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			</style>[an error occurred while processing this directive]<div class="content-width"><ol class="breadcrumb text-uppercase"><li><a href="/">Home</a></li><li><a href="/aboutus/">About Us</a></li><li><a href="/people/">People</a></li><li><a href="/people/faculty.html">Faculty</a></li><li><a href="/people/Joe.Pitt-Francis"><span itemprop="name">Joe Pitt-Francis</span></a></li><li class="active">Publications</li></ol></div><!-- MOBILE NAVIGATION --><div class="content-width space-below mobile-menu-placeholder visible-xs visible-sm"></div><!-- COLUMNS --><div class="container-fluid content-width"><div class="row"><div class="col-xs-12 col-md-9 col-md-push-3" id="maincontent"><!-- CONTENT (Column 2) --><div class="page-title"><h1>Joe Pitt-Francis : Publications
</h1></div><div role="toolbar" class="btn-toolbar"><div class="btn-group"><a href="/people/publications/date/Joe.Pitt-Francis.html" aria-hidden="true" type="button" class="btn btn-default"><span class="glyphicon glyphicon-sort-by-attributes"></span> By date</a><a href="/people/publications/title/Joe.Pitt-Francis.html" aria-hidden="true" type="button" class="btn btn-default"><span class="glyphicon glyphicon-sort-by-attributes"></span> By title</a><a href="/people/publications/type/Joe.Pitt-Francis.html" aria-hidden="true" type="button" class="btn btn-oxford-blue"><span class="glyphicon glyphicon-sort-by-attributes"></span> By type</a><a href="/people/publications/bibtex/Joe.Pitt-Francis.html" aria-hidden="true" type="button" class="btn btn-default"><span class="glyphicon glyphicon-file"></span> BibTex</a></div></div><p></p><h2>
      Journal papers
      </h2><ul class="list-unbulleted list-unbulleted-spaced"><li>
	
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	<p class="publicationTitle"> <strong>
            A mathematical framework for the emergence of winners and losers in cell competition </strong> </p>
	    <p class="publicationAuthors"> <em> Thomas F Pak&#x201a; Joe Pitt&#x2212;Francis and Ruth E Baker  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of Theoretical Biology</em>.
        
            Vol. 577.
        
                Pages 111666.
            2024.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16176-abstract.html">
			Details <span class="sr-only" > about <em> A mathematical framework for the emergence of winners and losers in cell competition  </em></span> </a> |
			<a href="/publications/publication16176.bib">
			BibTeX  <span class="sr-only" > data for <em> A mathematical framework for the emergence of winners and losers in cell competition  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Structural Features of Microvascular Networks Trigger Blood Flow Oscillations </strong> </p>
	    <p class="publicationAuthors"> <em> Yaron Ben&#x2212;Ami&#x201a; George W Atkinson&#x201a; Joe M Pitt&#x2212;Francis&#x201a; Philip K Maini and Helen M Byrne  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Bulletin of Mathematical Biology</em>.
        
            Vol. 84.
        
            No. 8.
        
                Pages 85.
            2022.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16174-abstract.html">
			Details <span class="sr-only" > about <em> Structural Features of Microvascular Networks Trigger Blood Flow Oscillations  </em></span> </a> |
			<a href="/publications/publication16174.bib">
			BibTeX  <span class="sr-only" > data for <em> Structural Features of Microvascular Networks Trigger Blood Flow Oscillations  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Dependence of cell&#x2212;free&#x2212;layer width on rheological parameters: Combining empirical data on flow separation at microvascular bifurcations with geometrical considerations </strong> </p>
	    <p class="publicationAuthors"> <em> Jakub K&#xf6;ry&#x201a; Philip K Maini&#x201a; Joe M Pitt&#x2212;Francis and Helen M Byrne  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Physical Review E</em>.
        
            Vol. 105.
        
            No. 1.
        
                Pages 014414.
            2022.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16173-abstract.html">
			Details <span class="sr-only" > about <em> Dependence of cell&#x2212;free&#x2212;layer width on rheological parameters: Combining empirical data on flow separation at microvascular bifurcations with geometrical considerations  </em></span> </a> |
			<a href="/publications/publication16173.bib">
			BibTeX  <span class="sr-only" > data for <em> Dependence of cell&#x2212;free&#x2212;layer width on rheological parameters: Combining empirical data on flow separation at microvascular bifurcations with geometrical considerations  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            A DNA&#x2212;structured mathematical model of cell&#x2212;cycle progression in cyclic hypoxia </strong> </p>
	    <p class="publicationAuthors"> <em> Giulia L Celora&#x201a; Samuel B Bader&#x201a; Ester M Hammond&#x201a; Philip K Maini&#x201a; Joe M Pitt&#x2212;Francis and Helen M Byrne  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of Theoretical Biology</em>.
        
            Vol. 545.
        
                Pages 111104.
            2022.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16171-abstract.html">
			Details <span class="sr-only" > about <em> A DNA&#x2212;structured mathematical model of cell&#x2212;cycle progression in cyclic hypoxia  </em></span> </a> |
			<a href="/publications/publication16171.bib">
			BibTeX  <span class="sr-only" > data for <em> A DNA&#x2212;structured mathematical model of cell&#x2212;cycle progression in cyclic hypoxia  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Chaste: cancer&#x201a; heart and soft tissue environment </strong> </p>
	    <p class="publicationAuthors"> <em> Fergus R Cooper&#x201a; Ruth E Baker&#x201a; Miguel O Bernabeu&#x201a; Rafel Bordas&#x201a; Louise Bowler&#x201a; Alfonso Bueno&#x2212;Orovio&#x201a; Helen M Byrne&#x201a; Valentina Carapella&#x201a; Louie Cardone&#x2212;Noott&#x201a; Cooper Jonatha and others  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of Open Source Software</em>.
        
            Vol. 5.
        
            No. 47.
        2020.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16169-abstract.html">
			Details <span class="sr-only" > about <em> Chaste: cancer&#x201a; heart and soft tissue environment  </em></span> </a> |
			<a href="/publications/publication16169.bib">
			BibTeX  <span class="sr-only" > data for <em> Chaste: cancer&#x201a; heart and soft tissue environment  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Pakman: a modular&#x201a; efficient and portable tool for approximate Bayesian inference </strong> </p>
	    <p class="publicationAuthors"> <em> Thomas Pak&#x201a; Ruth Baker and Joe Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of Open Source Software</em>.
        
            Vol. 5.
        
            No. 47.
        2020.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16168-abstract.html">
			Details <span class="sr-only" > about <em> Pakman: a modular&#x201a; efficient and portable tool for approximate Bayesian inference  </em></span> </a> |
			<a href="/publications/publication16168.bib">
			BibTeX  <span class="sr-only" > data for <em> Pakman: a modular&#x201a; efficient and portable tool for approximate Bayesian inference  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Abnormal morphology biases hematocrit distribution in tumor vasculature and contributes to heterogeneity in tissue oxygenation </strong> </p>
	    <p class="publicationAuthors"> <em> Miguel O Bernabeu&#x201a; Jakub K&#xf6;ry&#x201a; James A Grogan&#x201a; Bostjan Markelc&#x201a; Albert Beardo&#x201a; Mayeul d&#xfffd;Avezac&#x201a; Romain Enjalbert&#x201a; Jakob Kaeppler&#x201a; Nicholas Daly&#x201a; James Hetherington and others  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Proceedings of the National Academy of Sciences</em>.
        
            Vol. 117.
        
            No. 45.
        
                Pages 27811&#x2013;27819.
            2020.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16166-abstract.html">
			Details <span class="sr-only" > about <em> Abnormal morphology biases hematocrit distribution in tumor vasculature and contributes to heterogeneity in tissue oxygenation  </em></span> </a> |
			<a href="/publications/publication16166.bib">
			BibTeX  <span class="sr-only" > data for <em> Abnormal morphology biases hematocrit distribution in tumor vasculature and contributes to heterogeneity in tissue oxygenation  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Cooperation&#x201a; competition and antibiotic resistance in bacterial colonies </strong> </p>
	    <p class="publicationAuthors"> <em> Isabel Frost&#x201a; William PJ Smith&#x201a; Sara Mitri&#x201a; Alvaro San Millan&#x201a; Yohan Davit&#x201a; James M Osborne&#x201a; Joe M Pitt&#x2212;Francis&#x201a; R Craig MacLean and Kevin R Foster  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>The ISME journal</em>.
        
            Vol. 12.
        
            No. 6.
        
                Pages 1582&#x2013;1593.
            2018.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16154-abstract.html">
			Details <span class="sr-only" > about <em> Cooperation&#x201a; competition and antibiotic resistance in bacterial colonies  </em></span> </a> |
			<a href="/publications/publication16154.bib">
			BibTeX  <span class="sr-only" > data for <em> Cooperation&#x201a; competition and antibiotic resistance in bacterial colonies  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            The importance of geometry in the corneal micropocket angiogenesis assay </strong> </p>
	    <p class="publicationAuthors"> <em> James A Grogan&#x201a; Anthony J Connor&#x201a; Joe M Pitt&#x2212;Francis&#x201a; Philip K Maini and Helen M Byrne  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>PLoS computational biology</em>.
        
            Vol. 14.
        
            No. 3.
        
                Pages e1006049.
            2018.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16153-abstract.html">
			Details <span class="sr-only" > about <em> The importance of geometry in the corneal micropocket angiogenesis assay  </em></span> </a> |
			<a href="/publications/publication16153.bib">
			BibTeX  <span class="sr-only" > data for <em> The importance of geometry in the corneal micropocket angiogenesis assay  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Bayesian calibration&#x201a; validation and uncertainty quantification for predictive modelling of tumour growth: a tutorial </strong> </p>
	    <p class="publicationAuthors"> <em> Joe Collis&#x201a; Anthony J Connor&#x201a; Marcin Paczkowski&#x201a; Pavitra Kannan&#x201a; Joe Pitt&#x2212;Francis&#x201a; Helen M Byrne and Matthew E Hubbard  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Bulletin of mathematical biology</em>.
        
            Vol. 79.
        
                Pages 939&#x2013;974.
            2017.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16151-abstract.html">
			Details <span class="sr-only" > about <em> Bayesian calibration&#x201a; validation and uncertainty quantification for predictive modelling of tumour growth: a tutorial  </em></span> </a> |
			<a href="/publications/publication16151.bib">
			BibTeX  <span class="sr-only" > data for <em> Bayesian calibration&#x201a; validation and uncertainty quantification for predictive modelling of tumour growth: a tutorial  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Microvessel chaste: an open library for spatial modeling of vascularized tissues </strong> </p>
	    <p class="publicationAuthors"> <em> James A Grogan&#x201a; Anthony J Connor&#x201a; Bostjan Markelc&#x201a; Ruth J Muschel&#x201a; Philip K Maini&#x201a; Helen M Byrne and Joe M Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Biophysical Journal</em>.
        
            Vol. 112.
        
            No. 9.
        
                Pages 1767&#x2013;1772.
            2017.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16150-abstract.html">
			Details <span class="sr-only" > about <em> Microvessel chaste: an open library for spatial modeling of vascularized tissues  </em></span> </a> |
			<a href="/publications/publication16150.bib">
			BibTeX  <span class="sr-only" > data for <em> Microvessel chaste: an open library for spatial modeling of vascularized tissues  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Cell morphology drives spatial patterning in microbial communities </strong> </p>
	    <p class="publicationAuthors"> <em> William PJ Smith&#x201a; Yohan Davit&#x201a; James M Osborne&#x201a; Wook Kim&#x201a; Kevin R Foster and Joe M Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Proceedings of the National Academy of Sciences</em>.
        
            Vol. 114.
        
            No. 3.
        
                Pages E280&#x2013;E286.
            2017.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16149-abstract.html">
			Details <span class="sr-only" > about <em> Cell morphology drives spatial patterning in microbial communities  </em></span> </a> |
			<a href="/publications/publication16149.bib">
			BibTeX  <span class="sr-only" > data for <em> Cell morphology drives spatial patterning in microbial communities  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Comparing individual&#x2212;based approaches to modelling the self&#x2212;organization of multicellular tissues </strong> </p>
	    <p class="publicationAuthors"> <em> James M Osborne&#x201a; Alexander G Fletcher&#x201a; Joe M Pitt&#x2212;Francis&#x201a; Philip K Maini and David J Gavaghan  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>PLoS computational biology</em>.
        
            Vol. 13.
        
            No. 2.
        
                Pages e1005387.
            2017.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16146-abstract.html">
			Details <span class="sr-only" > about <em> Comparing individual&#x2212;based approaches to modelling the self&#x2212;organization of multicellular tissues  </em></span> </a> |
			<a href="/publications/publication16146.bib">
			BibTeX  <span class="sr-only" > data for <em> Comparing individual&#x2212;based approaches to modelling the self&#x2212;organization of multicellular tissues  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Predicting the influence of microvascular structure on tumor response to radiotherapy </strong> </p>
	    <p class="publicationAuthors"> <em> James A Grogan&#x201a; Bostjan Markelc&#x201a; Anthony J Connor&#x201a; Ruth J Muschel&#x201a; Joe M Pitt&#x2212;Francis&#x201a; Philip K Maini and Helen M Byrne  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>IEEE Transactions on Biomedical Engineering</em>.
        
            Vol. 64.
        
            No. 3.
        
                Pages 504&#x2013;511.
            2016.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16148-abstract.html">
			Details <span class="sr-only" > about <em> Predicting the influence of microvascular structure on tumor response to radiotherapy  </em></span> </a> |
			<a href="/publications/publication16148.bib">
			BibTeX  <span class="sr-only" > data for <em> Predicting the influence of microvascular structure on tumor response to radiotherapy  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            VENI&#x201a; VIDI&#x201a; Voronoi: Attacking Viruses with Spherical Voronoi Diagrams </strong> </p>
	    <p class="publicationAuthors"> <em> Tyler Reddy&#x201a; Ross Hemsley&#x201a; Edd Edmondson&#x201a; Nikolai Nowaczyk&#x201a; Joe Pitt&#x2212;Francis and Mark SP Sansom  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Biophysical Journal</em>.
        
            Vol. 110.
        
            No. 3.
        
                Pages 36a.
            2016.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16145-abstract.html">
			Details <span class="sr-only" > about <em> VENI&#x201a; VIDI&#x201a; Voronoi: Attacking Viruses with Spherical Voronoi Diagrams  </em></span> </a> |
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			BibTeX  <span class="sr-only" > data for <em> VENI&#x201a; VIDI&#x201a; Voronoi: Attacking Viruses with Spherical Voronoi Diagrams  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Development and analysis of patient&#x2212;based complete conducting airways models </strong> </p>
	    <p class="publicationAuthors"> <em> Rafel Bordas&#x201a; Christophe Lefevre&#x201a; Bart Veeckmans&#x201a; Joe Pitt&#x2212;Francis&#x201a; Catalin Fetita&#x201a; Christopher E Brightling&#x201a; David Kay&#x201a; Salman Siddiqui and Kelly S Burrowes  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>PloS one</em>.
        
            Vol. 10.
        
            No. 12.
        
                Pages e0144105.
            2015.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16144-abstract.html">
			Details <span class="sr-only" > about <em> Development and analysis of patient&#x2212;based complete conducting airways models  </em></span> </a> |
			<a href="/publications/publication16144.bib">
			BibTeX  <span class="sr-only" > data for <em> Development and analysis of patient&#x2212;based complete conducting airways models  </em></span>   </a>
			
			
		
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	<p class="publicationTitle"> <strong>
            Cognac: a chaste plugin for the multiscale simulation of gene regulatory networks driving the spatial dynamics of tissues and cancer </strong> </p>
	    <p class="publicationAuthors"> <em> Simone Rubinacci&#x201a; Alex Graudenzi&#x201a; Giulio Caravagna&#x201a; Giancarlo Mauri&#x201a; James Osborne&#x201a; Joe Pitt&#x2212;Francis and Marco Antoniotti  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Cancer informatics</em>.
        
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        		<p class="publicationlinks"> <a
        
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			Details <span class="sr-only" > about <em> Cognac: a chaste plugin for the multiscale simulation of gene regulatory networks driving the spatial dynamics of tissues and cancer  </em></span> </a> |
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            An integrated approach to quantitative modelling in angiogenesis research </strong> </p>
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	<p class="publicationTitle"> <strong>
            A parallel implementation of an off&#x2212;lattice individual&#x2212;based model of multicellular populations </strong> </p>
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	<p class="publicationDetails"> 
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	<p class="publicationTitle"> <strong>
            Application of stochastic phenomenological modelling to cell&#x2212;to&#x2212;cell and beat&#x2212;to&#x2212;beat electrophysiological variability in cardiac tissue </strong> </p>
	    <p class="publicationAuthors"> <em> John Walmsley&#x201a; Gary R Mirams&#x201a; Joe Pitt&#x2212;Francis&#x201a; Blanca Rodriguez and Kevin Burrage  </em> </p>
	
	<p class="publicationDetails"> 
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	<p class="publicationTitle"> <strong>
            Ten simple rules for effective computational research </strong> </p>
	    <p class="publicationAuthors"> <em> Miguel Bernabeu&#x201a; Maria Bruna&#x201a; Jonathan Cooper&#x201a; Sara&#x2212;Jane Dunn&#x201a; Alexander Fletcher&#x201a; David Gavaghan&#x201a; Greg McInerny&#x201a; Gary Mirams&#x201a; James Osborne and Joe Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
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        		<p class="publicationlinks"> <a
        
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	<p class="publicationTitle"> <strong>
            Clinical validation of a CT&#x2212;based impulse oscillometry model </strong> </p>
	    <p class="publicationAuthors"> <em> Rafel Bordas&#x201a; Sherif Gonem&#x201a; Christophe Lefevre&#x201a; Bart Veeckmans&#x201a; Ruth Hartley&#x201a; Joe Pitt&#x2212;Francis&#x201a; Catalin Fetita&#x201a; Chris Brightling&#x201a; John Owers&#x2212;Bradley&#x201a; David Kay and others  </em> </p>
	
	<p class="publicationDetails"> 
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	<p class="publicationTitle"> <strong>
            Relationship between heterogeneous bronchoconstriction and impulse oscillometry resistance: A simulation study </strong> </p>
	    <p class="publicationAuthors"> <em> Rafel Bordas&#x201a; Sherif Gonem&#x201a; Wim Vos&#x201a; Ruth Hartley&#x201a; Joe Pitt&#x2212;Francis&#x201a; Jan De Backer&#x201a; Chris Brightling&#x201a; John Owers&#x2212;Bradley&#x201a; David Kay&#x201a; Salman Siddiqui and others  </em> </p>
	
	<p class="publicationDetails"> 
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	<p class="publicationTitle"> <strong>
            Multiscale cardiac modelling reveals the origins of notched T waves in long QT syndrome type 2 </strong> </p>
	    <p class="publicationAuthors"> <em> Arash Sadrieh&#x201a; Luke Domanski&#x201a; Joe Pitt&#x2212;Francis&#x201a; Stefan A Mann&#x201a; Emily C Hodkinson&#x201a; Chai&#x2212;Ann Ng&#x201a; Matthew D Perry&#x201a; John A Taylor&#x201a; David Gavaghan&#x201a; Rajesh N Subbiah and others  </em> </p>
	
	<p class="publicationDetails"> 
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	<p class="publicationTitle"> <strong>
            Chaste: a case study of parallelisation of an open source finite&#x2212;element solver with applications to computational cardiac electrophysiology simulation </strong> </p>
	    <p class="publicationAuthors"> <em> Miguel O Bernabeu&#x201a; James Southern&#x201a; Nicholas Wilson&#x201a; Peter Strazdins&#x201a; Jonathan Cooper and Joe Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
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			Details <span class="sr-only" > about <em> Chaste: a case study of parallelisation of an open source finite&#x2212;element solver with applications to computational cardiac electrophysiology simulation  </em></span> </a> |
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	<p class="publicationTitle"> <strong>
            Ten simple rules for effective computational research </strong> </p>
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			Details <span class="sr-only" > about <em> Ten simple rules for effective computational research  </em></span> </a> |
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	<p class="publicationTitle"> <strong>
            Hydrodynamic dispersion within porous biofilms </strong> </p>
	    <p class="publicationAuthors"> <em> Yohan Davit&#x201a; Helen Byrne&#x201a; J Osborne&#x201a; Joe Pitt&#x2212;Francis&#x201a; David Gavaghan and Michel Quintard  </em> </p>
	
	<p class="publicationDetails"> 
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            Validity of the Cauchy&#x2212;Born rule applied to discrete cellular&#x2212;scale models of biological tissues </strong> </p>
	    <p class="publicationAuthors"> <em> Yohan Davit&#x201a; James M Osborne&#x201a; HM Byrne&#x201a; David Gavaghan and Joe Pitt&#x2212;Francis  </em> </p>
	
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	<p class="publicationTitle"> <strong>
            Computational assessment of drug&#x2212;induced effects on the electrocardiogram: from ion channel to body surface potentials </strong> </p>
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			Details <span class="sr-only" > about <em> Computational assessment of drug&#x2212;induced effects on the electrocardiogram: from ion channel to body surface potentials  </em></span> </a> |
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	<p class="publicationTitle"> <strong>
            Chaste: a case study of parallelisation of an open source finite&#x2212;element solver with applications to computational cardiac electrophysiology simulation </strong> </p>
	    <p class="publicationAuthors"> <em> Miguel O Bernabeu&#x201a; James Southern&#x201a; Nicholas Wilson&#x201a; Peter Strazdins&#x201a; Jonathan Cooper and Joe Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>International Journal of High Performance Computing Applications</em>.
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        		<p class="publicationlinks"> <a
        
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			Details <span class="sr-only" > about <em> Chaste: a case study of parallelisation of an open source finite&#x2212;element solver with applications to computational cardiac electrophysiology simulation  </em></span> </a> |
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	<p class="publicationTitle"> <strong>
            Chaste: an open source C++ library for computational physiology and biology </strong> </p>
	    <p class="publicationAuthors"> <em> Gary R Mirams&#x201a; Christopher J Arthurs&#x201a; Miguel O Bernabeu&#x201a; Rafel Bordas&#x201a; Jonathan Cooper&#x201a; Alberto Corrias&#x201a; Yohan Davit&#x201a; Sara&#x2212;Jane Dunn&#x201a; Alexander G Fletcher&#x201a; Daniel G Harvey and others  </em> </p>
	
	<p class="publicationDetails"> 
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        		<p class="publicationlinks"> <a
        
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			 | <a
		href="http://dx.doi.org/10.1371/journal.pcbi.1002970">
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	<p class="publicationTitle"> <strong>
            Computational assessment of drug&#x2212;induced effects on the electrocardiogram: from ion channel block to body surface potentials </strong> </p>
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	<p class="publicationDetails"> 
        In <em>British Journal of Pharmacology</em>.
        
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			Details <span class="sr-only" > about <em> Computational assessment of drug&#x2212;induced effects on the electrocardiogram: from ion channel block to body surface potentials  </em></span> </a> |
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	<p class="publicationTitle"> <strong>
            Stochasticity in action potential duration enhances dispersion of repolarisation at fast pacing rates </strong> </p>
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	<p class="publicationTitle"> <strong>
            Solute transport within porous biofilms: diffusion or dispersion? </strong> </p>
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	<p class="publicationDetails"> 2012.
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	<p class="publicationTitle"> <strong>
            Anisotropic mesh adaptivity for cardiac electrophysiology </strong> </p>
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	<p class="publicationTitle"> <strong>
            Stimulus protocol determines the most computationally efficient preconditioner for the bidomain equations </strong> </p>
	    <p class="publicationAuthors"> <em> Miguel O Bernabeu&#x201a; Pras Pathmanathan&#x201a; Joe Pitt&#x2212;Francis and David Kay  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>IEEE transactions on biomedical engineering</em>.
        
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                Pages 2806&#x2013;2815.
            2010.
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	<p class="publicationTitle"> <strong>
            Simulating cardiac electrophysiology using anisotropic mesh adaptivity </strong> </p>
	    <p class="publicationAuthors"> <em> James Southern&#x201a; Gerard J Gorman&#x201a; MD Piggott&#x201a; Patrick E Farrell&#x201a; Miguel O Bernabeu and Joe Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of computational science</em>.
        
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	<p class="publicationTitle"> <strong>
            High&#x2212;throughput cardiac science on the Grid </strong> </p>
	    <p class="publicationAuthors"> <em> David Abramson&#x201a; Miguel O Bernabeu&#x201a; Blair Bethwaite&#x201a; Kevin Burrage&#x201a; Alberto Corrias&#x201a; Colin Enticott&#x201a; Slavisa Garic&#x201a; David Gavaghan&#x201a; Tom Peachey&#x201a; Joe Pitt&#x2212;Francis and others  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Philosophical Transactions of the Royal Society A: Mathematical&#x201a; Physical and Engineering Sciences</em>.
        
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	<p class="publicationTitle"> <strong>
            Simulating cardiac electrophysiology using anisotropic mesh adaptivity </strong> </p>
	    <p class="publicationAuthors"> <em> J Pitt&#x2212;Francis J Southern GJ Gorman MD Piggott PE Farrell MO Bernabeu  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of computational science</em>.
        
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	<p class="publicationTitle"> <strong>
            Stimulus protocol determines the most computationally&#x2212;efficient preconditioner for the bidomain equations </strong> </p>
	    <p class="publicationAuthors"> <em> D. Kay M. Bernabeu P. Pathmanathan J. Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Transactions of Biomedical Engineering</em>.
        
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	<p class="publicationTitle"> <strong>
            A numerical guide to the solution of the bidomain equations of cardiac electrophysiology </strong> </p>
	    <p class="publicationAuthors"> <em> Pras Pathmanathan&#x201a; Miguel O Bernabeu&#x201a; Rafel Bordas&#x201a; Jonathan Cooper&#x201a; Alan Garny&#x201a; Joe M Pitt&#x2212;Francis&#x201a; Jonathan P Whiteley and David J Gavaghan  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Progress in biophysics and molecular biology</em>.
        
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	<p class="publicationTitle"> <strong>
            An integrative computational model for intestinal tissue renewal </strong> </p>
	    <p class="publicationAuthors"> <em> Jon Chapman&#x201a; Jonathan Cooper&#x201a; Alexander Fletcher&#x201a; David Gavaghan&#x201a; Philip Maini&#x201a; Gary Mirams&#x201a; James Osborne&#x201a; Pras Pathmanathan&#x201a; Joe Pitt&#x2212;Francis and Jonathan Whiteley  </em> </p>
	
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            A computational study of discrete mechanical tissue models </strong> </p>
	    <p class="publicationAuthors"> <em> P Pathmanathan&#x201a; Jonathan Cooper&#x201a; Alexander Fletcher&#x201a; Gary Mirams&#x201a; P Murray&#x201a; J Osborne&#x201a; Joe Pitt&#x2212;Francis&#x201a; Alex Walter and SJ Chapman  </em> </p>
	
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            Grid Computing Simulations of Ion Channel Block Effects on the ECG Using 3D Anatomically&#x2212;Based Models </strong> </p>
	    <p class="publicationAuthors"> <em> Gavaghan D Bernabeu MO Corrias A Pitt&#x2212;Francis J Rodriguez B Bethwaite B Enticott C Garic S Peachey T Tan J Abramson D  </em> </p>
	
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            Chaste: a test&#x2212;driven approach to software development for biological modelling </strong> </p>
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	    <p class="publicationAuthors"> <em> P Pathmanathan&#x201a; J Cooper&#x201a; A Fletcher&#x201a; G Mirams&#x201a; P Murray&#x201a; J Osborne&#x201a; J Pitt&#x2212;Francis&#x201a; A Walter and S J Chapman  </em> </p>
	
	<p class="publicationDetails"> 
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            Simulation of cardiac electrophysiology on next&#x2212;generation high&#x2212;performance computers </strong> </p>
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            An integrative computational model for intestinal tissue renewal </strong> </p>
	    <p class="publicationAuthors"> <em> Van Leeuwen&#x201a; Ingeborg MM&#x201a; GR Mirams&#x201a; Alex Walter&#x201a; A Fletcher&#x201a; P Murray&#x201a; J Osborne&#x201a; S Varma&#x201a; SJ Young&#x201a; J Cooper&#x201a; B Doyle and others  </em> </p>
	
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        In <em>Cell proliferation</em>.
        
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            Chaste: Incorporating a Novel Multiscale Spatial and Temporal Algorithm into a Large Scale Open Source Library </strong> </p>
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            High performance computer simulations for the study of biological function in 3D heart models incorporating fibre orientation and realistic geometry at para&#x2212;cellular resolution </strong> </p>
	    <p class="publicationAuthors"> <em> Rodriguez B Bernabeu MO Bishop MJ Pitt&#x2212;Francis J Gavaghan DJ Grau V  </em> </p>
	
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            Multi&#x2212;scale computational modelling in biology and physiology </strong> </p>
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            Chaste: using agile programming techniques to develop computational biology software </strong> </p>
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            Integrative Biology&#xfffd;the challenges of developing a collaborative research environment for heart and cancer modelling </strong> </p>
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            Vol. 23.
        
            No. 3.
        
                Pages 457&#x2013;465.
            2007.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16113-abstract.html">
			Details <span class="sr-only" > about <em> Integrative Biology&#xfffd;the challenges of developing a collaborative research environment for heart and cancer modelling  </em></span> </a> |
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				[54] 
			</div>

		
        
		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Multimodal imaging techniques for the extraction of detailed geometrical and physiological information for use in multi&#x2212;scale models of colorectal cancer and treatment of individual patients </strong> </p>
	    <p class="publicationAuthors"> <em> Joe Pitt&#x2212;Francis&#x201a; Dan Chen&#x201a; Mark Slaymaker&#x201a; Andrew Simpson&#x201a; Michael Brady&#x201a; Ingeborg Van Leeuwen&#x201a; Fiona Reddington&#x201a; Phil Quirke&#x201a; Gina Brown and David Gavaghan  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Computational and Mathematical Methods in Medicine</em>.
        
            Vol. 7.
        
            No. 2&#x2212;3.
        
                Pages 177&#x2013;188.
            2006.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16114-abstract.html">
			Details <span class="sr-only" > about <em> Multimodal imaging techniques for the extraction of detailed geometrical and physiological information for use in multi&#x2212;scale models of colorectal cancer and treatment of individual patients  </em></span> </a> |
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        </li><li>
	
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				[55] 
			</div>

		
        
		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Enabling computer models of the heart for high&#x2212;performance computers and the grid </strong> </p>
	    <p class="publicationAuthors"> <em> Joe Pitt&#x2212;Francis&#x201a; Alan Garny and David Gavaghan  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Philosophical Transactions of the Royal Society A: Mathematical&#x201a; Physical and Engineering Sciences</em>.
        
            Vol. 364.
        
            No. 1843.
        
                Pages 1501&#x2013;1516.
            2006.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16109-abstract.html">
			Details <span class="sr-only" > about <em> Enabling computer models of the heart for high&#x2212;performance computers and the grid  </em></span> </a> |
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				[56] 
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		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Development of a functional magnetic resonance imaging simulator for modeling realistic rigid&#x2212;body motion artifacts </strong> </p>
	    <p class="publicationAuthors"> <em> Ivana Drobnjak&#x201a; David Gavaghan&#x201a; Endre S&#xfc;li&#x201a; Joe Pitt&#x2212;Francis and Mark Jenkinson  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Magnetic Resonance in Medicine: An Official Journal of the International Society for Magnetic Resonance in Medicine</em>.
        
            Vol. 56.
        
            No. 2.
        
                Pages 364&#x2013;380.
            2006.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16108-abstract.html">
			Details <span class="sr-only" > about <em> Development of a functional magnetic resonance imaging simulator for modeling realistic rigid&#x2212;body motion artifacts  </em></span> </a> |
			<a href="/publications/publication16108.bib">
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				[57] 
			</div>

		
        
		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Using oxsim for path planning </strong> </p>
	    <p class="publicationAuthors"> <em> Stephen Cameron and Joe Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>Journal of Robotic Systems</em>.
        
            Vol. 18.
        
            No. 8.
        
                Pages 421&#x2013;431.
            2001.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16116-abstract.html">
			Details <span class="sr-only" > about <em> Using oxsim for path planning  </em></span> </a> |
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				[58] 
			</div>

		
        
		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Geometric Modelling and Robotics </strong> </p>
	    <p class="publicationAuthors"> <em> Stephen Cameron and Joe Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
        In <em>International Journal of Shape Modeling</em>.
        
            Vol. 6.
        
            No. 02.
        
                Pages 145&#x2013;164.
            2000.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16130-abstract.html">
			Details <span class="sr-only" > about <em> Geometric Modelling and Robotics  </em></span> </a> |
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				[59] 
			</div>

		
        
		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            The importance of geometry in the corneal micropocket assay </strong> </p>
	    <p class="publicationAuthors"> <em> James A Grogan&#x201a; Anthony J Connor&#x201a; Joe M Pitt&#x2212;Francis&#x201a; Philip K Maini and Helen M Byrne  </em> </p>
	
	<p class="publicationDetails"> </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16175-abstract.html">
			Details <span class="sr-only" > about <em> The importance of geometry in the corneal micropocket assay  </em></span> </a> |
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				[60] 
			</div>

		
        
		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            An integrated approach to quantitative modelling in angiogenesis research </strong> </p>
	    <p class="publicationAuthors"> <em> Tom Quaizer&#x201a; Eliezer Shochat&#x201a; Joe Pitt&#x2212;Francis&#x201a; Jonathan Cooper&#x201a; Philip K Maini and Helen M Byrne  </em> </p>
	
	<p class="publicationDetails"> </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16152-abstract.html">
			Details <span class="sr-only" > about <em> An integrated approach to quantitative modelling in angiogenesis research  </em></span> </a> |
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				[61] 
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			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Comparison of parallel solution techniques for the Eikonal equation </strong> </p>
	    <p class="publicationAuthors"> <em> Joe Pitt&#x2212;Francis and James Anderson  </em> </p>
	
	<p class="publicationDetails"> </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16125-abstract.html">
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        </li></ul><h2>
      Conference papers
      </h2><ul class="list-unbulleted list-unbulleted-spaced"><li>
	
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				[1] 
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		>
			
	
	<p class="publicationTitle"> <strong>
            Simulating tumour vasculature at multiple scales </strong> </p>
	    <p class="publicationAuthors"> <em> James A Grogan&#x201a; Philip K Maini&#x201a; Joe Pitt&#x2212;Francis and Helen M Byrne  </em> </p>
	
	<p class="publicationDetails"> 
            In  
            <em>
            Proceedings of the 2014 6th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation&#x2212;The CHIC Project Workshop (IARWISOCI)</em>.
        
                Pages 1&#x2013;4.
            IEEE.
        2014.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16138-abstract.html">
			Details <span class="sr-only" > about <em> Simulating tumour vasculature at multiple scales  </em></span> </a> |
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				[2] 
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		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Grid computing simulations of ion channel block effects on the ECG using 3D anatomically&#x2212;based models </strong> </p>
	    <p class="publicationAuthors"> <em> MO Bernabeu&#x201a; A Corrias&#x201a; J Pitt&#x2212;Francis&#x201a; B Rodriguez&#x201a; B Bethwaite&#x201a; C Enticott&#x201a; S Garic&#x201a; T Peachey&#x201a; J Tan&#x201a; D Abramson and others  </em> </p>
	
	<p class="publicationDetails"> 
            In  
            <em>
            2009 36th Annual Computers in Cardiology Conference (CinC)</em>.
        
                Pages 213&#x2013;216.
            IEEE.
        2009.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16117-abstract.html">
			Details <span class="sr-only" > about <em> Grid computing simulations of ion channel block effects on the ECG using 3D anatomically&#x2212;based models  </em></span> </a> |
			<a href="/publications/publication16117.bib">
			BibTeX  <span class="sr-only" > data for <em> Grid computing simulations of ion channel block effects on the ECG using 3D anatomically&#x2212;based models  </em></span>   </a>
			
			
		
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				[3] 
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			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            High performance computer simulations for the study of biological function in 3D heart models incorporating fibre orientation and realistic geometry at para&#x2212;cellular resolution </strong> </p>
	    <p class="publicationAuthors"> <em> MO Bernabeu&#x201a; MJ Bishop&#x201a; J Pitt&#x2212;Francis&#x201a; DJ Gavaghan&#x201a; V Grau and B Rodriguez  </em> </p>
	
	<p class="publicationDetails"> 
            In  
            <em>
            2008 Computers in Cardiology</em>.
        
                Pages 721&#x2013;724.
            IEEE.
        2008.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16115-abstract.html">
			Details <span class="sr-only" > about <em> High performance computer simulations for the study of biological function in 3D heart models incorporating fibre orientation and realistic geometry at para&#x2212;cellular resolution  </em></span> </a> |
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				[4] 
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		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Gathering requirements for an Integrative Biology project </strong> </p>
	    <p class="publicationAuthors"> <em> David Gavaghan&#x201a; Jonathan Whiteley&#x201a; Joe Pitt&#x2212;Francis&#x201a; Mark Slaymaker&#x201a; David Boyd&#x201a; Damian Mac Randal&#x201a; Kerstin Kleese van Dam and Lakshmi Sastry  </em> </p>
	
	<p class="publicationDetails"> 
            In  
            <em>
            Proc. UK e&#x2212;Science All Hands Meeting</em>.
        
                Pages 99&#x2013;105.
            2004.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16120-abstract.html">
			Details <span class="sr-only" > about <em> Gathering requirements for an Integrative Biology project  </em></span> </a> |
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			BibTeX  <span class="sr-only" > data for <em> Gathering requirements for an Integrative Biology project  </em></span>   </a>
			
			
		
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				[5] 
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		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Directions in the use and computation of proximity queries </strong> </p>
	    <p class="publicationAuthors"> <em> Stephen Cameron&#x201a; Tristam Fenton&#x2212;May and Joe Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
            In  
            <em>
            Geometric Modeling and Processing. Theory and Applications. GMP 2002. Proceedings</em>.
        
                Pages 43&#x2013;52.
            IEEE.
        2002.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16122-abstract.html">
			Details <span class="sr-only" > about <em> Directions in the use and computation of proximity queries  </em></span> </a> |
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				[6] 
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			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Motion planning for real problems </strong> </p>
	    <p class="publicationAuthors"> <em> S Cameron and J Pitt&#x2212;Francis  </em> </p>
	
	<p class="publicationDetails"> 
            In  
            <em>
            Advanced robotics: beyond 2000 (Birmingham&#x201a; 27 April&#x2212;1 May 1998)</em>.
        1998.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16167-abstract.html">
			Details <span class="sr-only" > about <em> Motion planning for real problems  </em></span> </a> |
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				[7] 
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		<div
			class="col-xs-11"
		>
			
	
	<p class="publicationTitle"> <strong>
            Automatic generation of sphere hierarchies from cad data </strong> </p>
	    <p class="publicationAuthors"> <em> Joe Pitt&#x2212;Francis and R Feathertone  </em> </p>
	
	<p class="publicationDetails"> 
            In  
            <em>
            Proceedings. 1998 IEEE International Conference on Robotics and Automation (Cat. No. 98CH36146)</em>.
        
            Vol. 1.
        
                Pages 324&#x2013;329.
            IEEE.
        1998.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16112-abstract.html">
			Details <span class="sr-only" > about <em> Automatic generation of sphere hierarchies from cad data  </em></span> </a> |
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      Miscellaneous
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				[1] 
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		>
			
	
	<p class="publicationTitle"> <strong>
            Ten simple rules for a successful cross&#x2212;disciplinary collaboration </strong> </p>
	    <p class="publicationAuthors"> <em> Bernhard Knapp&#x201a; R&#xe9;mi Bardenet&#x201a; Miguel O Bernabeu&#x201a; Rafel Bordas&#x201a; Maria Bruna&#x201a; Ben Calderhead&#x201a; Jonathan Cooper&#x201a; Alexander G Fletcher&#x201a; Derek Groen&#x201a; Bram Kuijper and others  </em> </p>
	
	<p class="publicationDetails"> 2015.
        </p>
	
        		<p class="publicationlinks"> <a
        
            		href="/publications/publication16139-abstract.html">
			Details <span class="sr-only" > about <em> Ten simple rules for a successful cross&#x2212;disciplinary collaboration  </em></span> </a> |
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