0000000000300220

AUTHOR

Francisco Llaneras

showing 3 related works from this author

MCR-ALS on metabolic networks: Obtaining more meaningful pathways

2015

[EN] With the aim of understanding the flux distributions across a metabolic network, i.e. within living cells, Principal Component Analysis (PCA) has been proposed to obtain a set of orthogonal components (pathways) capturing most of the variance in the flux data. The problems with this method are (i) that no additional information can be included in the model, and (ii) that orthogonality imposes a hard constraint, not always reasonably. To overcome these drawbacks, here we propose to use a more flexible approach such as Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) to obtain this set of biological pathways through the network. By using this method, different constraint…

Mathematical optimizationProcess Chemistry and TechnologyESTADISTICA E INVESTIGACION OPERATIVAMetabolic networkMetabolic networkLeast SquaresVariance (accounting)Least squaresINGENIERIA DE SISTEMAS Y AUTOMATICAComputer Science ApplicationsAnalytical ChemistrySet (abstract data type)Constraint (information theory)OrthogonalityPichia pastorisPrincipal component analysisA priori and a posterioriMultivariate Curve Resolution-AlternatingGrey modellingSpectroscopySoftwareMathematics
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Metabolic flux understanding of Pichia pastoris grown on heterogenous culture media

2014

[EN] Within the emergent field of Systems Biology, mathematical models obtained from physical chemical laws (the so-called first principles-based models) of microbial systems are employed to discern the principles that govern cellular behaviour and achieve a predictive understanding of cellular functions. The reliance on this biochemical knowledge has the drawback that some of the assumptions (specific kinetics of the reaction system, unknown dynamics and values of the model parameters) may not be valid for all the metabolic possible states of the network. In this uncertainty context, the combined use of fundamental knowledge and data measured in the fermentation that describe the behaviour…

Principal Component AnalysisbiologyMathematical modelManufacturing processComputer scienceProcess Chemistry and TechnologySystems biologyMonte Carlo samplingESTADISTICA E INVESTIGACION OPERATIVACellular functionsMetabolic networkMetabolic networkMissing-data methods for Exploratory Data AnalysisContext (language use)biology.organism_classificationINGENIERIA DE SISTEMAS Y AUTOMATICAComputer Science ApplicationsAnalytical ChemistryPichia pastorisEconometricsBiochemical engineeringPossibilistic consistency analysisFlux (metabolism)SpectroscopySoftware
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Estimation of recombinant protein production in Pichia pastoris base don a constraint-based model

2012

[EN] A previously validated constraint based model and possibilistic MFA have been used to design a simple estimator of protein production rate in Pichia pastoris cultures. A structured model of the yeast P. pastoris metabolism is used to predict the balance of key energetic equivalents such as ATP from available measurements, mainly substrate consumption, gases exchange rates and biomass specific growth. It has been shown that ATP flux can be related to biomass growth and protein productivity specific rates by linear regression. Cross-validation has been applied for robust parameter fitting on the basis of chemostat, steady-state experimental conditions. In this way, protein estimation can…

Constraint-based modelbiologyUncertaintyfood and beveragesEstimatorBiomassProtein productivity predictionChemostatPossibilistic metabolic flux analysisBioinformaticsbiology.organism_classificationIndustrial and Manufacturing EngineeringYeastINGENIERIA DE SISTEMAS Y AUTOMATICAComputer Science ApplicationsPichia pastorisConstraint (information theory)Pichia pastorisControl and Systems EngineeringModeling and SimulationLinear regressionBiological systemFlux (metabolism)Mathematics
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