European Communications in Mathematical and Theoretical Biology 2019 · No. 22

European teams in mathematical biology

In each issue we present some of the Europeangroups working in the field of mathematical bi-ology. We try to cover di↵erent subjects andgeography. If you think some group should beportrayed in the next issue, please let us know.Enjoy!

StAMBio University of St AndrewsMathematical Biology Group

The research group is based within the Schoolof Mathematics and Statistics of the Univer-sity of St Andrews. We are an interdisciplinarygroup of mathematicians who develop, analyseand simulate mathematical models to study thekey mechanisms that underpin the dynamics ofbiological systems. Our current research inter-ests include multiscale models of cancer growthand treatment, models of infectious diseases andimmune competition, biological pattern forma-tion and morphogenesis, free boundary prob-lems in biology, stochastic models of signallingand gene regulatory networks, evolutionary dy-namics in structured populations and mathe-matical models arising from theoretical ecology.

At present the group consists of five membersof sta↵, four postdoctoral fellows and three PhDstudents, whose research profiles are briefly de-scribed below.

STAFF MEMBERS

Mark A. J. Chaplain (Head of the Group)My main area of research is

Mathematical Oncology theapplication of mathematicalmodelling to cancer growthand treatment. I am inter-ested in all aspects of can-cer modelling gene regulatory

networks, avascular growth, the immune re-sponse to cancer, angiogenesis, invasion andmetastasis, multiscale modelling techniques,chemotherapy and radiotherapy treatment. Iam also interested in theoretical ecology, specif-ically host-parasitoid systems.

Jochen Kursawe

I develop and apply math-ematical and computationalmethodology to understandembryonic development. I col-laborate with experimental bi-ologists to research how in-dividual cells make decisions

(e.g. to divide or di↵erentiate) and how mul-tiple cells interact to form healthy and viabletissues. My work includes analysing the dy-namics of gene regulatory interactions and mod-elling mechanics of single cells and cell-cell in-teractions. My aim is to decipher fundamentalmechanisms that underlie the robustness of em-bryonic patterning and morphogenesis.

Tommaso Lorenzi

The focus of my researchis on mathematical models ofcomplex living systems for-mulated in terms of nonlinearpartial di↵erential equationsand corresponding stochas-tic individual-based models.

These models can support a deeper theoreticalunderstanding of the mechanisms underlyinga variety of emergent behaviours observedin nature. Moreover, they pose a series ofanalytical and numerical challenges whichmake them interesting mathematical objectsper se.

Giorgos Minas

I study noisy, dynamic andcomplex biological processes,such as gene regulation, sig-nalling and development. Thetarget is to develop an in-tegrated, multi-level approachthat combines stochastic mod-

elling and mathematical analysis with compu-tational, statistical and machine learning meth-ods. The ultimate goal is to answer fundamen-tal biological questions such as how cells adaptto multi-dimensional signals received in theirever-changing environments.

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Nikolaos SfakianakisThe focus of my research is

the multiscale study of cancerand spans from lamellipodiumdynamics and live cell motil-ity, to cancer growth and tissueformation, and to the role ofstemness in health and disease.

The tools I employ come from several (sub-)fields of Applied Mathematics: modelling, sci-entific computing, numerical analysis, and anal-ysis of partial di↵erential equations.

POSTDOCTORAL FELLOWS

Ruth BownessI am a Medical Research

Council Fellow and Academyof Medical Sciences Spring-board Award Holder. My re-search involves using di↵eren-tial equations and individual-based models to describe infec-

tious disease spread within the human body,and to simulate and compare treatment strate-gies. My current projects include multiscalewithin-host modelling of tuberculosis diseaseprogression and treatment, and within-hostmodelling of antimicrobial resistant infections.

Sara HamisAs part of an interdisci-

plinary team with researchersat Ninewells hospital, I amcurrently working on develop-ing new paradigms for over-coming drug resistance in can-cer. Mathematical and compu-

tational biology are my main research interests,and I work with multiscale, hybrid individual-based models.

Fiona R. MacfarlaneThe main focus of my re-

search is the development ofindividual-based models de-scribing tumour-immune com-petition and tumour growth.More recently, I have been

working on the derivationof partial di↵erential equation models fromstochastic individual-based models of cell pop-ulations.

Cicely K. MacnamaraCurrently I am working as

part of SofTMech an EPSRC-funded centre for Mathemati-cal Sciences in Healthcare. Iwork on an individual-based,force-based model for tumourgrowth and the interactions

with the extra-cellular matrix. My other re-search interests include cancer-immune dynam-ics; intracellular dynamics, including gene reg-ulatory networks and cancer invasion.

PHD STUDENTS

Linnea C. FranssenI am an EPSRC-funded PhD

student in my final year.I focus on modelling cancercell invasion and secondarymetastatic spread. For this,I use spatially explicit hybridmodelling techniques to ac-

count for the evolution of individual cancer cellsand connected clusters of cancer cells, and forthe transition between those states. I havedeveloped the first cell-based spatially explicitframework of metastatic spread and currentlywork on a 3D in silico model that captures can-cer cell invasion observed in in vitro assays.

Chiara VillaI started my PhD in 2018,

under the supervision ofMark Chaplain and TommasoLorenzi. I am originally fromItaly and I studied in St An-drews for an MMath degree inApplied Mathematics. I work

on continuous models of phenotypic selectionin vascular tumours, and mechanochemicalmodels of pattern formation and tumourinvasion.

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European Communications in Mathematical and Theoretical Biology 2019 · No. 22

Yunchen XiaoI started my PhD in 2018,

under the supervision of MarkChaplain and Len Thomas(Statistics). My interestin Mathematical Biology be-gan during a summer re-search internship with Tom-

maso Lorenzi. My Masters dissertation wasentitled ’Mathematical models of cell dynam-ics in acute myeloid leukaemia’. My currentresearch interests are: parameterising mathe-matical models of tumour-induced angiogenesisand tumour invasion & metastasis, along withparameter estimations and selecting amongcompeting models using Approximate BayesianComputation methods.

More about our research and possible PhDand postdoc opportunities can be found athttp://www.mcs.st-and.ac.uk/mathbiol/

MAMBA (Inria, CNRS and SorbonneUniversite)

MAMBA is not only a fast moving ven-omous snake but also the name of our team,an acronym for “Modelling and Analysis forMedical and Biological Applications”. Locatedboth in the Jacques-Louis Lions Laboratory ofSorbonne Universite and in the Inria Paris Re-search Centre, our team gathers 8 permanentresearchers, and 20 post-doctoral and Ph.Dstudents. It aims at developing mathemat-ical models, simulations and numerical algo-rithms to solve problems from life sciences in-volving dynamics of biological systems such asprotein intracellular spatio-temporal dynamics,cell motion, early embryonic development, tis-sue growth and regeneration, cancer evolution,healthy and tumour growth control by pharma-cological means, protein polymerisation occur-ring in neurodegenerative disorders and controlof mosquito populations (to prevent epidemicsof vector-borne diseases like zika or dengue).It is the evolution of the BANG project-team,headed by Benoıt Perthame during 11 years(2003-2013).

Data and image analysis, statistical, ODE,PDE, SDE, stochastic processes and agent-based approaches are used either individuallyor in combination, with a strong focus on PDEanalysis and agent-based approaches. In orderto develop a unified framework to describe thesystems of interest at di↵erent scales (micro-scopic to macroscopic scales), a large activityof the team consists in investigating the linkbetween these di↵erent models.

Many projects within our team are guidedor directly address questions or applicationsin biology, biotechnology or medicine and arecarried out in close collaboration with spe-cialists in biology or medicine. In this con-text, our ongoing collaborations with biolo-gists and physicians, the collaboration withSt Antoine Hospital within the Institut Uni-versitaire de Cancerologie of Sorbonne Uni-versite and Hopital Paul Brousse (IUC, LuisAlmeida, Jean Clairambault, Dirk Drasdo,Benoıt Perthame) and close experiment-theorycollaborations characterized by associated re-searchers at the Leibniz Institute for Work-ing Environment and Human Factors in Dort-mund (Dirk Drasdo), Germany, are key pointsin our project. A very strong link has alsobeen developed with the Wolfgang Pauli Insti-tute in Vienna, especially with C. Schmeiserand his collaborators (Marie Doumic, BenoıtPerthame, Diane Peurichard), through an Inria“associated team”, a format to promote closeinteractions and exchanges with other institu-tions. The mosquito population control studies(Luis Almeida, Pierre-Alexandre Bliman) arealso developed in close collaboration with lifescientists from Institut Louis Malarde (FrenchPolynesia), Instituto de Medicina Tropical Pe-dro Kouri (Cuba) and Instituto Oswaldo Cruz(Brazil).

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Our main objective is the creation, inves-tigation and transfer of new models, meth-ods and algorithms. In selected cases softwaredevelopment as that of CellSys and TiQuant(Dirk Drasdo and Stefan Hoehme) is performed.More frequently, the team develops “proof ofconcept” numerical codes in order to test theadequacy of our models to experimental biol-ogy.

Some very recent research examples:

Cancer:

• Proposal of strategical principles in cancertherapeutics using asymptotic analysis andoptimal control for cell population dynamicmodels. Ref.: C. Pouchol, J. Clairambault,A. Lorz, E. Trlat, JMPA, 2018.

• Quantitative cell-based model predicts me-chanical stress response of growing tumorspheroids over various growth conditionsand cell lines, Ref: P Van Liedekerke, JNeitsch, T Johann, K Alessandri, P Nas-soy, D. Drasdo. PLoS Comp Biol, 2019.

Protein polymerisation:

• On the asymptotic distribution of nucle-ation times of polymerization processes.Ref : P. Robert and W. Sun, SIAM AppMath., 2019.

• A new variant of the Becker-Doring sys-tem, to model sustained oscillations ob-served in protein fibrils depolymerisationexperiments, Ref: M. Doumic, K. Fellner,M. Mezache, H. Rezaei, JTB, 2019.

Vector-borne diseases:

• Implementation of control strategies forsterile insect techniques, P.-A. Bliman,D. Cardona-Salgado, Y. Dumont, O.Vasilieva, Math Biosci., 2019.

• Preventing epidemics of vector-borne dis-eases (like dengue or zika) thanks to thecontrol of mosquito populations, Ref: L.Almeida, Y. Privat, M. Strugarek, N.Vauchelet SIAM J. Math. Anal., 2019

Cell multiscale models:

• Particle interactions mediated by dynam-ical networks: assessment of macroscopicdescriptions, Ref : J. Barre, J.A. Carrillo,P. Degond, E. Zatorska, D. Peurichard,Journal of Nonlinear Science, 2017 (+ il-lustration)

• Traveling wave and aggregation in a flux-limited Keller-Segel model, V Calvez, BPerthame, S Yasuda, 2019.

• Developing a new mathematical frameworkto model reaction-di↵usion in developingorganisms: Ref : F. Rossi, N. PouradierDuteil, N. Yakoby, B. Piccoli, Proc. 2016IEEE CDC, 2016.

Photos from left to right then up to bottom: LuisAlmeida, Federica Bubba, Marie Doumic, GaetanVignoud, Jean Clairambault, Jieling Zhao, MarkusSchmidtchen, Dirk Drasdo, Julia Delacour, Math-ieu Mezache, Cecile della Valle, Pierre-AlexandreBliman, Adrien Ellis, Alexandre Poulain, Nas-tassia Pouradier-Duteil, Philippe Robert, BenoıtPerthame, Xinran Ruan, Valeria Caliaro, DianePeurichard

Other members: Jules Dichamp, Florian Joly,

Noemi David, Jorge Estrada Hernandez, Emma

Leschiera, Jesus Bellver Arnau, Giorgia Ciavolella,

Gisselle Estrada Rodriguez.

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