Professor Andrew Francis
Interim Dean  School of Computer, Data and Mathematical Sciences,
Dean's Unit, Computer, Data & Math Sciences
Interim Dean  School of Computer, Data and Mathematical Sciences,
Dean's Unit, Computer, Data & Math Sciences
Professor,
Mathematics & Statistics
Professor,
Mathematics & Statistics
Biography
Professor Andrew Francis is the Deputy Dean of the School of Computer, Data, and Mathematical Sciences.
He is a former ARC Future Fellow, who works on a wide range of research problems in algebra and mathematical biology. He joined Western Sydney in the year 2000 as a Lecturer in Mathematics, after a postdoctoral position at the University of Virginia, and was Director of the Centre for Research in Mathematics and Data Science from 2015 to 2019.
His research can be characterized as the development of discrete and combinatorial mathematics, such as reflection groups and graph theory, to address problems both within and outside mathematics. Apart from algebra itself, these problems have chiefly been in phylogenetics, epidemiology, bacterial genome structure, and statistics. Aside from his Future Fellowship 20102014, he has held four ARC Discovery Project grants.
Professor Francis has held a number of governance posts, including serving on the Academic Senate 20072011. He chaired the Senate's Mathematics Expert Advisory Group in 2010 that reviewed issues relating to all levels of mathematics at the University and made many recommendations. He has served on the Council of the Australian Mathematical Society (201214), on the ARC Research Evaluation Committee for the 2015 and 2018 Excellence in Research for Australia exercises, and on the ARC College of Experts (20182021). He continues to sit on several ARC committees.
This information has been contributed by Professor Francis.
Qualifications
 PhD University of New South Wales
 BSc University of Sydney
Professional Memberships
 American Mathematical Society (1998)
 Combinatorial Mathematics Society of Australasia (CMSA) (2020)
 Society for Mathematical Biology (2011)
 Australian Mathematical Society (1995)
Awards
 Fellow of the Australian Mathematical Society 20151001
 Erskine Fellow, Canterbury University 20160901
 ARC Future Fellow 20110101
Organisational Unit (School / Division)
 Dean's Unit, Computer, Data & Math Sciences
 Dean's Unit, Computer, Data & Math Sciences
 Mathematics & Statistics
 Mathematics & Statistics
Contact
Email:  A.Francis@westernsydney.edu.au 

Phone:  (02) 9685 9236 
Mobile:  0439893637 
Location:  EN.1.42 Parramatta 
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Publications
Chapters in Books
 Rodrigues, G., Francis, A., Sisson, S. and Tanaka, M. (2019), 'Inferences on the acquisition of multidrug resistance in Mycobacterium tuberculosis using molecular epidemiological data', Handbook of Approximate Bayesian Computation, CRC Press 9781439881507.
Journal Articles
 Francis, A. and Steel, M. (2023), 'Labellable phylogenetic networks', Bulletin of Mathematical Biology, vol 85, no 6 .
 Clark, C., Jonusas, J., Mitchell, J. and Francis, A. (2023), 'An algebraic model for inversion and deletion in bacterial genome rearrangement', Journal of Mathematical Biology, vol 87, no 2 .
 Fischer, M., Francis, A. and Wicke, K. (2023), 'Phylogenetic diversity rankings in the face of extinctions : the robustness of the fair proportion index', Systematic Biology, vol 72, no 3 , pp 606  615.
 Francis, A., Huber, K., Moulton, V. and Wu, T. (2022), 'Encoding and ordering Xcactuses', Advances in Applied Mathematics, vol 142 .
 Erdos, P., Francis, A. and Mezei, T. (2021), 'Rooted NNI moves and distance1 tail moves on treebased phylogenetic networks', Discrete Applied Mathematics, vol 294 , pp 205  213.
 Francis, A., Huson, D. and Steel, M. (2021), 'Normalising phylogenetic networks', Molecular Phylogenetics and Evolution, vol 163 .
 Aandahl, R., Bhatia, S., Vaudagnotto, N., Street, A., Francis, A. and Tanaka, M. (2020), 'MERCAT : visualising molecular epidemiology data combining genetic markers and drug resistance profiles', Infection, Genetics and Evolution, vol 77 .
 Fischer, M. and Francis, A. (2020), 'How treebased is my network? : proximity measures for unrooted phylogenetic networks', Discrete Applied Mathematics, vol 283 , pp 98  114.
 Hendriksen, M. and Francis, A. (2020), 'A partial order and clustersimilarity metric on rooted phylogenetic trees', Journal of Mathematical Biology, vol 80, no 5 , pp 1265  1290.
 Francis, A. and Wynn, H. (2020), 'A mean first passage time genome rearrangement distance', Journal of Mathematical Biology, vol 80, no 6 , pp 1971  1992.
 Fischer, M. and Francis, A. (2020), 'The space of treebased phylogenetic networks', Bulletin of Mathematical Biology, vol 82, no 6 .
 Bhatia, S., EgriNagy, A., Serdoz, S., Praeger, C., Gebhardt, V. and Francis, A. (2020), 'A pathdeformation framework for determining weighted genome rearrangement distance', Frontiers in Genetics, vol 11 .
 Clark, C., EgriNagy, A., Francis, A. and Gebhardt, V. (2019), 'Bacterial phylogeny in the Cayley graph', Discrete Mathematics, Algorithms and Applications, vol 11, no 5 .
 Hendriksen, M. and Francis, A. (2019), 'Treemetrizable HGT networks', Mathematical Biosciences, vol 318 .
 Francis, A., Semple, C. and Steel, M. (2018), 'New characterisations of treebased networks and proximity measures', Advances in Applied Mathematics, vol 93 , pp 93  107.
 Francis, A., Huber, K. and Moulton, V. (2018), 'Treebased unrooted phylogenetic networks', Bulletin of Mathematical Biology, vol 80, no 2 , pp 404  416.
 Francis, A., Huber, K., Moulton, V. and Wu, T. (2018), 'Bounds for phylogenetic network space metrics', Journal of Mathematical Biology, vol 76, no 5 , pp 1229  1248.
 Francis, A. and Moulton, V. (2018), 'Identifiability of treechild phylogenetic networks under a probabilistic recombinationmutation model of evolution', Journal of Theoretical Biology, vol 446 , pp 160  167.
 Bhatia, S., Feijao, P. and Francis, A. (2018), 'Position and content paradigms in genome rearrangements : the wild and crazy world of permutations in genomics', Bulletin of Mathematical Biology, vol 80, no 12 , pp 3227  3246.
 Serdoz, S., EgriNagy, A., Sumner, J., Holland, B., Jarvis, P., Tanaka, M. and Francis, A. (2017), 'Maximum likelihood estimates of pairwise rearrangement distances', Journal of Theoretical Biology, vol 423 , pp 31  40.
 Francis, A., Stehlik, M. and Wynn, H. (2017), '"Building" exact confidence nets', Bernoulli, vol 23, no 4B , pp 3145  3165.
 Bryant, D., Francis, A. and Steel, M. (2017), 'Can we "futureproof" consensus trees?', Systematic Biology, vol 66, no 4 , pp 611  619.
 Sumner, J., Jarvis, P. and Francis, A. (2017), 'A representationtheoretic approach to the calculation of evolutionary distance in bacteria', Journal of Physics A: Mathematical and Theoretical, vol 50, no 33 .
 Bhatia, S., EgriNagy, A. and Francis, A. (2015), 'Algebraic double cut and join : a grouptheoretic approach to the operator on multichromosomal genomes', Journal of Mathematical Biology, vol 71, no 5 , pp 1149  1178.
 Francis, A. and Steel, M. (2015), 'Treelike reticulation networks : when do treelike distances also support reticulate evolution?', Mathematical Biosciences, vol 259 , pp 12  19.
 Francis, A. and Steel, M. (2015), 'Which phylogenetic networks are merely trees with additional arcs?', Systematic Biology, vol 64, no 5 , pp 768  777.
 Francis, A. and Wynn, H. (2014), 'Subgroup majorization', Linear Algebra and Its Applications, vol 444 , pp 53  66.
 Bak, T., Chu, D., Francis, A., Li, W. and Nowotny, J. (2014), 'Concentration of electrons at grain boundaries in TiO2 (rutile) : impact on charge transport and reactivity', Catalysis Today, .
 EgriNagy, A., Gebhardt, V., Tanaka, M. and Francis, A. (2014), 'Grouptheoretic models of the inversion process in bacterial genomes', Journal of Mathematical Biology, vol 69, no 1 , pp 243  265.
 Francis, A. (2014), 'An algebraic view of bacterial genome evolution', Journal of Mathematical Biology, vol 69, no 67 , pp 1693  1718.
 Francis, A. and Tanaka, M. (2012), 'Evolution of variation in presence and absence of genes in bacterial pathways', BMC Evolutionary Biology, vol 12, no 55 , pp 1  11.
 Francis, A. and Jones, L. (2011), 'Monomial bases for the centres of the group algebra and iwahorihecke algebra of the symmetric group', Far East Journal of Mathematical Sciences, vol 58, no 2 , pp 119  143.
 Ballouz, S., Francis, A., Lan, R. and Tanaka, M. (2010), 'Conditions for the Evolution of Gene Clusters in Bacterial Genomes', PLoS Computational Biology, vol 6, no 2 , pp 1  10.
 Stevenson, P., Mnatsakanyan, M., Francis, A. and Shalliker, R. (2010), 'A discussion on the process of defining 2D separation selectivity', Journal of Separation Science, vol 33, no 10 , pp 1405  1413.
 Francis, A. and Jones, L. (2009), 'A new integral basis for the centre of the IwahoriHecke algebra of type A', Journal of Algebra, vol 321, no 3 , pp 866  878.
 Luciani, F., Sisson, S., Jiang, H., Francis, A. and Tanaka, M. (2009), 'The epidemiological fitness cost of drug resistance in Mycobacterium tuberculosis', Proceedings of the National Academy of Sciences of the United States of America, vol 106, no 34 , pp 14711  14715.
 Luciani, F., Francis, A. and Tanaka, M. (2008), 'Interpreting genotype cluster sizes of Mycobacterium tuberculosis isolates typed with IS6110 and spoligotyping', Infection, Genetics and Evolution, vol 8, no 2 , pp 182  190.
 Reyes, J., Francis, A. and Tanaka, M. (2008), 'Models of deletion for visualizing bacterial variation : an application to tuberculosis spoligotypes', BMC Bioinformatics, vol 9 .
 Tang, C., Reyes, J., Luciani, F., Francis, A. and Tanaka, M. (2008), 'spolTools : online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex', Bioinformatics, vol 24, no 20 , pp 2414  2415.
 Francis, A. and Jones, L. (2007), 'On the square root of the centre of the Hecke algebra of type A', Journal of the Australian Mathematical Society, vol 82, no 2 , pp 209  220.
 Tanaka, M. and Francis, A. (2006), 'Detecting emerging strains of tuberculosis by using spoligotypes', Proceedings of the National Academy of Sciences of the United States of America, vol 103, no 41 , pp 15266  15271.
 Tanaka, M., Phong, R. and Francis, A. (2006), 'An evaluation of indices for quantifying tuberculosis transmission using genotypes of pathogen isolates', BMC Infectious Diseases, vol 6, no 92 .
 Francis, A. and Graham, J. (2006), 'Centres of Hecke algebras: the DipperJames conjecture', Journal of Algebra, vol 306, no 1 , pp 244  267.
 Tanaka, M., Francis, A., Luciani, F. and Sisson, S. (2006), 'Using Approximate Bayesian Computation to Estimate Tuberculosis Transmission Parameters From Genotype Data', Genetics, vol 173, no 3 , pp 1511  1520.
 Tanaka, M. and Francis, A. (2005), 'Methods of quantifying and visualising outbreaks of tuberculosis using genotypic information', Infection, Genetics and Evolution, vol 5, no 1 , pp 35  43.
 Francis, A. and Jones, L. (2005), 'On bases of centres of IwahoriHecke algebras of the symmetric group', Journal of Algebra, vol 289, no 1 , pp 42  69.
 Francis, A. (2003), 'Centralizers of IwahoriHecke algebras II: the general case', Algebra Colloquium, vol 10 , pp 95  100.
 Francis, A. (2001), 'The Brauer Homomorphism and the minimal basis for centres of IwahoriHecke algebra', Communications in Algebra, vol 29, no 1 , pp 85  97.
Conference Papers
 Trescak, T., Simoff, S., Francis, A. and Berry, L. (2021), 'Empowering graduate success with careerdriven modular curriculum', International Academic Forum Conference on Education, online.
 EgriNagy, A., Francis, A. and Gebhardt, V. (2014), 'Bacterial genomics and computational group theory : the BioGAP package for GAP', International Congress of Mathematical Software, Seoul, South Korea.
 Francis, A. and Jones, L. (2012), 'Multiplicative bases for the centres of the group algebra and IwahoriHecke algebra of the symmetric group', Southeastern Lie Theory Workshop: Finite and Algebraic Groups, University of Virginia.
 Francis, A. and Wang, W. (2009), 'The centers of IwahoriHecke algebras are filtered', Fourth International Conference on Representation Theory, Lhasa, China.
My research interests are in applications of algebra, combinatorics, and discrete mathematics to biology and anywhere I find interesting questions. My algebraic training was in the structure of Hecke algebras, that arise in the representation theory of finite groups, and especially I enjoy working with reflection groups. My mathematical biology interests are to do with understanding the evolutionary processes of bacterial organisms, as well as in epidemiology (the spread of disease), and phylogenetics (the study of historical evolutionary relationships). I am interested in thinking about "the way things work" and using mathematical ways of thinking to clarify problems.
This information has been contributed by Professor Francis.
Previous Projects
Title:  Algebraic algorithms for investigating the space of bacterial genomes 

Funder: 

Western Researchers:  Andrew Francis and Volker Gebhardt 
Years:  20130101  20151231 
ID:  P00020822 
Title:  Evolutionary models and bioinformatic analyses of genetic variation in pathogens [via UNSW] 
Funder: 

Western Researchers:  Andrew Francis 
Years:  20050101  20071231 
ID:  P0014704 
Title:  Internship for Geoscience Australia project 
Funder: 

Western Researchers:  Andrew Francis 
Years:  20150101  20151231 
ID:  P00024648 
Title:  Mathematical models and bioinformatic analyses of bacterial genome evolution [via UNSW] 
Funder: 

Western Researchers:  Andrew Francis 
Years:  20090106  20140530 
ID:  P00016641 
Title:  Algebraic evolution and evolutionary algebra 
Funder: 

Western Researchers:  Andrew Francis 
Years:  20101230  20150630 
ID:  P00018766 
Title:  An efficient approach to the computation of bacterial evolutionary distance (via UTAS) 
Funder: 

Western Researchers:  Andrew Francis 
Years:  20180101  20201231 
ID:  P00023905 
Supervision
Professor Francis is available to be a principal supervisor for doctoral projects
Current Supervision
Thesis Title:  The Evolution of Multiple Drug Resistance in Mycobacterium Tuberculosis 

Field of Research:  
Thesis Title:  Algebraic Models of Bacterial Genomes Evolving by Inversions and Deletions 
Field of Research: 
Media
Title:  We resigned from the ARC College of Experts  political meddling gave us no choice 

Description:  Article in The Guardian describing my decision to resign from the ARC College of Experts 