Mathematical Biology and Medicine

Erik van Doorn
Seminars
Wednesdays 12 noon in the MALL (School of Maths, level 8)Mathbiomedicine seminars are intended to be of interest to a wide audience. MSc and PhD students are strongly encouraged to participate.

- Audrey Gerard (Oxford)
CD8 T cell collective behaviour in health and disease
Wed 11 Dec
CD8 T cell responses are key to eradicate virus, intracellular bacteria and cancer cells. A crucial feature of this response is to recruit T cells that will kill pathogen-infected cells or tumour cells while sparing healthy tissues. A multitude of CD8 T cell clones are recruited during an immune response, each with distinct T cell antigen receptors (TCR) with different affinity for their antigen. This clonal breadth is consistently observed despite factors favouring dominance of one or a few clones. How and why this diversity exists is unclear. Our central hypothesis is that T cells integrate individual responses into a collective response through direct communication to preserve T cell clonal breadth. We propose that T cells behave collectively in part through direct co-regulation through cytokines, allowing for lower-affinity clones to emerge and survive despite the competitive environment. I will discuss the consequences of direct T cell communication through the cytokine IFNγ on anti-bacterial responses, and how it impedes anti-tumour responses.
Current and forthcoming programs, conferences and workshops
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QuanTII



Jobs News
Recent seminars
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Oscar Rodriguez de Rivera Ortega (Kent)
Spatial and spatio-temporal models to understand ecological processes
Wed 23rd October 2019, 12:00-13:00 -
Systems Pharmacology and Pharmacometrics: How Mathematics, Statistics and Data Science Are Impacting Drug Discovery and Development
Paolo Vicini (Kymab Ltd)
18 October 2019 13.30
Modern drug discovery and development are rapidly becoming more reliant on rigorously quantitative approaches. In addition to established statistical testing and experimental design techniques, new approaches include pharmacometrics and systems pharmacology. Pharmacometrics is a collection of quantitative tools applied to clinical drug development and trial design, including mixed effect models for drug exposure and response, and covariate selection methods to quantify the impact of demographic, disease status and genetic variation on drug dosing, concentration and effect. Systems pharmacology is an evolution of systems biology, which seeks to harness quantitative, time-dependent pathway models to predict and quantify the effects of pharmacological interventions on downstream biomarkers, ultimately aiding rationalize target and drug candidate selection. This presentation will describe modern drug discovery and development pipelines and the role of pharmacometrics and systems pharmacology, highlighting in particular their interdisciplinary nature and the extent to which they borrow from other discipline, including mathematics, statistics and computer science.
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Damian Clancy (Heriot-Watt University, UK)
Approximating persistence time for SIS infections in heterogeneous populations
Wed 9th October 2019, 12:00-13:00 -
Prof. Uwe C Tauber (Department of Physics, Virginia Tech, USA)
Stochastic Spatial Predator-Prey Models
Wednesday 2nd October 2019, 12:00-13:00 -
A mathematical adventure in immunology Carmen Molina-París
International Centre for Theoretical Sciences, Bangalore. 7 July 2019 - Thursday 23rd May
Dr Maria Nowicka (Department of Pathology and Cell Biology, Columbia University, US)
Differential impact of self and environmental antigens on the ontogeny and maintenance of CD4+ T cell memory
Laboratory mice not exposed to overt infections nevertheless develop populations of circulating memory phenotype (MP) CD4+ T cells, presumably in response to environmental, commensal or self-antigens. The relative importance and timing of the forces that generate these populations remain unclear. We combine mathematical models with data from studies tracking the generation of CD4+ MP T cell subsets in mice of different ages, housed in facilities that differ in their `dirtiness'. We infer that both central and effector CD4+ MP T cell populations derive directly from naive CD4 T cells, and are heterogeneous in their rates of turnover. We also infer that early exposure to self and environmental antigens establishes persistent memory populations at levels determined largely, but not exclusively, by the dirtiness of the environment. After the first few weeks of life, however, these populations are continuously supplemented by new memory cells at rates that appear to be independent of environment, likely in response to self or ubiquitous commensal antigens.
Current and recent visitors




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Joe Gillard and Tom Laws
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Mario Castro works on mathematical models of systems where
fluctuations are relevant (cellular and receptor immunology) and on
pattern formation in spatially extended systems (from tumour cell
modelling to cauliflower morphogenesis or nano-structuring). The figure
shows comparisons of different mathematical models with real
experiments.
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Applications for research leading to a PhD are welcome. Please apply here, naming a potential project and supervisor. Sample projects are as follows:
- Analysis of high-throughput genomic data applied to diseases
such as cancer
Arief Gusnanto, Charles Taylor, Jeanine Houwing-Duistermaat
Statistical modelling of copy number alteration in cancer: using statistical methodology to discover patterns within the genomic copy number alteration profiles in cancer patients and how the pattern can be utilised for improved prediction of cancer survival and patients' clinical characteristics.
Genetic association in complex diseases and cancer: a collaboration with research groups in the School of Medicine to perform fine mapping around a previously identified location to identify genetic variants that are associated with cancer. - Mathematical immunology
Grant Lythe and Carmen Molina-París
Development of stochastic mathematical and computational models of the immune system in health and disease, of intra-cellular signalling to understand cell fate, and development of diffusive motion models of cell-cell interactions and receptor-ligand interactions. - Modelling biodiversity and ecosystems
Sandro Azaele
In this project you will be developing mathematical and computational tools for modelling spatial and temporal patterns in ecosystems, understanding their principal drivers across different scales, at population and community level. This will also help developing methodologies for upscaling biodiversity information from fine-scale sampling. - Modelling evolution on molecular and macroscopic scales
Mauro Mobilia
Inspired by recent results in biology, and also in behavioural sciences, we will combine notions of non-linear dynamics and evolutionary game together with the theory of stochastic processes and numerical simulations to investigate how noise and mobility influences the formation of coherent patterns. - Modelling of biomolecules
Oliver Harlen and Daniel Read, in collaboration with the Astbury Centre
Simulating the motions of large biomolecules such molecular motors and also soft colloidal particles, entities that are large enough to be beyond the scope of atomistic simulations (that model the motion of individual atoms), but small enough to be affected by thermal fluctuations (Brownian motion).
Recent programs, conferences and workshops
- Numerical analysis and applied mathematics Rhodes, Greece. 23-28 September 2019.
- Immunology of human diseases Santa Fe, NM. 28-31 Jul 2019.
- Society for Mathematical Biology annual conference Montréal. 21-26 July 2019
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Fluctuations, tipping points and emergence in eco-evolutionary dynamics
Leeds. 2-5 July 2019
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Mathematical and Statistical Explorations in Disease Modelling and Public Health
Bangalore, India. 1-11 July 2019
- Mathematical and statistical challenges in viral dynamic models: Ebola virus as a paradigm ICMS Edinburgh. 10-28 June 2019
- Systems Biology of Human Disease Berlin, Germany. 27-29 May
- Mathematical modelling in immunology Cambridge, 9-10 May 2019.
- Systems Immunology Cold Spring Harbour, 13-16 March 2019.
- T-cell memory: thinking outside the blood Trippenhuis KNAW, Amsterdam. 28-30 Nov2018
- Stochasticity and Control in the Dynamics and Diversity of Immune Repertoires Institut des Systèmes Complexes, Paris. 28-31 Oct 2018
- Advanced asymptotics of PDEs, modeling and extreme statistics and their applications to data analysis in cell biology Pisa, 15 September - 31 Oct 2018
- Frontiers in Basic Immunology NIH, Bethesda, MD 27-28 Sep 2018
- Systems Biology London, 3-4 Sep 2018
- PiNE
- Synthetic immunity Santa Fe, NM. 10-14 Jul 2018
- Quantitative Analysis of Immune Cell Migration and Spatial Processes in Health and Disease BIRS Oaxaca, 24-29 June 2018
- British Society for Immunology: Mathematical Modelling affinity group meeting Cambridge, 7-8 June 2018.
- Systems immunologySurrey, 27-28 Mar 2018.
- PiNE Leeds, 16 Feb 2018
- Modelling infectious diseases in the cell and host Singapore, 22-24 Jan 2018.
- Quantitative Principles in Biology at EBML Heidelberg, 2-4 Nov 2017
- Systems out of equilibrium Warwick. 27 Nov 2017
- Synthetic Immunity Santa Fe, NM. 10-14 July 2017.
- Network Dynamics and Structure Leeds, 25 July 2017.
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Climate Fluctuations and Non-equilibrium Statistical Mechanics: An Interdisciplinary Dialogue
10 July to 4 August at the MPIPKS in Dresden, Germany. -
Biostatistics and machine learning methods in omics research
The 34th Leeds Annual Statistical Research Workshop, joint with the EU MIMOmics network.
Leeds, Monday 26 - Wednesday 28 June 2017. - CoSyDy 26 Jun 2017 at Imperial College London.
- Theoretical and Experimental Immunology hosted by Microsoft Research Cambridge, 8-9 Jun 2017.
- Viral Dynamics: Past, Present and Future 5-7 May in Santa Fe, NM
- Modeling Viral Infections and Immunity 1-4 May in Estes Park CO.
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QuanTI closing meeting 19-21 April
- Probability in the North-East
University of Leeds, Thursday 27th April 2017
Programme- 10.00 - 10.30 Welcome and Coffee
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10.30 - 11.20 Corina Constantinescu (University of Liverpool)
Ruin probabilities in insurance models -
11.20 - 12.10 Ronnie Loeffen (University of Manchester)
Spectral representations for affine processes - 12.10 - 13.10 Lunch
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13.10 - 14.00 Vicky Henderson (University of Warwick)
Probability weighting, stop-loss and the disposition effect -
14.00 - 14.50 Adrian Pratt (Public Health England)
Back-calculation techniques and other models to inform mitigation strategies of non-transmissible acute infections - 14.50 - 15.20 Coffee Break
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15.20 - 16.10 Theodore Kypraios (University of Nottingham)
Recent developments in Bayesian non-parametric inference for epidemic models -
16.10 - 17.00 Antonio Gómez-Corral (Complutense University of Madrid, Spain)
On perturbation analysis of quasi-birth-death processes with applications to multi-type epidemic models
- Quantitative T cell Immunology Symposium
Hosted by AstraZeneca, Cancer Research UK Cambridge Institute, 21-22 Sep 2016
Wednesday 21st September- 14:35 Ton Schumacher, Netherlands Cancer Institute
T cell recognition and tumor resistance in human cancer - 15:35 Simon Dovedi Medimmune
Modelling the immunobiology of radiotherapy in cancer - 16:00
Ken Duffy, Hamilton Institute NUI Maynooth
T cell signal integration and an algebra of tree concatenation
- 09:30 Melania Barile, German Cancer Research Centre, Heidelberg
Quantifying the flux through haematopoiesis - 10:00 Sarah Teichmann, Wellcome Trust Sanger Institute
Understanding cellular heterogeneity - 11:10 Cathal Seoighe, NUI Galway
Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells - 12:00 Mariona Baliu Piqué, UMC Utrecht
Is long-lasting memory provided by short-lived cells? A closer look at CD8+ memory T cell dynamics
- Robustness, Adaptability and Critical Transitions in Living Systems
Amsterdam, The Netherlands. 19-22 Sep 2016- Systems Immunology Santa Fe. 27-28 Sep 2016.
- International Congress of Immunology Melbourne 21-26 Aug 2016
- Mathematical and Systems Immunology session at ECMTB Nottingham, 11-15 Jul 2016.
- Stochastic Dynamical Systems in Biology: Numerical Methods and Applications
Isaac Newton Institute, Cambridge. Jan-Jun 2016- Theoretical and experimental immunology Cambridge. 16-17 June 2016
- Big Data Analytics at Leeds
Wednesday 11 May 2016.- Be curious 19 Mar 2016
- Spring school on lymphocyte dynamics Unilever. 17-18 Mar 2016
- Single-cell biology EBI Hinxton. 8-10 Mar 2016
- Quantitative Immunology KITP Santa Barbara. 1-19 Feb 2016
- PiNE Probability in the North-East
Friday 6 November 2015
Complex stochastic systems arising in applications and interdisciplinary research
School of Mathematics, University of Leeds. Room: MALL 1
Programme 2015 - 13.30 -- 14.20 Carmen Molina-París (University of Leeds)
Stochastic modelling of T cell receptor clonotype competition - 14.20 -- 15.10 Malwina Luczak (Queen Mary, University of London)
SIR epidemics on random graphs with a given degree sequence - 15.30 -- 16.20 Anton Camacho (London School of Hygiene and Tropical Medicine)
The impact of dynamical modelling on public-health decisions made during the 2013-2015 Ebola outbreak - 16.20 -- 17.10 Alexandre Veretennikov (University of Leeds)
On convergence in Erlang-Sevastyanov queueing systems and in reliability theory
- Numerical Modeling in Evolutionary Problems: perspectives and applications Salerno, 26-27 Nov 2015
- Workshop on Physics of Living Systems San Servolo island, Venice, Italy. 16-19 September, 2015
- Stochastic Single-Cell Dynamics in Immunology Amsterdam, 17-19 June 2015
- British Society for Immunology: Mathematical Modelling Microsoft Research Cambridge. 4-5 Jun 2015
- Mathematics for health and disease ICMS Edinburgh. 13-17 Apr 2015
- LIVING -- Robustness, adaptability and critical transition in living systems
Satellite conference at the annual European Conference on Complex Systems (ECCS14)- Stochastic modelling and immunology Ecology, Evolution and Dynamics of Dengue and other Related Diseases Arizona, 4-5 Aug 2014
- BSI Mathematical Modelling, Microsoft Research Cambridge, 19-20 May 2014.
- Novel Applications of Statistical Mechanics Boston, 10-11 may 2014
- Dynamics of Active Matter Imperial College London, Wednesday 7th May .
- Quantitative immunology Les Houches, France. 9-14 Mar 2014
- Systems Approaches in Immunology Santa Fe, USA. 10-11 Jan 2014
- Mathematical modelling affinity group session at the BSI congress 2013
- Modelling the Complexity of the Immune System Barcelona, 16-20 September 2013.
- Stochastic, statistical and computational approaches to Immunology
International Centre for Mathematical Sciences, Edinburgh. 22-26 July 2013- Complexity Systems Dynamics Leeds, 5 June 2013.
- Mathematical and computational modelling in immunology
Cambridge, 8-9 May 2013.- Simulation Models of Infectious Disease Transmission and Control Processes
Antwerp, 17-18 April.- BAMC 2013
- Systems biology of T cells Baeza, Spain. 21-24 Oct 2012
- Multiscale physics of lymphocyte development
Max Planck Institute for the Physics of Complex Systems,
Dresden, Germany. 5-31 Aug 2012- New Statistics and Modern Natural Sciences Leeds, 3-5 Jul 2012
- Theoretical and experimental immunology 25-26 Jun 2012 poster
- Synchronisation in Complex Systems 11 May, London.
- Computational Immunology
WEHI Melbourne, 11-13 Apr 2012- Evolution and diversity in complex systems Leeds, 2 Mar 2012.
- Theoretical and Experimental Immunology IISc Bangalore, 16 August 2011 Abstracts
- Theoretical immunology network meeting on 16 May 2011 at the University of Leeds
- Imaging, Interpretation and Modeling in Modern Immunology Banff, 10-15 April 2011
- Physics of Immunity: Complexity Approach 4-8 April 2011, Max-Planck-Institut Dresden
- Experimental and theoretical immunology on 18 March 2011 at the University of Leeds
- Experimental and theoretical immunology in the real world at the University of Leeds 10 January 2011.
- Yorkshire Immunology Group "Pattern recognition receptors in the immune system" 24 November 2010, Leeds Institute of Molecular Medicine, University of Leeds
- Movement in Models of Mathematical Biology 15 November 2010, University of Warwick
- Stochastic dynamics and applications Monday 18 October 2010, University of Leeds
- Immunology, Imaging and Modelling Network Summer School at the University of Leeds 13-17 September 2010.
- High-throughput Sequencing, Proteins and Statistics (29th Leeds Annual Statistical Research Workshop) 6th-8th July 2010
- Probability in the North-East