Mathematical Biology and Medicine
Jobs News
- Research Fellow in Mathematical Modelling of Infection University of Leeds, part of a European consortium.
Seminars

- 12 Dec 2023 (3pm, Roger Stevens LT8)
Giulia Belluccini Los Alamos
Mathematical models of hepatitis B infection Nearly 300 million of people are chronically infected with hepatitis B virus (HBV). Currently no cure has been developed, leading to more than 800,000 HBV-related deaths annually. The focus of therapies is on eliminating the template for HBV replication, i.e. covalently closed circular DNA (cccDNA). However, HBV surface antigens (HBsAg) derive also from integrated DNA (iDNA). The presence of HBsAg activates the immune response, which leads to an inflammatory state and eventually to liver damage. Our collaborators at the Viral Hepatitis Center of John Hopkins University considered a cohort of 10 HBV-HIV co-infected participants on nucleos(t)ide analogue (NUC) therapy for a short or long time (from a few months to almost 12 years). Liver biopsies were obtained from each individual at 2 time points and single cell analysis was performed, measuring the genetic material inside each cell. First, we quantify the decay/growth of the number of cells with viral genetic material, and its timescale, with the aim of understanding how NUC therapy affects this dynamics. Then, we build a stochastic model that accounts for hepatocytes spatial distribution to study the distribution of infected cells and how the viral genetic material accumulates inside each cell.- 12 Dec 2023 (12 noon, Roger Stevens LT14) Luís Hernandez-Navarro Leeds
Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance
The rise of antimicrobial resistance (AMR) is a global threat responsible for millions of deaths, and we therefore have a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate AMR cells. The inactivation of antimicrobials by resistant microbes can often be viewed as a cooperative behaviour, leading to the long-lived coexistence of resistant and sensitive cells in static environments. In this talk, I will discuss how this picture is greatly altered in more realistic, volatile environments, where microbial communities commonly evolve. By combining analytical and computational means, we characterise the environmental conditions for the long-lived coexistence or extinction of each type of cells, and we unveil a novel fluctuation-driven AMR eradication mechanism, where resistant microbes experience bottlenecks leading to extinction.- 7 Dec 2023 Wasiur Khuda Bukhsh Nottingham
Approximations and parameter inference for epidemic models
In this presentation, I will talk about a recently developed method, called the dynamical survival analysis (DSA), for parameter inference of models of infectious disease epidemiology. In a nutshell, the DSA method allows us to interpret mean-filed ordinary or partial differential equations for proportions of individuals in different compartments as probabilistic quantities, such as the survival function, density etc, by virtue of an application of the Sellke construction. I will provide example applications to both network-based and mass-action models. I will discuss when those two types of models are equivalent in some precise sense, and when one class of models can be approximated by another one, e.g., an SEIR model by an SIR model.- 16 Nov 2023 Adrianne Jenner QUT
Using virtual clinical trials to improve our understanding of diseases
Mathematical and computational techniques can improve our understanding of diseases. In this talk, I'll present ways in which data from cancer patients can be combined with mathematical modelling and used to improve cancer treatments.
Given the variability in individual responses to cancer treatments, agent-based modelling has been a useful technique for accurately capturing cellular behaviours that may lead to stochasticity in patient outcomes. Using a hybrid agent-based model and partial differential equation system, we developed a model for brain cancer (glioblastoma) growth informed by ex-vivo patient samples. Extending the model to capture patient treatment with an oncolytic virus rQNestin, we used our model to propose reasons for treatment failure, which was later confirmed with further patient samples. More recently, we extended this model to investigate the effectiveness of combination treatments (chemotherapy, virotherapy and immunotherapy) informed by individual patient imaging mass cytometry.
This talk hopes to provide examples of ways mathematical and computational modelling can be used to run ``virtual'' clinical trials with the goal of obtaining more effective treatments for diseases.- 26 Oct 2023 Helena Stage Bristol
The role of superinfection in evolutionary epidemiology
The study of evolutionary epidemiology is vital to understand and control the spread of e.g. anti-microbial resistance, but poses serious challenges due to the multi-scale presence of the forces driving pathogen evolution. For example, selection for high within-host fitness may reduce between-host transmission. Time-since-infection models are much more flexible than ODEs in capturing aspects of both within- and between-host scales, but studying the feedback loops between such scales remains non-trivial. We will discuss how a general theory for time-since-infection models that allow for superinfection (e.g. multi-strain systems with partial cross-immunity) can capture recent infection history and quantify the system's steady states. This will be explored through a series of toy models which admit the same qualitative features as are observed in more complex model descriptions. We will distinguish between the cases when superinfection of the host facilitates the coexistence of two (or more) infections that interact synergistically by fuelling each other's spread (syndemic), and when these infections hinder each other.- 19 Oct 2023 Katie Link Pfizer
Mathematical modeling of extended-release pre-exposure prophylasis and drug-resistant HIV\em>
The pharmacologic tail of long-acting cabotegravir (CAB-LA), an injectable Pre-Exposure Prophylaxis (PrEP), allows for months-long intervals between injections, but it may facilitate the emergence of drug-resistant human immunodeficiency virus (HIV) strains during the acute infection stage. In this study, we present a within-host, mechanistic ordinary differential equation model of the HIV latency and infection cycle in CD4+ T cells to investigate the impact of CAB-LA on drug-resistant mutations in both humans and macaques. We develop a pharmacokinetic/pharmacodynamic model for CAB-LA to correlate the inhibitory drug response with the drug concentration in plasma. After validating our model against experimental results, we conduct in-silico trials. First, we separately administer CAB-LA to the in-silico macaque and human patients prior to and post-simian-human immunodeficiency virus (SHIV)/HIV exposure, to observe SHIV and HIV infectivity dynamics, respectively. Although the model does not incorporate a mechanism for CAB-LA-induced HIV mutations, we analyze the outcomes when mutations occur naturally. Our findings suggest that CAB-LA may enhance the growth of drug-resistant strains over the wild-type strains during the acute stage. The in-silico trials demonstrate that the effectiveness of CAB-LA against mutations and the fitness of the drug-resistant strain to infect T cells determine the course of the mutated strain.- 5 Oct 2023 Simone De Reggi University of Udine
A journey through structured populations: stability analysis of infinite-dimensional dynamical systems and relevant numerics
Population dynamics are often described by means of structures, i.e., variables representing individual traits (e.g., age, size, immunity, spatial position). These models can be formulated as (integro-)partial differential equations which, as a result, lead to deal with abstract evolution equations. In this talk I will present some basic concepts on continuously structured populations, starting from the well known McKendrick-von Foerster equation. I will introduce the basic tools for the stability analysis of infinite-dimensional dynamical systems by drawing a parallel with well-known approaches for Ordinary Differential Equations (including the concept of the basic reproduction number). In the last part I will discuss some numerical methods for the stability analysis of equilibria. Numerical results attesting the validity of the approaches and applications to models from epidemiology and ecology are presented.- 21 Sep 2023 Mohit Kumar Jolly IISc Bangalore
Design principles of decision-making networks in cancer cell plasticity and T cell differentiation
Decoding the emergent dynamics of cellular differentiation is crucial in understanding how cells make decisions during development and modulate those decisions for cellular reprogramming. Decision-making is often driven by complex interconnected networks, whose design principles remain poorly understood. I will present examples from our work on CD4+ T-cell differentiation into Th1, Th2, Th17 and hybrid states, as well as from cancer cell plasticity during metastasis. These networks exhibit multistability, thus enabling cells to reversibly alter their phenotypes. Moreover, the specific dynamical features seen in these networks are largely unique to them, indicating evolutionary selection of these networks in enabling multicellularity. Analysis of transcriptomic data analysis from relevant datasets validates our model predictions, and highlight how an integration of dynamical modeling with transcriptomic data can quantitatively map the cellular decision-making landscape.- 11 Sep 2023 Chang Liu Maynooth
PACESS: Practical AI-based Cell Extraction and Spatial Statistics for large 3D biological images
Efficient methodologies to fully extract and analyse large datasets remain the Achilles heels of 3D tissue imaging. Here we present PACESS a pipeline for large-scale data extraction and spatial statistical analysis from 3D biological images. First, using 3D object detection neural networks trained on annotated 2D data, we identify and classify the location of hundreds of thousands of cells contained in large biological images. Then, we introduce a series of statistical techniques tailored to work with spatial data, resulting in a 3D statistical map of the tissue from which multi-cellular interactions can be clearly understood. As illustration of the power of this new approach, we apply this analysis pipeline to an organ known to have a complex and still poorly understood cellular structure: the bone marrow. The analysis reveals coherent, useful biological information on multiple cell population interactions. This novel and powerful spatial analysis pipeline can be broadly used to unravel complex multi-cellular interaction towards unlocking tissue complexity.- 18 May 2023 Chris Overton Liverpool
Modelling the 2022 mpox outbreak
During the 2022 mpox outbreak, modelling has provided support to policy makers and the incident management team. In this talk, I will give an overview of some of the key modelling work. Firstly, we consider real-time estimation of epidemiological parameters. Such estimation is challenging due to right-truncation and interval-censoring in the real-time data. Through this, we provided the first evidence of pre-symptomatic transmission of mpox. This will be followed by an overview of novel nowcasting models that were developed during the outbreak. With substantial delays between infections occurring and being reported, the epidemic curve suffered from substantial backfilling. Nowcasting methods attempt to account for this backfilling, allowing the epidemic curve to be evaluated in real-time. This is essential for reliable surveillance and timely decision making.- 17 May Philip Maini Oxford
Modelling collective cell movement in development and disease
Collective movement is ubiquitous in nature, occurring across a vast range of scales, from whales to bacteria. This talk will review some of our work on collective movement at the cell level. It will include (i) a novel partial differential equation (PDE) model derived from consideration of the classical snail-trail model for angiogenesis; (ii) a PDE model that views cancer cell invasion as a co-operative phenomenon; (iii) a hybrid agent-based model for cranial neural crest migration which, coupled with experiments, has led to new biological insights on this phenomenon.- 11 May Eva Deinum Wageningen
Zebrastripes for thirsty plants: the same story twice over?
The plant cell wall is a versatile material that can meet a wide range of mechanical requirements. The banded patterns in protoxylem form a striking example, enabling these vessels withstand substantial negative pressure and allow for extension at the same time. The required anisotropic material properties largely derive from the location and orientation of the constituting cellulose microfibrils. These, in turn are deposited along the cortical microtubule cytoskeleton. So, using the case of protoxylem as a model system for complex cell wall patterns, the question becomes how cortical microtubules can self-organize into banded patterns. This happens in interaction with another well-known patterning system, the ROP proteins.
We address this interaction from both sides: how can dynamic microtubules collectively adjust to a predefined ROP pattern and how can an –implicitly microtubule derived– field of diffusion anisotropy orient and change ROP patterns?
The ROPs can be described as a reaction-diffusion system, which we study using PDEs, complemented with an ODE model of slowly interacting peaks/clusters. The microtubule part of the work extends a long tradition of combined analytical and stochastic simulation approaches, with a close link to experimental quantification. Whereas the simulations are more easily adapted to relevant biological detail, the analytical foundation aids in efficient investigation and interpretation.
Despite the very different modelling frameworks and proteins involved, our work on ROP proteins provides critical insights into a problem in the stochastic microtubule simulations: there is a deep link between the stable coexistence of multiple clusters of active ROP and maintaining a sufficiently homogeneous distribution of microtubules across the cell cortex.- 4 May Samuel Relton Leeds
Prediction Modelling in the Healthcare System: From Patient to Production
In this talk we'll go through the full production cycle of building statistical models that are actually used by clinicians within the NHS. Most modelling work takes place using pre-cleaned data and doesn't need to be production-ready, so there are many extra issues to consider when going the extra mile. In particular we'll discuss the modelling for the electronic frailty index+ (eFI+) work which will imminently go live within the SystmOne and EMIS GP systems (totalling over 30M patients). In addition to the usual modelling issues we'll touch on various sources of bias, robust external validation, MHRA registration, and patient/stakeholder engagement that all need to be taken care of to make direct clinical impact on the frontline. - 12 Dec 2023 (12 noon, Roger Stevens LT14) Luís Hernandez-Navarro Leeds
Recent theses

Flavia Feliciangeli Stochastic compartmental models and CD8+ T cell exhaustion Sep 2023 ![]() |
Léa Sta Mathematical models of cell signalling in heterogeneous populations Mar 2023 ![]() |
Daniel Luque Duque Network models of T cell receptor repertoires, cross-reactivity, and viral infection Mar 2023 ![]() |
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Bevelynn Williams Mechanistic intracellular and within-host models of bacterial and viral infections Feb 2023 ![]() |
Giulia Belluccini Stochastic models of cell population dynamics and tick-borne virus transmission Feb 2023 ![]() |
Polly-Anne Jeffrey Mathematical Modelling of Cellular Receptor-Ligand Dynamics Oct 2021 ![]() |
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Recent programs, conferences and workshops
ECMTB 2022 Immunoctoberfest 2022![]() |
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- Sensing and Signaling in Immune Systems: Mathematics meets Biology BIRS Banff, Feb 2022
- NEPA 2020-21
- PiNEJan2021
- PiNE 10-14 Sep 2020
- Society for mathematical biology 17-20 Aug 2020
- British Early Career Mathematicians' Colloquium (virtual colloquium) 14-15 Jul 2020
- Mathematical and Computational Biomedicine Oaxaca. 3-8 Nov 2019
- Cancer and Inflammation: From Micro to Macro NIH. 17-18 Oct 2019
- Viral dynamics Paris, France. 21-23 Oct 2019.
- The mathematics of biology and medicine Leeds. 30 Sep 2019
- Numerical analysis and applied mathematics Rhodes, Greece. 23-28 Sep 2019.
- Stochastic modelling in Health and Disease Leeds. 11-13 Sep 2019
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50 Years of Stochastic Processes at UCSD: a symposium in honor of Katja Lindenberg
15-16 Aug 2019.
- Immunology of human diseases Santa Fe, NM. 28-31 Jul 2019.
- Society for Mathematical Biology annual conference Montréal. 21-26 Jul 2019
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Fluctuations, tipping points and emergence in eco-evolutionary dynamics
Leeds. 2-5 Jul 2019
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Mathematical and Statistical Explorations in Disease Modelling and Public Health
Bangalore, India. 1-11 Jul 2019
- Mathematical and statistical challenges in viral dynamic models: Ebola virus as a paradigm ICMS Edinburgh. 10-28 Jun 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 Mar 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 Durham, 12 Sep 2018
- 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 Jun 2018
- British Society for Immunology: Mathematical Modelling affinity group meeting Cambridge, 7-8 Jun 2018.
- Systems immunology Surrey, 27-28 Mar 2018.
- Host-pathogen dynamics Ohio, 19-23 Feb 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 Jul 2017.
- Network Dynamics and Structure Leeds, 25 Jul 2017.
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Climate Fluctuations and Non-equilibrium Statistical Mechanics: An Interdisciplinary Dialogue
10 Jul to 4 Aug 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 Jun 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 2017 in Santa Fe, NM
- Modeling Viral Infections and Immunity 1-4 May 2017
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QuanTI closing meeting 19-21 Apr 2017
- Probability in the North-East
University of Leeds, Thursday 27th Apr 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
- Lessons to be learnt from mathematical models of T cells University of Glasgow, 17 Nov, 2016.
- 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 Jul 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 Apr- 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 Aug 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 Apr 2011
- Physics of Immunity: Complexity Approach 4-8 Apr 2011, Max-Planck-Institut Dresden
- Experimental and theoretical immunology on 18 Mar 2011 at the University of Leeds
- Experimental and theoretical immunology in the real world at the University of Leeds 10 Jan 2011.
- Yorkshire Immunology Group "Pattern recognition receptors in the immune system" 24 Nov 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 Jul 2010
- Probability in the North-East