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60

Rafael Muñoz-Tamayo


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 Inra (FR) on modelling fermentation by human gut microbiota. Further, I participated in various research projects in the domains of biotechnology, agriculture and life sciences at Inra, Wageningen University (NL) and Inria (FR). My research motivation is to develop a quantitative understanding of complex biological processes using modelling to combine and structure knowledge across disciplines. In 2014, I was appointed as researcher at the MoSAR team (Inra).  My current research project aims to enhance understanding of the dynamic interplay between the diet, the rumen microbiota and the ruminant animal via and interdisciplinary approach covering microbiology, chemistry, thermodynamics, animal science and mathematical modelling.  For more information about my research please visit my web site


Journal articles20 documents

  • Rafael Munoz Tamayo, J. Ramírez Agudelo, R. Dewhurst, G. Miller, T. Vernon, et al.. A parsimonious software sensor for estimating the individual dynamic pattern of methane emissions from cattle. animal, Published by Elsevier (since 2021) / Cambridge University Press (until 2020), 2019, 13 (06), pp.1180-1187. ⟨10.1017/S1751731118002550⟩. ⟨hal-02369429⟩
  • Rafael Munoz Tamayo, Milka Popova, Maxence Tillier, Diego Morgavi, Jean-Pierre Morel, et al.. Hydrogenotrophic methanogens of the mammalian gut: Functionally similar, thermodynamically different—A modelling approach. PLoS ONE, Public Library of Science, 2019, 14 (12), pp.e0226243. ⟨10.1371/journal.pone.0226243⟩. ⟨hal-02473686⟩
  • Manuel Revilla Sanchez, Nicolas Friggens, Laurent Broudiscou, Gaetan Lemonnier, Fany Blanc, et al.. Towards the quantitative characterisation of piglets’ robustness to weaning: a modelling approach. animal, Published by Elsevier (since 2021) / Cambridge University Press (until 2020), 2019, First view (11), pp.1-11. ⟨10.1017/S1751731119000843⟩. ⟨hal-02192515⟩
  • Laura Lema-Perez, Rafael Munoz Tamayo, Jose Garcia-Tirado, Hernan Alvarez. On parameter interpretability of phenomenological-based semiphysical models in biology. Informatics in Medicine Unlocked, 2019, 15, pp.100158. ⟨10.1016/j.imu.2019.02.002⟩. ⟨hal-02192507⟩
  • Rafael Munoz Tamayo, Laurence Puillet, J. Daniel, Daniel Sauvant, O. Martin, et al.. Review: to be or not to be an identifiable model. Is this a relevant question in animal science modelling?. animal, Published by Elsevier (since 2021) / Cambridge University Press (until 2020), 2018, 12 (04), pp.701 - 712. ⟨10.1017/S1751731117002774⟩. ⟨hal-01526307⟩
  • Carlos Robles Rodriguez, Rafael Munoz Tamayo, Carine Bideaux, Nathalie Gorret, Stéphane Guillouet, et al.. Modeling and optimization of lipid accumulation by Yarrowia lipolytica from glucose under nitrogen depletion conditions. Biotechnology and Bioengineering, Wiley, 2018, 115 (5), pp.1-15. ⟨10.1002/bit.26537⟩. ⟨hal-01713779⟩
  • Sharon A. Huws, Christopher J. Creevey, Linda B. Oyama, Itzhak Mizrahi, Stuart E. Denman, et al.. Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present, and future. Frontiers in Microbiology, Frontiers Media, 2018, 9, ⟨10.3389/fmicb.2018.02161⟩. ⟨hal-01890696⟩
  • Rafael Munoz Tamayo, Sylvie Giger-Reverdin, Daniel Sauvant. Mechanistic modelling of in vitro fermentation and methane production by rumen microbiota. Animal Feed Science and Technology, Elsevier Masson, 2016, 220, pp.1-21. ⟨10.1016/j.anifeedsci.2016.07.005⟩. ⟨hal-01349548⟩
  • Caroline Baroukh, Rafael Munoz Tamayo, Olivier Bernard, Jean-Philippe Steyer. Reply to the Comment on “Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production” by Baroukh et al. [Curr. Opin. Biotechnol. 2015, 33:198–205]. Current Opinion in Biotechnology, Elsevier, 2016, 38, pp.200 - 202. ⟨10.1016/j.copbio.2016.02.018⟩. ⟨hal-01410975⟩
  • Francis Mairet, Rafael Munoz Tamayo, Olivier Bernard. Adaptive control of light attenuation for optimizing microalgae production. Journal of Process Control, Elsevier, 2015, 30, pp.117-124. ⟨10.1016/j.jprocont.2015.03.010⟩. ⟨hal-01163455⟩
  • Caroline Baroukh, Rafael Munoz Tamayo, Jean-Philippe Steyer, Olivier Bernard. A state of the art of metabolic networks of unicellular microalgae and cyanobacteria for biofuel production. Metabolic Engineering, Elsevier, 2015, 30, pp.49-60. ⟨10.1016/j.ymben.2015.03.019⟩. ⟨hal-01163453⟩
  • Caroline Baroukh, Rafael Munoz Tamayo, Olivier Bernard, Jean-Philippe Steyer. Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production. Current Opinion in Biotechnology, Elsevier, 2015, 33, pp.198-205. ⟨10.1016/j.copbio.2015.03.002⟩. ⟨hal-01163456⟩
  • Rafael Munoz Tamayo, Pierre Martinon, Gaël Bougaran, Francis Mairet, Olivier Bernard. Getting the most out of it: optimal experiments for parameter estimation of microalgae growth models. Journal of Process Control, Elsevier, 2014, 24 (6), pp.991-1001. ⟨10.1016/j.jprocont.2014.04.021⟩. ⟨hal-00998525⟩
  • Caroline Baroukh, Rafael Munoz Tamayo, Jean-Philippe Steyer, Olivier Bernard. DRUM: A new framework for metabolic modeling under non-balanced growth. Application to the carbon metabolism of unicellular microalgae. PLoS ONE, Public Library of Science, 2014, 9 (8), pp.e104499. ⟨10.1371/journal.pone.0104499⟩. ⟨hal-01123224⟩
  • Rafael Munoz Tamayo, Francis Mairet, Olivier Bernard. Optimizing microalgal production in raceway systems. Biotechnology Progress, Wiley, 2013, 29 (2), pp.543--552. ⟨10.1002/btpr.1699⟩. ⟨hal-00850376⟩
  • Rafael Munoz Tamayo, Jolan de Groot, Peter A. Wierenga, Harry Gruppen, Marcel H. Zwietering, et al.. Modeling peptide formation during the hydrolysis of β-casein by Lactococcus lactis. Process Biochemistry, Elsevier, 2012, 47 (1), pp.83-93. ⟨10.1016/j.procbio.2011.10.012⟩. ⟨hal-02643666⟩
  • Rafael Munoz Tamayo, Jolan de Groot, Edwin Bakx, Peter A. Wierenga, Harry Gruppen, et al.. Hydrolysis of β-casein by the cell-envelope-located PI-type protease of Lactococcus lactis: A modelling approach. International Dairy Journal, Elsevier, 2011, 21 (10), pp.755-762. ⟨10.1016/j.idairyj.2011.03.012⟩. ⟨hal-02648605⟩
  • Rafael Munoz Tamayo, Béatrice Laroche, Eric Walter, Sylvia Duncan, Harry Flint, et al.. Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species. FEMS Microbiology Ecology, Wiley-Blackwell, 2011, 76 (3), pp.615-624. ⟨10.1111/j.1574-6941.2011.01085.x⟩. ⟨hal-00655932⟩
  • Rafael Munoz Tamayo, Béatrice Laroche, Eric Walter, Joel Doré, Marion Leclerc. Mathematical modelling of carbohydrate degradation by human colonic microbiota. Journal of Theoretical Biology, Elsevier, 2010, 266 (1), pp.189-20. ⟨10.1016/j.jtbi.2010.05.040⟩. ⟨hal-00521148⟩
  • Julien Tap, Stanislas Mondot, Florence Levenez, Eric Pelletier, Christophe Caron, et al.. Towards the human intestinal microbiota phylogenetic core. Environmental Microbiology, Society for Applied Microbiology and Wiley-Blackwell, 2009, 11 (10), pp.2574-2584. ⟨10.1111/j.1462-2920.2009.01982.x⟩. ⟨hal-02667864⟩

Conference papers23 documents

  • Rafael Munoz Tamayo. The shades of gray in model building and its opportunities for precision livestock farming. 72. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2021, Davos, Switzerland. ⟨hal-03347173⟩
  • Rafael Munoz Tamayo, Helen Kettle, Baptiste Ruiz, Richard Williams, Peter J. Moate, et al.. How complex does a mathematical model need to be to describe the dynamics of methane production in cattle?. MODNUT, 2019. ⟨hal-02790648⟩
  • Rafael Munoz Tamayo, Alberto Stanislao Atzori, Antonello Cannas, Francesco Masoero, Sylvie Giger-Reverdin, et al.. Predictive capabilities of a dynamic mechanistic model of in vitro fermentation by rumen microbiota. 61. Annual Meeting of the European Associationfor Animal Production (EAAP), 2019, NA, France. ⟨hal-02193905⟩
  • Helen Kettle, Rafael Munoz Tamayo, R.J. Dewhurst. Combining a process-based model of rumen fermentation with methane production data from respiration chambers. 75. Annual Conference of the British Society of Animal Science (BSAS), Apr 2019, Edinburgh, United Kingdom. ⟨10.1017/S2040470019000013⟩. ⟨hal-02193900⟩
  • Rafael Munoz Tamayo, Manuel Revilla Sanchez, Nicolas Friggens, Laurent Broudiscou, Gaetan Lemonnier, et al.. Towards a quantitative characterization of robustness of piglets at weaning period: An animal growth modelling approach. Journées 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. ⟨hal-01840967⟩
  • Rafael Munoz Tamayo, Milka Popova, Diego Morgavi, Dominique Graviou, Jean-Pierre Morel, et al.. Rumen methanogens display species-specific energetic and growth dynamics: a thermodynamic and kinetic based modelling approach. Journées 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. ⟨hal-01840971⟩
  • Yuliaxis Ramayo Caldas, Aurélien Bernard, Laura Zingaretti, Milka Popova, Nuria Mach Casellas, et al.. Identification of microbial taxa linked to methane emission in Holstein and Charolais cattle by an integrative approach. Gut Microbiology: No longer the forgotten organ - 11. INRA-Rowett Symposium, Jun 2018, Aberdeen, United Kingdom. ⟨hal-02738326⟩
  • Yuliaxis Ramayo Caldas, Aurélien Bernard, Laura M. Zingaretti, Milka Popova, Nuria Mach Casellas, et al.. Multivariate and network analysis identified microbial biomarkers linked to methane emission. 69. Annual Meeting of the European Federation of Animal Science, European Federation of Animal Science, Aug 2018, Dubrovnik, Croatia. ⟨hal-02881487⟩
  • Rafael Munoz Tamayo, Pierre Blavy, Laurence Puillet, Olivier Martin, Jean-Baptiste Daniel, et al.. 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. ⟨hal-01840968⟩
  • Caroline Baroukh, Rafael Munoz Tamayo, Jean-Philippe Steyer, Olivier Bernard. Metabolic modeling of microalgae growth and lipids production during day/night cycles and nitrogen starvation. Metabolic Pathway Analysis 2015, Jun 2015, Braga, Portugal. ⟨hal-01603450⟩
  • Caroline Baroukh, Olivier Bernard, Jean-Philippe Steyer, Rafael Munoz Tamayo, Benoit Chachuat. A new approach to unravel metabolic regulations. Application to microalgae growth and lipid production under day/night cycles and nitrogen starvation. BioSynSys 2015 : 1er colloque du GDR "Biologie de Synthèse et des Systèmes", Sep 2015, Paris, France. ⟨hal-01601441⟩
  • Rafael Munoz Tamayo, Cesar Arturo Aceves-Lara, Carine Bideaux. Optimization of lipid production by oleaginous yeast in continuous culture. 19. World Congress of the International Federation of Automatic Control, Aug 2014, Cape Town, South Africa. ⟨hal-01268860⟩
  • Francis Mairet, Rafael Munoz Tamayo, Olivier Bernard. Driving Species Competition in a Light-limited Chemostat. 9th IFAC Symposium on Nonlinear Control Systems (NOLCOS), Sep 2013, Toulouse, France. ⟨hal-00852258⟩
  • Rafael Munoz Tamayo, Francis Mairet, Olivier Bernard. Driving microalgal production in raceway systems to near optimal productivities.. European Control Conference (ECC13), Jul 2013, Zurich, Switzerland. ⟨hal-00852259⟩
  • Caroline Baroukh, Rafael Munoz Tamayo, Jean-Philippe Steyer, Olivier Bernard. A new framework for metabolic modeling under non-balanced growth. Application to carbon metabolism of unicellular microalgae: Application to carbon metabolism of unicellular microalgae. CAB 2013 - International on Computer Applications to Biotechnology, Dec 2013, Mumbai, India. ⟨hal-00856042v2⟩
  • Rafael Munoz Tamayo, Francis Mairet, Olivier Bernard. A closed-loop controller for optimizing nitrogen removal in a microalgal outdoor pond. 11. IWA Conference on Instrumentation Control and Automation, Sep 2013, Narbonne, France. ⟨hal-02747879⟩
  • Caroline Baroukh, Rafael Munoz Tamayo, Jean-Philippe Steyer, Olivier Bernard. 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. ⟨hal-01601779⟩
  • Rafael Munoz Tamayo, Pierre Martinon, Gaël Bougaran, Francis Mairet, Olivier Bernard. Design of Optimal Experiments for Parameter Estimation of Microalgae Growth Models. International Symposium on Computer Applications to Biotechnology (CAB 2013), Dec 2013, Mumbai, India. ⟨hal-00856749⟩
  • Francis Mairet, Rafael Munoz Tamayo, Olivier Bernard. Adaptive control for optimizing microalgae production. Computer Application in Biotechnology (CAB2013), Dec 2013, Mumbai, India. ⟨hal-00921486⟩
  • Rafael Munoz Tamayo, Béatrice Laroche, Marion Leclerc, Eric Walter. IDEAS: a parameter identification toolbox with symbolic analysis of uncertainty and its application to biological modelling. 15. IFAC Symposium on System Identication (SYSID 2009), Jul 2009, Saint Malo, France. ⟨10.3182/20090706-3-FR-2004.00211⟩. ⟨hal-01204242⟩
  • Rafael Munoz Tamayo, Béatrice Laroche, Marion Leclerc, Eric Walter. Modelling and identification of in vitro homoacetogenesis by human-colon bacteria. 16. Mediterranean Conference on Control and Automation, 2008, Ajaccio, France. ⟨hal-01204248⟩
  • Rafael Munoz Tamayo, Jean-Philippe Steyer, Béatrice Laroche, Marion Leclerc. Human colon: a complex bioreactor. Conceptual modelling for the anaerobic digestion of the functional trophic chain. 11. World Congress on Anaerobic Digestion, Sep 2007, Brisbane, Australia. 6 p. ⟨hal-01204246⟩
  • Fabiola Angulo, Rafael Munoz Tamayo, Gerard Olivar. Control of a bioreactor using feedback linearization. 2007 Mediterranean Conference on Control & Automation (MED 2007), Jun 2007, Athènes, Greece. ⟨10.1109/MED.2007.4433763⟩. ⟨hal-02755197⟩

Poster communications3 documents

  • Pierre Blavy, Laurence Puillet, Jean-Baptiste Daniel, Daniel Sauvant, Olivier Martin, et al.. Animal modelling meets identifiability: a practioner perspective. Journées d'Animation Scientifique du département Phase (JAS Phase 2018), Apr 2018, Rennes, France. 2018, Journées d’animation scientifiques du département Phase - Recueil des résumés. ⟨hal-02738243⟩
  • Rafael Munoz Tamayo, Milka Popova, Diego Morgavi, Dominique Graviou, Jean Pierre Morel, et al.. Rumen methanogens exhibit specific energetic and growth dynamics: a modelling approach. 10. International Symposium on the Nutrition of Herbivores (ISNH10), Sep 2018, Clermont-Ferrand, France. Cambridge University Press, Advances in Animal Biosciences, 9 (3), 2018, 10th. International Symposium on the Nutrition of Herbivores (ISNH10). ⟨hal-02734246⟩
  • Rafael Munoz Tamayo, Sylvie Giger-Reverdin, Daniel Sauvant. Predicting ruminal pH dynamics by linking microbial metabolism and the host: a theoretical study. 10. INRA-Rowett symposium on gut microbiology “Twenty years and counting”, Jun 2016, Clermont-Ferrand, France. 2016. ⟨hal-01351516⟩

Book sections1 document

  • Rafael Munoz Tamayo. Breve elogio a la lentitud en ciencia. Ciencia y Humanismo 50 años Revista Aleph (1996-2016), Carlos Enrique Ruiz, 594 p., 2016, 978-958-8730-75-2. ⟨hal-02797416⟩

Other publications1 document

  • Rafael Munoz Tamayo, Béatrice Laroche, Eric Walter, Marion Leclerc. IDEAS. 2009. ⟨hal-01204255⟩

Preprints, Working Papers, ...10 documents

  • Manuel Revilla, Guillaume Lenoir, Loïc Flatres-Grall, Rafael Munoz Tamayo, Nicolas Friggens. Quantifying growth perturbations over the fattening period in swine via mathematical modelling. 2021. ⟨hal-03165841⟩
  • Manuel Revilla, Guillaume Lenoir, Loïc Flatres-Grall, Rafael Munoz Tamayo, Nicolas Friggens. Quantifying growth perturbations over the fattening period in swine via mathematical modelling. 2021. ⟨hal-03346812⟩
  • P Blavy, O Dhumez, B Nielsen, Rafael Munoz Tamayo, Nicolas Friggens, et al.. A filtering algorithm for accurate determination of feed intake dynamics. 2020. ⟨hal-02959928⟩
  • Rafael Munoz Tamayo, Juana Chagas, Mohammad Ramin, Sophie J. Krizsan. Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation. 2020. ⟨hal-03024873⟩
  • Rafael Munoz Tamayo. A brief tribute to slowness in science *. 2019. ⟨hal-02369434⟩
  • Rafael Munoz Tamayo. A brief tribute to slowness in science. 2018. ⟨hal-02786714⟩
  • Laura Lema Perez, Rafael Munoz Tamayo, Jose Fernando Garcia Tirado, Hernan Alvarez. On Parameter Interpretability of Phenomenological-Based Semiphysical Models. 2018. ⟨hal-02788220⟩
  • Manuel Revilla, Nicolas Friggens, Laurent Broudiscou, G. Lemonnier, F. Blanc, et al.. Towards the quantitative characterization of piglets' robustness to weaning: A modelling approach. 2018. ⟨hal-02369432⟩
  • Rafael Munoz Tamayo, J Ramírez Agudelo, R. Dewhurst, G Miller, T Vernon, et al.. A parsimonious software sensor for estimating the individual dynamic pattern of methane emissions from cattle. 2018. ⟨hal-02369431⟩
  • Rafael Munoz Tamayo, Milka Popova, Maxence Tillier, Diego Morgavi, Gérard Fonty, et al.. Hydrogenotrophic methanogens of the mammalian gut: functionally similar, thermodynamically different -A modelling approach. 2018. ⟨hal-02369430⟩

Theses1 document

  • Rafael Munoz Tamayo. Modélisation mathématique de la dégradation des hydrates de carbone dans le côlon humain. Mathématiques [math]. Université Paris Sud - Paris 11, 2010. Français. ⟨tel-02822888⟩

Habilitation à diriger des recherches1 document

  • Rafael Munoz Tamayo. A modelling odyssey in the tree of life. Modeling and Simulation. Université Paris Sud (Paris 11), 2019. ⟨tel-02183063⟩