Mathematical Modelling with Multidisciplinary Applications (M3A)
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Computing Higher Leray–Serre Spectral Sequences of Towers of Fibrations
(20201027)The higher Leray–Serre spectral sequence associated with a tower of fibrations represents a generalization of the classical Leray–Serre spectral sequence of a fibration. In this work, we present algorithms to compute higher ... 
Critical fluctuations in epidemic models explain COVID‑19 post‑lockdown dynamics
(20210706)As the COVID19 pandemic progressed, research on mathematical modeling became imperative and very influential to understand the epidemiological dynamics of disease spreading. The momentary reproduction ratio r(t) of an ... 
A spacefractional bidomain framework for cardiac electrophysiology: 1D alternans dynamics
(2021)Cardiac electrophysiology modeling deals with a complex network of excitable cells forming an intricate syncytium: the heart. The electrical activity of the heart shows recurrent spatial patterns of activation, known as ... 
Variance Reduction with ArrayRQMC for TauLeaping Simulation of Stochastic Biological and Chemical Reaction Networks
(2021)We explore the use of ArrayRQMC, a randomized quasiMonte Carlo method designed for the simulation of Markov chains, to reduce the variance when simulating stochastic biological or chemical reaction networks with ... 
Targeting Impaired Antimicrobial Immunity in the Brain for the Treatment of Alzheimer’s Disease
(20210504)Alzheimer’s disease (AD) is the most common form of dementia and aging is the most common risk factor for developing the disease. The etiology of AD is not known but AD may be considered as a clinical syndrome with multiple ... 
Spikeadding and resetinduced canard cycles in adaptive integrate and fire models
(20210503)We study a class of planar integrate and fire (IF) models called adaptive integrate and fire (AIF) models, which possesses an adaptation vari able on top of membrane potential, and whose subthreshold dynamics is piece ... 
Predictive engineering and optimization of tryptophan metabolism in yeast through a combination of mechanistic and machine learning models
(2019)In combination with advanced mechanistic modeling and the generation of highquality multidimensional data sets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show ... 
Chemoinformaticguided engineering of polyketide synthases
(2019)Polyketide synthase (PKS) engineering is an attractive method to generate new molecules such as commodity, fine and specialty chemicals. A central challenge in PKS design is replacing a partially reductive module with a ... 
ART: A machine learning Automated Recommendation Tool for synthetic biology
(2019)Biology has changed radically in the last two decades, transitioning from a descriptive science into a design science. Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable ... 
Mathematical models for glioma growth and migration inside the brain
(202101)Gliomas are the most prevalent, aggressive, and invasive subtype of primary brain tumors, characterized by rapid cell proliferation and great infiltration capacity. De spite the advances of clinical research, these tumors ... 
Inflection, Canards and Folded Singularities in Excitable Systems: Application to a 3D FitzHugh–Nagumo Model
(20200907)Specific kinds of physical and biological systems exhibit complex MixedMode Oscillations mediated by foldedsingularity canards in the context of slowfast models. The present manuscript revisits these systems, specifically ... 
Why we should use topological data analysis in ageing: Towards defining the “topological shape of ageing”
(20201027)Living systems are subject to the arrow of time; from birth, they undergo complex transformations (selforganization) in a constant battle for survival, but inevitably ageing and disease trap them to death. Can ageing be ... 
Targeting Infectious Agents as a Therapeutic Strategy in Alzheimer’s Disease
(20200526)Alzheimer’s disease (AD) is the most prevalent dementia in the world. Its cause(s) are presently largely unknown. The most common explanation for AD, now, is the amyloid cascade hypothesis, which states that the cause of ... 
The Impact of Serotype CrossProtection on Vaccine Trials: DENVax as a Case Study
(202011)There is a growing public health need for effective preventive interventions against dengue, and a safe, effective and affordable dengue vaccine against the four serotypes would be a significant achievement for disease ... 
Modeling COVID19: Challenges and results
(202010)Weird times we are living in. While lots of technological, medical and scientific advances are generated in a short period of time, we are now fighting a pandemic, trying to stop the spread of a new virus that has not only ... 
SHAR and effective SIR models: from dengue fever toy models to a COVID19 fully parametrized SHARUCD framework
(2020)We review basic models of severe/hospitalized and mild/asymptomatic infection spreading (with classes of susceptibles S, hopsitalized H, asymptomatic A and recovered R, hence SHARmodels) and develop the notion of comparing ... 
Reproduction ratio and growth rates: Measures for an unfolding pandemic
(202005)The initial exponential growth rate of an epidemic is an important measure that follows directly from data at hand, commonly used to infer the basic reproduction number. As the growth rates λ(t) of tested positive COVID19 ... 
Conditionspecific mortality risk can explain differences in COVID19 case fatality ratios around the globe
(202009)Objectives With COVID19 infections resulting in death according to a hierarchy of risks, with age and preexisting health conditions enhancing disease severity, the objective of this study is to estimate the conditionspecific ... 
Ethics of a partially effective dengue vaccine: Lessons from the Philippines
(202007)Dengvaxia, a chimeric yellow fever tetravalent dengue vaccine developed by SanofiPasteur is widely licensed in dengueendemic countries. In a large cohort study Dengvaxia was found to partially protect children who had ... 
Modelling COVID 19 in the Basque Country from introduction to control measure response
(202010)In March 2020, a multidisciplinary task force (so‐called Basque Modelling Task Force, BMTF) was created to assist the Basque health managers and Government during the COVID‐19 responses. BMTF is a modelling team, working ...