Publications

Publications
Google Scholar

Bas Teusink, Robert Planqué and Frank J. Bruggeman. 2025. Making sense of gene expression control by flux sensing. Nature Metabolism. https://doi.org/10.1038/s42255-024-01182-w.
Maarten J. Droste, Maaike Remeijer, Robert Planqué, Frank J. Bruggeman. 2025. A trade-off between force and flow may lead to reduced entropy production rate during faster microbial growth. To appear in J. of Phys. Chemistry.
Robert Planqué, Josephus Hulshof and Frank J. Bruggeman. 2024. Sensing cellular growth rate facilitates its robust optimal adaptation to changing conditions. BioRXiv preprint.
Alicia Berkvens, Luis Salinas, Maaike Remeijer, Robert Planqué, Bas Teusink, and Frank J Bruggeman. 2024. Understanding and computational design of genetic circuits of metabolic networks. Essays in Biochemistry 68(1): 41-51.
R. Planqué. 2024. When is the inverse of an invertible convex function itself convex? J. of Convex Analysis 31(3): 847-852. ArXiv preprint.
Frank J. Bruggeman, Maaike Remijer, Maarten Droste, Luis Salinas, Meike Wortel, Robert Planqué, Bas Teusink, Herbert Sauro and Hans Westerhoff. 2023. Whole-cell metabolic control analysis. BioSystems: 105067. https://doi.org/10.1016/j.biosystems.2023.105067.
Zhaozheng Meng, Rebecca A. Capel, Samuel J. Bose, Erik Bosch, Sophia de Jong, Robert Planqué, Antony Galione, Rebecca A.B. Burton, Alfonso Bueno-Orovio. 2023. Lysosomal calcium loading promotes arrhythmias by potentiating ryanodine receptor release. Biophysical Journal 122: 1-16.
Odo Diekmann, Hans G. Othmer, Robert Planqué and Martin C.J. Bootsma. 2021. The discrete-time Kermack-McKendrick model: a versatile and computationally accessible framework for modelling epidemics. Proc. Nat. Acad. Sciences USA 118(39): e2106332118.
Tom J. Clement, Erik B. Baalhuis, Bas Teusink, Frank J. Bruggeman, Robert Planqué, Daan H. de Groot. 2020. Unlocking Elementary Conversion Modes: ecmtool unveils all capabilities of metabolic networks Patterns 2(1): 100177.
Age J. Tjalma, Robert Planqué and Frank J. Bruggeman. 2020. Poor sensing maximises microbial fitness when few out of many signals are sensed. BioRxiv preprint.
Frank J. Bruggeman, Robert Planqué Douwe Molenaar and Bas Teusink. 2020. Searching for principles of microbial physiology. FEMS Microbiology Reviews 44(6): 821-844.
Daan H. de Groot, Julia Lischke, Riccardo Muolo, Robert Planqué, Frank J. Bruggeman and Bas Teusink. 2020. The common message of constraint-based optimization approaches: overflow metabolism is caused by two growth-limiting constraints. Cell. Mol. Life Sciences. 77: 441-453.
Frank J Bruggeman, Jaap Schouten, Daan H. de Groot and Robert Planqué. 2020. Cell fate determination by Lamarckian molecule inheritance and chance. Preprint BioRxiv.
Daan H. de Groot, Josephus Hulshof, Bas Teusink, Frank J. Bruggeman and Robert Planqué. 2020. Elementary Growth Modes provide a molecular description of cellular self-fabrication. PLoS Comp Biol. 16(1):e1007559.
Gosse B Overal, Robert Planqué and Josephus Hulshof. 2020. Stability of an adaptive controlled pathway maximising specific flux under varying conditions. Preprint BioRxiv.
Odo Diekmann and Robert Planqué. 2020. The winner takes it all: how semelparous insects can become periodical. J. Math. Biology. 80: 283-301
Daan H. de Groot, Robert Planqué, Coco van Boxtel, Frank J. Bruggeman and Bas Teusink. 2019. The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates. PloS Comp Biol. 15(3): e1006858.
Robert Planqué, Josephus Hulshof, Bas Teusink, Johannes C. Hendriks, Frank J. Bruggeman. 2018. Maintaining maximal metabolic rates by gene expression control. PLoS Comp Biol. 14(9):e1006412.
Gosse B. Overal, Bas Teusink, Frank J. Bruggeman, Josephus Hulshof, Robert Planqué. 2018. Understanding startup problems in yeast glycolysis. Math Biosciences 299:117-126.
Robert Planqué, Scott Powell, Nigel R. Franks and Jan Bouwe van den Berg. 2016. Disruptive selection as a driver of evolutionary branching and caste evolution in social insects. J. Evol. Biol. doi 10.1111/jeb.12952
Robert Planqué, Frank J. Bruggeman, Bas Teusink and Josephus Hulshof. 2014. Understanding bistability in yeast glycolysis using general properties of metabolic pathways. Math. Biosciences. 255: 33-42.
Johan H. van Heerden, Meike T. Wortel, Frank J. Bruggeman, Joseph J. Heijnen, Yves J.M. Bollen, Robert Planqué, Josephus Hulshof, Tom G. O'Toole, S. Aljoscha Wahl and Bas Teusink. 2014. Fatal attraction in glycolysis: how Saccharomyces cervesiae manages sudden transitions to high glucose. Microbial Cell 1 (3): 103 - 106.
Johan H. van Heerden, Meike T. Wortel, Frank J. Bruggeman, Joseph J. Heijnen, Yves J.M. Bollen, Robert Planqué, Josephus Hulshof, Tom G. O'Toole, S. Aljoscha Wahl and Bas Teusink. 2014. Lost in transition: startup of glycolysis yields subpopulations of nongrowing cells. Science 343 (6174) : 987. DOI: 10.1126/science.1245114
Joseph A. Tobias, Robert Planqué, Dominic Cram, Nathalie Seddon. 2014. Species interactions and the structure of complex communication networks. Proc. Nat. Acad. Sciences USA. 111 (3):1020-1025.
Robert Planqué, Jan Bouwe van den Berg and Nigel R. Franks. 2013. The interplay between scent trails and group-mass recruitment systems in ants. Bull. Math. Biol. 75 (10):1912-1940. pdf.
Robert Planqué, Nicholas F. Britton and Hans Slabbekoorn. 2013. On the maintenance of bird song dialects. J. Math. Biol. 68 (1-2): 505-531. pdf
Robert Planqué, Jan Bouwe van den Berg and Nigel R. Franks. 2010. Recruitment strategies and colony size in social insects. PLoS ONE 5 (8): e11664.
Sander Idema, Clemens M. F. Dirven,Victor W. van Beusechem, Jan E. Carette, Robert Planqué, David P. Noske, Martine L. M. Lamfers, W. Peter Vandertop. 2010. Objective determination of the oncolytic potency of conditionally-replicating adenoviruses using mathematical modeling. J. Gene Medicine 12: 564-571.
Ana B. Sendova-Franks, Rebecca K. Hayward, Benjamin Wulf, Thomas Klimek, Richard James, Robert Planqué, Nicholas F. Britton, and Nigel R. Franks. 2009. Emergency networking: famine relief in ant colonies. Anim. Behav. 79 (2): 473-485..
James A.R. Marshall, Rafal Bogacz, Anna Dornhaus, Robert Planqué, Tim Kovacs, Nigel Franks. 2009. On optimal decision making in brains and social insect colonies. Proc. Roy. Soc. Interface 6: 1065-1074 pdf.
Sarina Macfadyen, Rachel Gibson, Andrew Polaszek, Rebecca J. Morris, Paul G. Craze, Robert Planqué, William O.C. Symondson, Jane Memmott. 2009. Do differences in food web structure between organic and conventional farms affect the ecosystem service of pest control? 2009. Ecology Letters 12: 229-238.
Robert Planqué and Hans Slabbekoorn. Spectral overlap in songs and temporal overlap in a Peruvian bird assemblage. 2008. Ethology 114: 262-271. pdf.
Robert Planqué, François-Xavier Dechaume-Moncharmont, Nigel Franks, Tim Kovacs, James Marshall. 2007. Why do house-hunting ants recruit in both directions? Naturwissenschaften 94 (11): 911-918.
Nick F. Britton, Robert Planqué, Nigel R. Franks. 2007. Evolution of defence portfolios in exploiter-victim systems. Bull. Math. Biol.. 69: 957-988.
Gert H.M. van der Heijden, Mark A. Peletier and Robert Planqué. 2007. On end rotation for open rods undergoing large deformations. Quarterly of Applied Mathematics. 65: 385-402 . Abstract, ps, pdf, journal reprint
Mark A. Peletier, Robert Planqué and Matthias Röger. 2007. Sobolev regularity via the rate of convergence of convolutions and Jensen's inequality. Annali della Scuola Superiore Normale di Pisa. 6: 499-510.
Robert Planqué, Anna Dornhaus, Nigel Franks, Tim Kovacs, James Marshall. 2006. Weighting waiting in collective decision making. Behav. Ecol. Sociobiol. 61 (3): 347-356. Abstract, pdf
Gert H.M. van der Heijden, Mark A. Peletier and Robert Planqué. 2006. Self-contact for rods on cylinders. Arch. Rat. Mech. Anal. 182 (3): 471-551. Abstract, pdf, journal link.
Robert Planqué, Nick F. Britton, Nigel R. Franks, and Mark A. Peletier. 2002. The adaptiveness of defense strategies against cuckoo parasitism. Bull. Math. Biol. 64: 1045-1068. Abstract, ps, pdf.

Conference proceedings, book chapters

Robert Planqué, Josephus Hulshof and Frank J. Bruggeman. 2019. Metabolic pathways and optimisation. Complexity Science. M. A. Peletier, R. van Santen and E. Steur (eds.). World Scientific.
Bas Teusink, Bob Planqué, Douwe Molenaar and Frank Bruggeman. 2018. Constraint-based models of microbial physiology: surprisingly versatile. Proceedings of FOODSIM 2018, pages 5-10.
Marshall, J. A. R., Bogacz, R., Dornhaus, A., Franks, N. R., Kovacs, T. & Planqué, R. (2006) Similar models of optimal decision making in social insect colonies and in the primate brain. In: T. Kovacs & J. Marshall (eds.) Proceedings of AISB'06: Adaptation in Artificial and Biological Systems (vol. 3), 205. AISB Press
Planqué, R. Marshall, J. A. R., Kovacs, T., Dechaume-Moncharmont, F. X., Franks, N. R., & Sendova-Franks, A. (2006) It takes two to tango: the role of late recruitment in collective decision making. In: T. Kovacs & J. Marshall (eds.) Proceedings of AISB'06: Adaptation in Artificial and Biological Systems (vol. 3), 207. AISB Press
Marshall, J. A. R., Bogacz, R., Planqué, R., Kovacs, T. & Franks, N. R. (2009) On optimal decision making in brains and social insect colonies. In: Seth et al. (eds.) Modelling Natural Action Selection. Cambridge University Press (in press).

Xeno-canto

Alexis Joly et al., 2025. LifeCLEF 2025 Teaser: Challenges on Species Presence Prediction and Identification, and Individual Animal Identification. In: Hauff, C., et al. Advances in Information Retrieval. ECIR 2025. Lecture Notes in Computer Science, vol 15576. Springer, Cham. https://doi.org/10.1007/978-3-031-88720-8_57.
Overview of BirdCLEF 2024: Acoustic Identification of Under-studied Bird Species in the Western Ghats Stefan Kahl, Tom Denton, Holger Klinck, Vijay Ramesh, Viral Joshi, Meghana Srivathsa, Akshay Anand, Chiti Arvind, Harikrishnan CP, Suyash Sawant, Robin V V, Hervé Glotin, Hervé Goëau, Willem-Pier Vellinga, Robert Planqué and Alexis Joly, CEUR Workshop Proceedings (CEUR-WS.org, ISSN 1613-0073), pdf
Burooj Ghani, Vincent J. Kalkman, Bob Planqué, Willem-Pier Vellinga, Lisa Gill, Dan Stowell. 2025. Impact of transfer learning methods and dataset characteristics on generalization in birdsong classification. Scientific Reports 15(1): 1-17.
Joly, A., et al., 2024. Overview of LifeCLEF 2024: Challenges on Species Distribution Prediction and Identification. In Experimental IR Meets Multilinguality, Multimodality, and Interaction.
Joly, A., et al., 2024. LifeCLEF 2024 Teaser: Challenges on Species Distribution Prediction and Identification. In European Conference on Information Retrieval. Springer Nature Switzerland. p. 19-27.
Joly, A., et al. Overview of LifeCLEF 2023: Evaluation of AI models for the identification and prediction of birds, plants, snakes and fungi. In International Conference of the Cross-Language Evaluation Forum for European Languages. Cham: Springer Nature Switzerland. 2023.
Kahl, S., Denton, T., Klinck, H., Reers, H., Cherutich, F., Glotin, H., Planqué, R., Vellinga, W.-P., ... ,Joly, A.. Overview of BirdCLEF 2023: Automated bird species identification in Eastern Africa. Working Notes of CLEF.
Joly, A., et al. Overview of lifeclef 2022: an evaluation of machine-learning based species identification and species distribution prediction. International Conference of the Cross-Language Evaluation Forum for European Languages. Cham: Springer International Publishing, 2022.
Stefan Kahl, et al., Overview of BirdCLEF 2022: Endangered bird species recognition in soundscape recordings. CLEF Working Notes 2022. CLEF: Conference and Labs of the Evaluation Forum, Sep. 2022, Bologna, Italy, 2022.
Alexis Joly et al. 2022. LifeCLEF 2022 Teaser: An Evaluation of Machine-Learning Based Species Identification and Species Distribution Prediction In: M. Hagen, et al. Advances in Information Retrieval. ECIR 2022. Lecture Notes in Computer Science, vol 13186. Springer, Cham.
Joly, Alexis, et al. Lifeclef 2022 teaser: An evaluation of machine-learning based species identification and species distribution prediction. European Conference on Information Retrieval. Cham: Springer International Publishing, 2022.
Alexis Joly et al. 2021. Overview of LifeCLEF 2021: An Evaluation of Machine-Learning Based Species Identification and Species Distribution Prediction. In book: Experimental IR Meets Multilinguality, Multimodality, and Interaction, 12th International Conference of the CLEF Association, CLEF 2021, Virtual Event, September 21-24, Proceedings.
Stefan Kahl, Mary Clapp, W. Alexander Hopping, Hervée Goëeau, Hervée Glotin, Robert Planqué, Willem-Pier Vellinga, and Alexis Joly. 2020. Overview of BirdCLEF 2020: Bird Sound Recognition in Complex Acoustic Environments. In CLEF2020 Working Notes.
Stefan Kahl, Fabian-Robert Stöter, Hervé Goëau, Hervé Glotin, Robert Planqué, Willem-Pier Vellinga, Alexis Joly. 2019. Overview of BirdCLEF 2019: large-scale bird recognition in soundscapes. In CLEF2019 Working Notes.
Alexis Joly, Hervé Goëau, Christophe Botella, Stefan Kahl, Marion Poupard, Maximillien Servajean, Hervé Glotin, Pierre Bonnet, Willem,-Pier Vellinga, Robert Planqué, Jan Schlüter, Fabian-Robert Stöter, Henning Müller. 2019. LifeCLEF 2019: Biodiversity identification and prediction challenges. In ECIR 2019 Advances in Information Retrieval. Lecture Notes in Computer Science 11438: 275-282.
Hervé Goëau, Stefan Kahl, Hervé Glotin, Robert Planqué, Willem-Pier Vellinga and Alexis Joly. 2018. Overview of BirdCLEF 2018: monospecies vs. soundscape bird identification. In CLEF2018 Working Notes.
Willem-Pier Vellinga, Bob Planqué, Sander Pieterse and Jonathon Jongsma. 2017. www.xeno-canto.org: a decade on. Neotropical birding 21: 40-47.
Alexis Joly, Hervé Goëau, Hervé Glotin, Concetto Spampinato, Pierre Bonnet, Willem-Pier Vellinga, Jean-Christophe Lombardo, Robert Planqué, Simone Palazzo, Henning Müller. 2016. LifeCLEF 2017: Multimedia Life Species Identification Challenges. In CLEF Proceedings 2017.
Hervé Goëau, Hervé Glotin, Willem-Pier Vellinga, Robert Planqué and Alexis Joly. 2017. LifeCLEF Bird Identification Task 2017. In CLEF Proceedings 2017.
Alexis Joly, Hervé Goëau, Hervé Glotin, Concetto Spampinato, Pierre Bonnet, Willem-Pier Vellinga, Julien Champ, Robert Planqué, Simone Palazzo, Henning Müller. 2016. LifeCLEF 2016: Multimedia Life Species Identification Challenges. In CLEF Proceedings 2016.
Hervé Goëau, Hervé Glotin, Willem-Pier Vellinga, Robert Planqué and Alexis Joly. 2016. LifeCLEF Bird Identification Task 2016. The arrival of deep learning. In CLEF2016 Working Notes 2016.
A. Joly, H. Goëau, H. Glotin, C. Spampinato, P. Bonnet, W.-P. Vellinga, R. Planqué, A. Rauber, S. Palazzo, B. Fisher. 2015. LifeCLEF 2015: Multimedia Life Species Identification, In Proceedings of CLEF 2015.
Hervé Goëau, Hervé Glotin, Willem-Pier Vellinga, Robert Planqué, Andreas Rauber and Alexis Joly. 2015. LifeCLEF Bird Identiﬁcation Task 2015. In Proceedings of CLEF 2015.
Willem-Pier Vellinga and Robert Planqué. 2015. The Xeno-canto collection and its relation to sound recognition and classification. In Proceedings of CLEF 2015.
Alexis Joly, Hervé Goëau, Hervé Glotin, Concetto Spampinato, Pierre Bonnet, Willem-Pier Vellinga, Andreas Rauber, Bob Fisher, Henning Müller and Robert Planqué. 2014. Are species identification tools biodiversity-friendly? A cross-tasks analysis of LifeCLEF 2014 results. 3rd ACM Int. Regular and Data Challenge Workshop on Multimedia Analysis for Ecological Data (MAED2014), Orlando.
Hervé Goëau, Hervé Glotin, Willem-Pier Vellinga, Robert Planqué, Andreas Rauber and Alexis Joly. 2014. LifeCLEF Bird Identiﬁcation Task 2014. In CLEF working notes 2014, ICMR-EMR Workshop Glasgow,UK.
A. Joly, H. Muller, H. Goeau, H. Glotin, C. Spampinato, A. Rauber, P. Bonnet, W.-P. Vellinga, B. Fisher, R. Planqué. 2014. LifeCLEF: Multimedia Life Species Identification, Int. Workshop on Environmental Multimedia Retrieval, Glasgow.
Alexis Joly, Hervé Goëau, Hervé Glotin, Concetto Spampinato, Pierre Bonnet, Willem-Pier Vellinga, Andreas Rauber, Bob Fisher, Henning Müller and Robert Planqué. 2014. LifeCLEF 2014: multimedia life species identification challenges. In Proceedings of CLEF 2014.
Bob Planqué & Willem-Pier Vellinga. Xeno-canto: a 21st century way of appreciating bird song. 2008. Neotropical Birding 3, 17-23. PDF available upon request.

Other publications

Erick Vermeulen en de Studiegroep Wiskunde met de Industrie (Geertje Hek, Misja Nuyens, Mark Peletier, Bob Planqué, Harmen van der Ploeg en Guido Terra), Het grote internationale eurodiffusie-experiment (in Dutch), Natuur & Techniek 01 (2002) p.11 and 22-25. pdf with pictures, html with corresponding page in section Actueel,
Geertje Hek, Misja Nuyens, Harmen van der Ploeg, Bob Planqué, Erick Vermeulen, Het grote internationale eurodiffusie-experiment (in Dutch), Natuur & Techniek 11 (2002) p.56-62. pdf, ps
Misja Nuyens en Bob Planqué, De wiskunde achter de eurodiffusie (in Dutch), Vakantiecursus 2003, Wiskunde in het Dagelijks Leven, CWI Syllabus 52 (2003) p.103-112.ps, pdf.

Studygroup Mathematics and Industry:

Jan Bouwe van den Berg, Natalia Davydova, Barbera van de Fliert, Frank Peeters, Bob Planqué, Harmen van der Ploeg en Guido Terra. Reconstruction of sea surface temperatures from the oxygen isotope composition of fossil planktic foraminifera.
in: Proceedings of the forty-second European study group with industry, G.M. Hek (ed.), CWI Syllabus 51 (2002) p.91-120. Abstract, ps, pdf.
Jan Bouwe van den Berg, Gregory Kozyreff, Hai-Xiang Lin, John McDarby, Mark A. Peletier, Robert Planqué, Philip Wilson. Japanese oysters in Dutch waters.
Abstract, ps, pdf.

Bob Planqué