Rafael Muñoz-Tamayo
- Modélisation Systémique Appliquée aux Ruminants (MoSAR)
Présentation
I am a mathematical modeller of biological systems. I am from Colombia. I have an undergraduate in chemical engineering and a MSc automatic control degree from Universidad Nacional de Colombia. I did my PhD in applied mathematics at Université Paris-Sud (France). I am a researcher at INRAE (France) in the MoSAR team since 2014. My research motivation is to develop a quantitative understanding of biological processes using modelling to combine and structure information across disciplines. My research project aims to enhance understanding of the dynamic interplay between the diet, the rumen microbiota and the ruminant animal via an interdisciplinary approach covering microbiology, chemistry, thermodynamics, animal nutrition, computational biology and mathematical modelling. My ultimate goal is to produce innovative model-based solutions to major challenges facing agriculture such as efficient ruminant production. I have an international path with significant experience in being the fulcrum in interdisciplinary projects within a network of more than 60 international scientists and 41 publications. I am strongly engaged in the open science movement with leading roles at institutional and international levels for enhancing open science practices and thus contributing to make open science the new normal. I am founder of the Open Science initiative Peer Community In ( PCI) Animal Science. For more information about my research please visit my web site.
Domaines de recherche
Compétences
Publications
Publications
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A theoretical optimal experiment design for accurate estimation of key parameters of a dynamic mechanistic model representing the effect of Asparagopsis taxiformis on rumen fermentation and methane production under in vitro continuous conditions11. Workshop on Modelling Nutrient Digestion and Utilization in Farm Animals (Modnut 2025), Agroscope, Sep 2025, Engelberg, Switzerland. pp.456, ⟨10.1016/j.anscip.2025.07.285⟩ |
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Use of a mechanistic model simulating in vitro rumen fermentation to evaluate the effect of nutritional strategies on rumen production and farm indices in intensive dairy farms11. Workshop on Modelling Nutrient Digestion and Utilization in Farm Animals (Modnut 2025), Agroscope, Sep 2025, Engelberg, Switzerland. pp.458-459, ⟨10.1016/j.anscip.2025.07.288⟩ |
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A conceptual model of the synergetic effect of combining the anti-methanogenic macroalgae Asparagopsis taxiformis with the hydrogen acceptor phloroglucinol: a strategy for methane mitigation with fermentation co-benefits for ruminants11. Workshop on Modelling Nutrient Digestion and Utilization in Farm Animals (Modnut 2025), Agroscope, Sep 2025, Engelberg, Switzerland. pp.482-483, ⟨10.1016/j.anscip.2025.07.315⟩ |
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Dynamic sensitivity analysis of a mathematical model describing the effect of the macroalgae Asparagopsis taxiformis on methane production in a rumen in vitro continuous system75. Annual Meeting of the European Federation of Animal Science (EAAP 2024), European Federation of Animal Science (EAAP), Jan 2024, Florence, Italy. pp.329 |
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Degré d'infection : Proposition d'un modèle pour prendre en compte le caractère dynamique de l'état de santé et le lien avec la résilience au travers de l'exemple d'une infection mammaire27. Rencontres autour des recherches sur les ruminants (3R 2024), Institut de l'élevage [IDELE], INRAE, Dec 2024, Paris, France |
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Exploring modelling approaches to address the dynamic nature of animal health75. Annual Meeting of the European Federation of Animal Science (EAAP 2024), European Federation of Animal Science (EAAP), Sep 2024, Florence, Italy. pp.805 |
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Using risk analysis to compare the accuracy of enteric methane emissions models of dairy cattle75. Annual Meeting of the European Federation of Animal Science (EAAP 2024), European Federation of Animal Science (EAAP), Jan 2024, Florence, Italy. pp.329 |
Reducing enteric methane emissions improves energy metabolism in livestock: is the tenet right?International Symposium on Energy and Protein Metabolism and Nutrition (ISEP 2022), EAAP, Sep 2022, Granada, Spain. pp.100830 |
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A dynamic mechanistic model of microbial fermentation and methane production in the cow rumenADSA Annual Meeting, ADSA, Jun 2023, Ottawa, Canada |
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A dynamic in silico model of rumen microbial fermentation and methane production74. Annual meeting of the european federation of animal science (EAAP), INRAE; EAAP, Aug 2023, Lyon, France. pp.325 |
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Peer Community In Animal Science: A free publication model for transparent and open science2022 ASAS-CSAS Annual Meeting, Jun 2022, Oklahoma City, United States. pp.80-81, ⟨10.1093/jas/skac247.158⟩ |
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The power of theoretical and practical identifiability analysis for modeling (micro-) biological processesASAS-CSAS Annual Meeting, Jun 2022, Oklahoma, United States. pp.33 |
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Sensitivity analysis of a mechanistic model of the rumen in-vitro fermentation: Study of the impact of 3 sampling methods on Sobol indices of accuracyModelling Nutrient Digestion and Utilization in Farm Animals (MODNUT), Sep 2022, Alghero, Italy. pp.532-533, ⟨10.1016/j.anscip.2022.07.411⟩ |
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Towards the characterisation of animal robustness by dynamic energy allocation indicators in fattening pigsWCGALP 2022, Jul 2022, Rotterdam, Netherlands |
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The shades of gray in model building and its opportunities for precision livestock farming72. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2021, Davos, Switzerland |
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Genome-scale network reconstruction of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S852021 - 12th International Symposium on Gut Microbiology, INRAE ; Rowett Institute UK, Oct 2021, En ligne, France. pp.1 P; |
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Combining a process-based model of rumen fermentation with methane production data from respiration chambers75. Annual Conference of the British Society of Animal Science (BSAS), Apr 2019, Edinburgh, United Kingdom. ⟨10.1017/S2040470019000013⟩ |
Predictive capabilities of a dynamic mechanistic model of in vitro fermentation by rumen microbiota61. Annual Meeting of the European Associationfor Animal Production (EAAP), 2019, NA, France |
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How complex does a mathematical model need to be to describe the dynamics of methane production in cattle?9. Workshop on Modelling Nutrient Digestion and Utilization in Farm Animals (Modnut), Sep 2019, Ubatuba, Brazil |
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Assessing the predictive capabilities of a dynamic mechanistic model of in vitro rumen fermentation and methane production9. Workshop on Modelling Nutrient Digestion and Utilization in Farm Animals (MODNUT), Sep 2019, Ubatuba, Brazil. pp.320, ⟨10.1017/S2040470019000025⟩ |
Rumen methanogens display species-specific energetic and growth dynamics: a thermodynamic and kinetic based modelling approachJournées d'Animation Scientifique du département PHASE, Institut National de Recherche Agronomique (INRA). UAR Département Physiologie Animale et Systèmes d'Elevage (0558)., Apr 2018, Rennes, France |
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Tous les modèles doivent-ils être identifiables ?Journées Animation Scientifique du département PHASE, Institut National de Recherche Agronomique (INRA). UAR Département Physiologie Animale et Systèmes d'Elevage (0558)., Apr 2018, Rennes, France. pp.1 |
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Multivariate and network analysis identified microbial biomarkers linked to methane emission69. Annual Meeting of the European Federation of Animal Science, European Federation of Animal Science, Aug 2018, Dubrovnik, Croatia |
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Towards a quantitative characterization of robustness of piglets at weaning period: An animal growth modelling approachJournées d'Animation Scientifique du département PHASE, Institut National de Recherche Agronomique (INRA). UAR Département Physiologie Animale et Systèmes d'Elevage (0558)., Apr 2018, Rennes, France |
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Identification of microbial taxa linked to methane emission in Holstein and Charolais cattle by an integrative approachGut Microbiology: No longer the forgotten organ - 11. INRA-Rowett Symposium, Jun 2018, Aberdeen, United Kingdom |
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Metabolic modeling of microalgae growth and lipids production during day/night cycles and nitrogen starvationMetabolic Pathway Analysis 2015, Jun 2015, Braga, Portugal |
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A new approach to unravel metabolic regulations. Application to microalgae growth and lipid production under day/night cycles and nitrogen starvationBioSynSys 2015 : 1er colloque du GDR "Biologie de Synthèse et des Systèmes", Sep 2015, Paris, France |
Model-based optimization of lipid production by the oleaginous yeast Yarrowia lipolytica10. European Symposium on Biochemical Engineering Sciences, Sep 2014, Lille, France |
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Optimization of lipid production by oleaginous yeast in continuous culture19. World Congress of the International Federation of Automatic Control, Aug 2014, Cape Town, South Africa |
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Design of Optimal Experiments for Parameter Estimation of Microalgae Growth ModelsInternational Symposium on Computer Applications to Biotechnology (CAB 2013), Dec 2013, Mumbai, India |
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A new framework for metabolic modeling under non-balanced growth. Application to carbon metabolism of unicellular microalgaeCAB 2013 - International on Computer Applications to Biotechnology, Dec 2013, Mumbai, India |
A new framework for metabolic modelling under non-balanced growth. Application to photoautotrophic microalgae in day/night cycle.Metabolic Pathway Analysis 2013, Sep 2013, Oxford, United Kingdom |
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Adaptive control for optimizing microalgae productionComputer Application in Biotechnology (CAB2013), Dec 2013, Mumbai, India |
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Driving Species Competition in a Light-limited Chemostat9th IFAC Symposium on Nonlinear Control Systems (NOLCOS), Sep 2013, Toulouse, France |
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Driving microalgal production in raceway systems to near optimal productivities.European Control Conference (ECC13), Jul 2013, Zurich, Switzerland |
A closed-loop controller for optimizing nitrogen removal in a microalgal outdoor pond11. IWA Conference on Instrumentation Control and Automation, Sep 2013, Narbonne, France |
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IDEAS: a parameter identification toolbox with symbolic analysis of uncertainty and its application to biological modelling15. IFAC Symposium on System Identication (SYSID 2009), Jul 2009, Saint Malo, France. ⟨10.3182/20090706-3-FR-2004.00211⟩ |
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Modelling and identification of in vitro homoacetogenesis by human-colon bacteria16. Mediterranean Conference on Control and Automation, 2008, Ajaccio, France |
Control of a bioreactor using feedback linearization2007 Mediterranean Conference on Control & Automation (MED 2007), Jun 2007, Athènes, Greece. ⟨10.1109/MED.2007.4433763⟩ |
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Human colon: a complex bioreactor. Conceptual modelling for the anaerobic digestion of the functional trophic chain11. World Congress on Anaerobic Digestion, Sep 2007, Brisbane, Australia. 6 p |
Breve elogio a la lentitud en cienciaCiencia y Humanismo 50 años Revista Aleph (1996-2016), Carlos Enrique Ruiz, 594 p., 2016, 978-958-8730-75-2 |
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Initier les primaires aux sciences animalesAutre publication scientifique hal-05386022v1 |
IDEAS2009 |
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Modélisation mathématique de la dégradation des hydrates de carbone dans le côlon humainMathématiques [math]. Université Paris Sud - Paris 11, 2010. Français. ⟨NNT : ⟩ |
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A modelling odyssey in the tree of lifeModeling and Simulation. Université Paris Sud (Paris 11), 2019 |