Mathematical Biology seminars

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General information:

Seminars are on Mondays at 2pm in room 5323 of the James Clerk Maxwell Building and are jointly organized by Tibor Antal and Michael Nicholson (Maths), Linus Schumacher (Medicine), Ramon Grima (SynthSys), Helen Alexander (Evolution), and Aidan Brown (Physics). Everybody is welcome to attend.

To be placed on the seminar announcement list, email sympa@mlist.is.ed.ac.uk with subject: sub mathbiol  or use subject: unsub mathbiol   to be removed from the list.

Upcoming events in 2025:

• 6 October Student talks with MAC-MIGS: Rodrigo Rivas Barbosa , Thanakorn Jaemthaworn, James Hayes, Caterina Lue, Kiran Wadhawan, Manon Savage, Josh Fogg, Keren Tapper, Ross Walker, Xell Brunet Guasch, Maame Ama Bainson, Rosario Capozza, Yannis Galanos, Alex Richardson, Zak Sattar
• 20 October Mark Chaplain, School of Mathematics and Statistics, University of St Andrews, Mathematical modelling of cancer invasion and metastatic spread
• 27 October Sara Jabbari, School of Mathematics, University of Birmingham, Mathematical modelling to understand microbial behaviour and suggest novel directions for treatment of bacterial infections
• 3 November Davide Marenduzzo, School of Physics and Astronomy, UoE, Biophysical principles of chromosome organisation and transcriptional dynamics
• 10 November Michael Boemo, Department of Pathology, University of Cambridge, Mapping DNA replication in cancer cells and parasites with mathematical modelling, long-read sequencing, and AI
• postponed: Timothy I. Cannings, School of Mathematics, UoE, An introduction to (isotonic) subgroup selection
• 24 November Katie Atkins, Usher Institute, UoE and London School of Hygiene and Tropical Medicine, Can we predict the evolution of antibiotic resistance?
• 1 December Sjoerd Viktor Beentjes, School of Mathematics, UoE
• 8 December Nikolaos Sfakianakis, School of Mathematics and Statistics, University of St Andrews

Past events in 2025:

• 13 January Student talks: Cameron Kerr, Xell Brunet Guasch, James Hayes, Laila Saliekh, Alannah Neff, Caterina Lue, Germander Soothill , Alex Richardson, Lucy Martin, Jessica Codling
• 20 January Luke K Davis, SoM, UoE, Mesoscopic heterogeneity in biomolecular condensates from sequence patterning
• 27 January Magnus Rattray, Institute for Data Science and Artificial Intelligence, University of Manchester, Uncovering how mRNA transcription and degradation shape embryonic development
• 29 january (Wednesday) Reidun Twarock, Department of Mathematics and Department of Biology, Universty of York, Mechanistic Virology: Where Structure Meets Function
• 3 February Bartlomiej Waclaw, Dioscuri Centre for Physics and Chemistry of Bacteria, Poland, Predicting the evolution of resistance to antibiotics – do simple models work?
• 17 February James Marshall, School of Computer Science, The University of Sheffield, Negative feedback as a noise suppression mechanism in collective foraging
• 24 February Matthew Silk, Institute of Ecology and Evolution, UoE, What can modeling networks tell us about animal social ecology and evolution?
• 3 March Claudia Igler, School of Biological Sciences, University of Manchester, Understanding the drivers of antimicrobial resistance evolution
• 10 March Andreas Tiffeau-Mayer,  Division of Infection and Immunity, University College London, Statistical Insights into the Immune Receptor Code
• 17 March Helen Alexander, Institute of Ecology and Evolution, UoE, Estimating non-homogeneous mutation rates in bacteria using fluctuation analysis
• 24 March Mariya Ptashnyk, School of Mathematical and Computer Sciences, Heriot Watt University, Multiscale modelling, analysis and simulation of intercellular signalling processes and mechanotransduction in biological tissues
• 31 March Jamie Dean, Department of Medical Physics and Biomedical Engineering, University College London, Revealing mechanisms of cell cycle regulation underlying radiotherapy resistance

Past events in 2024:

• 23 January Michael Nicholson, Institute of Genetics and Cancer, UoE, Quantifying the stochastic dynamics of transcription-coupled DNA repair
• 30 January Mariia Dvoriashyna, School of Mathematics, UoE, Fluid and solute transport across ocular epithelia
• 6 February Aidan Brown, School of Physics, UoE, Buckling instabilities in chaining bacterial colonies
• 20 February Linus Schumacher, Centre for Regenerative Medicine, UoE, Stochastic processes and inverse problems in stem cell and tissue dynamics
• 27 February Philip Greulich, Applied Mathematics, University Southampton, Universal laws in stem cell biology from graph theory and population dynamics
• 5 March Derek Setter, Institute of Evolutionary Biology, UoE, Breakups and Hookups: a Markov model for karyotype evolution
• 12 March Anastasia Ignatieva, School of Mathematics and Statistics, University of Glasgow, Signals of structural variation in reconstructed genealogies
• 19 March Giulio Caravagna, Cancer Data Science Laboratory, University of Trieste, Timing the origin of immune-escape from leukaemia after bone marrow transplant
• 26 March William Duncan Martinson, University of Oxford Mathematical Institute, Multiscale modelling of collective behaviour: insights, challenges, and future perspectives
• 16 April Ruben Perez-Carrasco, Department of Life Sciences, Imperial College London, Unlocking the dynamics of gene regulatory networks: Beyond the steady-state paradigm
• 22 April Weini Huang, Queen Mary University London, Mutation accumulation in cell populations
• 30 April Tim Rogers, Department of Mathematical Sciences, University of Bath, Overturning consensus in animals and humans  
• 30 September Ava Khamseh, Institute of Genetics & Cancer and School of Informatics, UoE, Stator: High order expression dependencies finely resolve cryptic states and subtypes in single cell data
• 7 October Peter Swain,  SynthSys, Centre for Synthetic and Systems Biology, UoE, The ups and downs of budding yeast's transport of glucose
• 21 October Nikola Popovic, School of Mathematics, UoE, Front propagation in two-component reaction-diffusion systems with a cut-off
• 28 October  Philip Pearce, Institute for the Physics of Living Systems, University College London, Multiscale modelling of blood flow in health and disease
• 4 November Chris Brackley, School of Physics & Astronomy, UoE, Simulating chromosome compaction and protein droplets: liquid phase separation?
• 11 November Andrea Weisse, School of Informatics, UoE, A mechanistic model of Rtc-regulated RNA repair suggests molecular targets to potentiate antibiotic effects
• 25 November Lyndsay Kerr, Mathematics and Statistics, Strathclyde, Cluster mean-field models: Applications in DNA and beyond
• 2 December Diego Oyarzún,  School of Informatics and School of Biological Sciences, UoE, Integration of dynamical systems and machine learning for cell factory design

Past events in 2019:

• 19 March, Lyuba Chumakova, School of Mathematics, UoE, Why are we not falling apart?
• 2 Apr, Linus Schumacher, MRC Centre for Regenerative Medicine, UoE, Collective behaviour at intermediate scales: aggregation and swarming of the roundworm C. elegans
• 23 April, Joachim Krug, Institute for Biological Physics, University of Cologne, Recombination promotes mutational robustness on neutral fitness landscapes
• 30 April, Matthew Hartfield, Institute of Evolutionary Biology, UoE, Adaptation and Self–Fertilisation
• 7 May, Alex Fletcher, School of Mathematics and Statistics, University of Sheffield, Modelling epithelial tissue patterning and morphogenesis
• 8 Oct, Alexander R.A. Anderson, Integrated Mathematical Oncology Department, Moffitt Cancer Center & Research Institute, Tampa, FL, USA, Exploiting evolution to design better cancer therapies
• 26 Nov, Daniele Avitabile; Vrije Universiteit Amsterdam, This is not a bump
• 3 Dec, Jochen Kursawe, School of Mathematics and Statistics, University of St Andrews, Quantitative modelling of embryonic development
• 10 Dec, Amaury Lambert, Stochastics & Biology Group, Laboratoire de Probabilités, Statistique & Modélisation, Sorbonne Université, The split-and-drift random graph, a null model for speciation

Past events in 2018:

• 16 Jan, Shiladitya Banerjee, Department of Physics and Astronomy, University College London, Adaptive size regulation and division control in bacterial cells
• 20 Feb, Caroline Kosiol, School of Biology, University of St Andrews, Estimating the evolutionary history of populations using boundary mutation models
• 20 March, Ben MacArthur, Mathematical Sciences, University of Southampton, Stochastic models of stem cells
• 27 March, Kit Yates, Department for Mathematical Sciences, University of Bath, Hybrid frameworks for modelling reaction-diffusion processes
• 1 May, Maria Rita D'Orsogna, Math Department, California State University, Northridge, USA, Swarms in two and three dimensions: patterns, stability and collapse
• 8 May, Carsten Marr, Institute of Computational Biology, Helmholtz Zentrum München, Quantifying cellular dynamics of stem cell decisions
• 22 May, Jerome Kelleher,  Wellcome Trust Centre for Human Genetics, University of Oxford
• 2 Oct, Pak-Wing Fok, Department of Mathematical Sciences, University of Delaware, Inference of Rates in a Birth-Death Process from Conditional Extinction Times
• 9 Oct, Carina Dunlop, Department of Mathematics, University of Surrey, Mechanical models for cell and tissue mechanotransduction
• 16 Oct, Simon Pearce, University of Manchester, How to curl a microtubule
• 30 Oct, Kevin Leder, Industrial and Systems Engineering, University of Minnesota-Twin Cities, A spatial model of cancer initiation
• 13 Nov, Jamie Blundell, Department of Oncology University of Cambridge, Hematopoietic Stem Cell Parameters and Clonal Dynamics Revealed by Applying Branching Process Models to Clonal Hematopoiesis Datasets
• 20 Nov, George Constable, Mathematical Sciences Department, University of Bath, Why do most isogamous species have so few mating types, yet some have so many?
• 27 Nov, Jasmine Foo, School of Mathematics, University of Minnesota-Twin Cities, Memory in trait macroevolution
• 4 Dec, Helen Alexander, Department of Zoology, University of Oxford, Modelling mutations in bacteria: causes and consequences of phenotypic delay
• 11 Dec, David Head, School of Computing, University of Leeds, Agent-based modelling of the dental plaque biofilm

Past events in 2017:

• 24 Jan, Chris Josephides, UoE, Predicting adaptive evolution in an eco-evolutionary model from graph-theoretic properties of mutational paths
• 7 Feb, Victoria Todd and Ian Todd, Directors of Ocean Science Consulting; Maximilian Ruffert, Scool of Mathematics, UoE; Clare Owen, Research Analyst at OSC, Passive Acoustic Monitoring of Porpoises in the North Sea
• 21 Feb,  Alessandro Moura, Institute of Medical Sciences, University of Aberdeen, Why are replication origins located where they are?
• 28 Feb, Rhoda J Hawkins, Department of Physics and Astronomy, University of Sheffield, Active matter droplets & applications to cell movement & deformation
• 7 March, Ben Goddard, School of Mathematics, UoE, Dynamic Density Functional Theory:  A Tool For Mathematical Biology?
• 21 March, Marco Archetti, School of Biological Sciences, University of East Anglia, Game theory of cancer
• 28 March, Andy Hoyle, Faculty of Natural Sciences, University of Stirling, Optimising antibiotic dosage regimens to treat bacterial infections
• 4 April, Trevor Graham, Barts Cancer Institute, Quantification of subclone fitness advantages in human cancers
• 16 May, Benedict Leimkuhler, School of Mathematics, UoE, Adaptive Brownian Dynamics
• 22 May, Alison Hill & Jeff Gerold, Program for Evolutionary Dynamics, Harvard University, Stochastic dynamics of latent HIV: barrier or path to a cure?  
• Sept 12, Ivana Bozic, Department of Applied Mathematics, University of Washington, Stochastic evolutionary modeling of cancer development and resistance to treatment
• Oct 17, Edward Cao, SynthSys, UoE, Linear Mapping Approximation of Nonlinear Gene Regulatory Networks
• Oct 24, Rebecca Hoyle, Mathematical Sciences, University of Southhampton,  Maternal effects and environmental change
• Oct 31, (joint SoM Colloquium) Simon Tavare, Cancer Research UK Cambridge Institute, The unreasonable effectiveness of the Ewens Sampling Formula
• Nov 7, Finn Lindgren, Shool of Mathematics, UoE, Stochastic space-time models, non-trivial observation mechanisms, and practical inference
• Nov 14, Daren Wilkinson,  School of Mathematics & Statistics, Newcastle University, Multiscale modelling of open engineered biological systems
• Nov 28, Ruth Baker, Mathematical Institute, University of Oxford, Collective cell invasion: mathematical models and biological insights

Past events in 2016:

• 12 Jan, Guido Sanguinetti, Informatics, UoE Cox process representation and inference for stochastic reaction-diffusion processes
• 26 Jan, Stephen Cornell, Institute of Integrative Biology, University of Liverpool Stochastic models in community ecology
• 9 Feb, Gavin Gibson, School of Mathematical & Computer Sciences, Heriot-Watt University, Latent processes and functional models for partially observed epidemics
• 16 Feb, Stefan Grosskinsky, Mathematics Institute, University of Warwick, Effect of non-Markovian dynamics on pattern formation and transport
• 23 Feb, Andy White, School of Mathematical & Computer Sciences, Heriot-Watt University, Mathematical Modelling Tools for Red Squirrel Conservation
• 8 March,  Paul Jenkins, Dept of Statistics, University of Warwick, Exact simulation of the Wright-Fisher diffusion
• 22 March,  Nick Savill, Institute of Immunology and Infection Research, UoE,  Chronobiology of malaria
• 29 March, Andrew Goryachev, SyntSys, UoE, Activator-inhibitor patterns on the scale of biological cells
• 3 May, Teuta Pilizota, Centre for Synthetic and Systems Biology, UoE, Achieving directional swimming by manipulating the diffusion constant
• 10 May, Kevin Burrage, University of Oxford and Queensland University of Technology, Australia, Coping with variability and heterogeneity when modelling the electrophysiology of the heart
• 24 May, Benjamin Allen, Mathematics, Emmanuel College, Boston, Neutral drift and weak selection on graphs
• 4 Oct, Kostas Zygalakis, School of Mathematics, UoE, Hybrid modelling of stochastic chemical kinetics
• 11 Oct, Andrea Sottoriva, Evolutionary Genomics and Modelling, The Institute of Cancer Research, London, Making sense of cancer genomic data in the light of tumour evolution: measuring clonal dynamics in individual patients from next-generation sequencing
• 18 Oct, Frits Veerman, School of Mathematics, UoE, Rapid evolution in plankton populations: a slow-fast model
• 25 Oct, Tim Rogers, Department of Mathematical Sciences, University of Bath, Strength in numbers: how demographic noise can reverse the direction of selection
• 1 Nov, Alexander Morozov, School of Physics, UoE, Swimming of microorganisms in viscoelastic fluids
• 15 Nov, Christina Cobbold, School of Mathematics and Statistics, University of Glasgow, From maladaptivity to adaptivity -the evolution of developmental timing
• 22 Nov, Juan Bonachela, Mathematics and Statistics, University of Strathclyde, Large-scale emergent patterns in semi-arid ecosystems
• 29 Nov, Juraj Szavits-Nossan, School of Physics, UoE,  Predicting mRNA translation rates from coding DNA sequences
• 9 Dec, Joachim Krug, Institute for Theoretical Physics, University of Cologne, Genotypes, phenotypes and Fisher's geometric model

Past events in 2015:

• 20 Jan, Magnus Richardson, Systems Biology Centre, Warwick University Neurons, synapses and neuromodulators
• 27 Jan, Fordyce A Davidson, Division of Mathematics, University of Dundee Applications of differential equations to spatio-temporal organisation in (micro)-biology
• 3 Feb, Nick Hill, School of Mathematics & Statistics, University of Glasgow Modelling the Human Circulation
• 10 Feb, (also Maxwell Colloquium) Philip K Maini, Mathematical Institute, Oxford University Case Studies in Modelling Collective Cell Motion
• 17 Feb, Ivana Gudelj, Biosciences, University of Exeter The role of trade-offs in the evolution of diversity and host specialisation
• 24 Feb, Jarrod Hadfield, Institute of Evolutionary Biology, UoE The Spatial Scale of Local Adaptation
• 26 Feb, (joint Applied Maths Seminar) David Kessler, Department of Physics, Bar-Ilan University, Israel Large population solution of the stochastic Luria–Delbrück evolution model
• 3 March, (Joint Probability Seminar)  Helen Byrne, Mathematical Institute, Oxford University Oxygen: A Careful Balancing Act
• 10 March, Jozsef Z Farkas, Computing Science and Mathematics, University of Stirling Structured models for disease dynamics
• 24 March, Kevin J Painter, Department of Mathematics, Heriot Watt University A user's guide to modelling chemotaxis
• 31 March, Andrea Weisse, SyntSys, UoE A mechanistic model of a cell to link cellular trade-offs, gene expression, and growth
• 3 Nov, Mariya Ptashnyk, Department of Mathematics, University of Dundee Gene Regulatory Network and Functional Analysis: Mathematical modelling and analysis of signalling processes in cells and tissues.
• 17 Nov, Gabriel Lord, School of Mathematical & Computer Sciences, Heriot-Watt University A numerical method for stochastic travelling waves in neural tissue
• 24 Nov, Florian Markowetz, University of Cambridge, CRUK Cambridge Institute Inferring cancer evolution
• 1 Dec, Axel Rossberg, School of Biological and Chemical Sciences, Queen Mary University of London Structural instability as the key to community ecology

Past events in 2014:

• 18 Feb, Bartek Waclaw, School of Physics, UoE Mathematical problems in the physics of growing bacterial populations
• 25 Feb, Michael Cates, School of Physics, UoE Phase separation in self-propelled organisms
• 4 March, Matteo Cavaliere, Synthsys, UoE The Rise and Fall of Cooperative Communities
• 11 March, Nikola Popovic, School of Maths, UoE A geometric analysis of fast-slow models for stochastic gene expression
• 18 March, Raluca Eftimie, Department of Mathematics, University of Dundee Mathematical mechanisms behind pattern formation in biological aggregations with nonlocal interactions
• 25 March, Karen M Page, Department of Mathematics, UCL Mathematical modelling of vertebrate neural tube patterning
• 1 April, Margaritis Voliotis, School of Mathematics, University of Bristol Information transfer by leaky, heterogeneous, protein kinase signaling systems
• 8 April, Charles Cockell, Astrobiology and Geobiology, UoE Life in Extremes
• 15 April, Konrad Lohse, Institute of Evolutionary Biology, UoE Calculating likelihoods under the coalescent
• 22 April, Reidun Twarock, Department of Mathematics, University of York Viruses and geometry – a new perspective on virus assembly and anti-viral therapy
• 29 April, Alan McKane, School of Physics and Astronomy, The University of Manchester Fast-mode elimination in stochastic metapopulation models
• 6 May, Martin Howard, Dept of Systems Biology, John Innes Centre How cells get to be the right size and put things at the right place inside them
• 13 May, Orkun Soyer, Life Sciences, University of Warwick Evolution as the designer in biology: From cellular networks to microbial communities
• 20 May, William Sloan, School of Engineering, University of Glasgow Modelling interactions between hydrodynamics and dispersalthat help shape biofilm community composition across a range of scales
• 27 May, Vincent Danos, CNRS and Synthsys, UoE Formal mean field theories for graph rewriting
• 26 June, Roderick C. Dewar, Research School of Biology, The Australian National University The statistical mechanics of savannas
• 25 August, Stan Leibler, The Rockefeller University On ethology and ecology of simple microbial systems
• 7 Oct, Davide Marenduzzo, School of Physics, UoE Modelling protein-driven DNA organisation, and chromatin self-assembly
• 14 Oct, Robert Beardmore, Biosciences, University of Exeter Observations of a Mathematician in an Evolutionary Microbiology LabTesting Theories of Biodiversity & Antibiotic-Resistance Adaptation
• 21 Oct, Kavita Jain, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India Rise and fall of asexual mutators in adapted populations
• 18 Nov, (joint Probability Seminar) Damian Clancy, Mathematical and Computer Sciences, Heriot Watt University The effects of population heterogeneities on spread of infection
• 25 Nov, Eva Deinum, Institute of Evolutionary Biology, UoE Understanding the paradoxical effects of microtubule severing on the self organization of the plant cortical array
• 2 Dec, Stefano Zapperi, CNR-IENI, Milano, Italy Mechanical stresses in tumor growth

Past events in 2013:

• 5 Feb, Brian Charlesworth, Institute of Evolutionary Biology, UoE Natural Selection and the Genome
• 12 Feb, Rosalind Allen, School of Physics, UoE Making models for microbial ecosystems
• 19 Feb, Peter Swain, SynthSys, School of Biological Sciences, UoE Identifying sources of variation in biochemical networks
• 26 Feb, Jonathan Sherratt, Department of Mathematics, Heriott-Watt How Does Seasonal Forcing Affect Vole Population Cycles?
• 12 March, Sam Brown, Institute of Evolutionary Biology, UoE Molecular, ecological and evolutionary dynamics of bacterial communication
• 19 March, Martin Evans, School of Physics, UoE Models of Switching in Biophysical Contexts
• 26 March, Peter Keller, School of Mathematics, UoE Time Symmetries in biological models -- a Markov Chain approach
• 7 May, Satya Majumdar, Laboratoire de Physique Théorique et Modèles Statistiques, Université de Paris-Sud Random Convex Hulls: Applications to Ecology and Animal Epidemics
• 14 May, Glenn Marion, Biomathematics & Statistics Scotland Understanding impacts of animal behaviour in wildlife-disease systems
• 21 May, Mark Chaplain, Division of Mathematics, University of Dundee Mathematical modelling of intracellular negative feedback systems
• 28 May, Timothy Newman, Cell and Developmental Biology, University of Dundee Approaching biology discretely
• 17 Sept, Joachim Krug, Physics Department, University of Cologne, Germany, Fitness landscapes and the predictability of evolution
• 24 Sept, Nick Barton, Institute of Science and Technology, Austria, What limits a species' range?
• 1 Oct, Radek Erban, Mathematical Institute, Oxford University Mathematical Methods for Multiscale Modelling in Molecular, Cell and Population Biology
• 8 Oct, Celso Grebogi, Institute of Pure and Applied Mathematics, University of Aberdeen Evolutionary game theory and the emergence of spatio-temporal order in ecological systems
• 22 Oct, Ramon Grima, SynthSys, School of Biological Sciences, UoE Inferring enzyme kinetic parameters from noisy time series data
• 29 Oct, Nacho Molina, SynthSys, School of Biological Sciences, UoE Model-based Bayesian analysis of time series: stochastic gene expression as a case study
• 19 Nov, (joint Probability Seminar) Alison M Etheridge, Dept Statistics, Oxford University Modelling evolution in a spatial continuum
• 26 Nov, Tom Leinster, School of Maths, UoE Measuring diversity: the importance of species similarity
• 3 Dec, M Carmen Romano, ICSMB, University of Aberdeen Modelling of ribosome recycling in S. Cerevisiae
• 10 Dec, Richard Blythe, School of Physics, UoE Evolution of communication by natural selection

Previous organizers: Rosalind Allen (Physics), Peter Swain (SynthSys).