwerf Klaas J.
Date Published: 1st Sep 2012
Journal: Not specified
DOI: 10.1111/j.1742-4658.2012.08608.x
Citation:
Presentation by Michael Ederer and Klaas Hellingwerf at the SysMO Conference 2013 (Feb 2013, Berlin)
Creator: Michael Ederer
Contributor: Michael Ederer
Presentation by Robert Pool at the SysMO Conference (Feb 2013 in Berlin)
Creator: Robert Poole
Contributor: Michael Ederer
Summary
1.1 modifying TFinfer to model the TFs using ON/OFF switches (fast response model),
1.2 trying to infer metabolites effect using a joint gene-tf-metabolite model,
2 analysing aerbiosis data using a similar model,
3 clustering genes for extending the EC network to obtain better fits to the data (feedback loop).
Creator: Botond Cseke
Contributor: Botond Cseke