Professor Andrew Francis

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Professor Andrew Francis

Head of School

PhD, University of New South Wales, 1999

BSc (Hons I), University of Sydney, 1994.

Science

School of Mathematics & Statistics

I joined ��Ʊ in May 2024 as a Professor of Mathematics, and Head of the School of Mathematics and Statistics.

My academic career began with study in Pure Mathematics at the University of Sydney and the University of New South Wales, followed by a postdoctoral position at the University of Virginia. I worked at Western Sydney University from 2000 to early 2024, during which time I moved from Lecturer to Professor, and had a number of interesting opportunities. I held an ARC Future Fellowship from 2011 to 2014, to develop algebraic models of bacterial genome evolution; led a research centre in mathematics and data science; and spent the covid years (2020-23) as the Deputy Dean of my School. I have had further significant involvement with the Australian Research Council, for instance serving on ERA panels in 2015 and 2018, and on the College of Experts 2018-2021. I continue to serve roles for the ARC, and for the Australian Mathematical Society.

E-mail

a.francis@unsw.edu.au

Location

School of Mathematics and Statistics ��Ʊ Sydney Anita B. Lawrence Centre Room 3075

Book Chapters | 2023

Chowdhury TK; Park LAF; Stone G; Tanaka MM; Francis A, 2023, 'Estimating the relative contribution of transmission to the prevalence of drug resistance in tuberculosis', in Data Driven Science for Clinically Actionable Knowledge in Diseases, pp. 64 - 91,

Book Chapters | 2018

Rodrigues G; Francis A; Sisson S; Tanaka M, 2018, 'Inferences on the acquisition of multidrug resistance in Mycobacterium tuberculosis using molecular epidemiological data', in Sisson S; Fan Y; Beaumont M (ed.), Approximate Bayesian Computation Likelihood-Free Methods for Complex Models, Chapman & Hall

Book Chapters | 2014

Egri-Nagy A; Francis AR; Gebhardt V, 2014, 'Bacterial genomics and computational group theory: The BioGAP package for GAP', in , pp. 67 - 74,
Journal articles | 2024

Francis A; Marchei D; Steel M, 2024, 'Phylogenetic network classes through the lens of expanding covers', Journal of Mathematical Biology, 88, pp. 58,

Journal articles | 2023

Clark C; Jonušas J; Mitchell JD; Francis A, 2023, 'An algebraic model for inversion and deletion in bacterial genome rearrangement', Journal of Mathematical Biology, 87, pp. 34,

Journal articles | 2023

Fischer M; Francis A; Wicke K, 2023, 'Phylogenetic Diversity Rankings in the Face of Extinctions: The Robustness of the Fair Proportion Index', Systematic Biology, 72, pp. 606 - 615,

Journal articles | 2023

Francis A; Steel M, 2023, 'Labellable Phylogenetic Networks', Bulletin of Mathematical Biology, 85,

Journal articles | 2022

Francis A; Huber KT; Moulton V; Wu T, 2022, 'Encoding and ordering X-cactuses', Advances in Applied Mathematics, 142,

Journal articles | 2022

Francis A; Jarvis PD, 2022, 'Brauer and partition diagram models for phylogenetic trees and forests', Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 478,

Journal articles | 2022

Pons JC; Coronado TM; Hendriksen M; Francis A, 2022, 'A polynomial invariant for a new class of phylogenetic networks', PLoS ONE, 17,

Journal articles | 2021

Erdős PL; Francis A; Mezei TR, 2021, 'Rooted NNI moves and distance-1 tail moves on tree-based phylogenetic networks', Discrete Applied Mathematics, 294, pp. 205 - 213,

Journal articles | 2021

Francis A; Huson DH; Steel M, 2021, 'Normalising phylogenetic networks', Molecular Phylogenetics and Evolution, 163,

Journal articles | 2020

Aandahl RZ; Bhatia S; Vaudagnotto N; Street AG; Francis AR; Tanaka MM, 2020, 'MERCAT: Visualising molecular epidemiology data combining genetic markers and drug resistance profiles', Infection, Genetics and Evolution, 77, pp. 104043,

Journal articles | 2020

Bhatia S; Egri-Nagy A; Serdoz S; Praeger CE; Gebhardt V; Francis A, 2020, 'A Path-Deformation Framework for Determining Weighted Genome Rearrangement Distance', Frontiers in Genetics, 11,

Journal articles | 2020

Fischer M; Francis A, 2020, 'How tree-based is my network? Proximity measures for unrooted phylogenetic networks', Discrete Applied Mathematics, 283, pp. 98 - 114,

Journal articles | 2020

Fischer M; Francis A, 2020, 'The Space of Tree-Based Phylogenetic Networks', Bulletin of Mathematical Biology, 82,

Journal articles | 2020

Francis AR; Wynn HP, 2020, 'A mean first passage time genome rearrangement distance', Journal of Mathematical Biology, 80, pp. 1971 - 1992,

Journal articles | 2020

Hendriksen M; Francis A, 2020, 'A partial order and cluster-similarity metric on rooted phylogenetic trees', Journal of Mathematical Biology, 80, pp. 1265 - 1290,

Journal articles | 2019

Clark C; Egri-Nagy A; Francis A; Gebhardt V, 2019, 'Bacterial phylogeny in the Cayley graph', Discrete Mathematics, Algorithms and Applications, 11,

Journal articles | 2019

Francis A; Huber KT; Moulton V, 2019, 'Correction to: Tree-Based Unrooted Phylogenetic Networks (Bulletin of Mathematical Biology, (2018), 80, 2, (404-416), 10.1007/s11538-017-0381-3)', Bulletin of Mathematical Biology, 81, pp. 936 - 937,

Journal articles | 2019

Hendriksen M; Francis A, 2019, 'Tree-metrizable HGT networks', Mathematical Biosciences, 318,

Journal articles | 2018

Bhatia S; Feijão P; Francis AR, 2018, 'Position and Content Paradigms in Genome Rearrangements: The Wild and Crazy World of Permutations in Genomics', Bulletin of Mathematical Biology, 80, pp. 3227 - 3246,

Journal articles | 2018

Francis A; Huber KT; Moulton V; Wu T, 2018, 'Bounds for phylogenetic network space metrics', Journal of Mathematical Biology, 76, pp. 1229 - 1248,

Journal articles | 2018

Francis A; Huber KT; Moulton V, 2018, 'Tree-Based Unrooted Phylogenetic Networks', Bulletin of Mathematical Biology, 80, pp. 404 - 416,

Journal articles | 2018

Francis A; Moulton V, 2018, 'Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution', Journal of Theoretical Biology, 446, pp. 160 - 167,

Journal articles | 2018

Francis A; Semple C; Steel M, 2018, 'New characterisations of tree-based networks and proximity measures', Advances in Applied Mathematics, 93, pp. 93 - 107,

Journal articles | 2017

Bryant D; Francis A; Steel M, 2017, 'Can We "future-Proof" Consensus Trees?', Systematic Biology, 66, pp. 611 - 619,

Journal articles | 2017

Francis AF; Stehlík M; Wynn HP, 2017, '"building" exact confidence nets', Bernoulli, 23, pp. 3145 - 3165,

Journal articles | 2017

Serdoz S; Egri-Nagy A; Sumner J; Holland BR; Jarvis PD; Tanaka MM; Francis AR, 2017, 'Maximum likelihood estimates of pairwise rearrangement distances', Journal of Theoretical Biology, 423, pp. 31 - 40,

Journal articles | 2017

Sumner JG; Jarvis PD; Francis AR, 2017, 'A representation-theoretic approach to the calculation of evolutionary distance in bacteria', Journal of Physics A: Mathematical and Theoretical, 50,

Journal articles | 2015

Bhatia S; Egri-Nagy A; Francis AR, 2015, 'Algebraic double cut and join: A group-theoretic approach to the operator on multichromosomal genomes', Journal of Mathematical Biology, 71, pp. 1149 - 1178,

Journal articles | 2015

Francis AR; Steel M, 2015, 'Tree-like reticulation networks-When do tree-like distances also support reticulate evolution?', Mathematical Biosciences, 259, pp. 12 - 19,

Journal articles | 2015

Francis AR; Steel M, 2015, 'Which phylogenetic networks are merely trees with additional arcs?', Systematic Biology, 64, pp. 768 - 777,

Journal articles | 2014

Bak T; Chu D; Francis AR; Li W; Nowotny J, 2014, 'Concentration of electrons at grain boundaries in TiO2 (rutile): Impact on charge transport and reactivity', Catalysis Today, 224, pp. 200 - 208,

Journal articles | 2014

Egri-Nagy A; Gebhardt V; Tanaka MM; Francis AR, 2014, 'Group-theoretic models of the inversion process in bacterial genomes', Journal of Mathematical Biology, 69, pp. 243 - 265,

Journal articles | 2014

Francis AR; Wynn HP, 2014, 'Subgroup majorization', Linear Algebra and Its Applications, 444, pp. 53 - 66,

Journal articles | 2014

Francis AR, 2014, 'An algebraic view of bacterial genome evolution', Journal of Mathematical Biology, 69, pp. 1693 - 1718,

Journal articles | 2013

Bak T; Li W; Nowotny J; Chu D; Francis AR, 2013, 'Concentration of electrons at grain boundaries in TiO (rutile): Impact on charge transport and reactivity', Catalysis Today,

Journal articles | 2012

Francis AR; Tanaka M, 2012, 'Evolution of variation in presence and absence of genes in bacterial pathways', BMC Evolutionary Biology, 12, pp. 1 - 11,

Journal articles | 2011

Francis A; Jones L, 2011, 'Monomial bases for the centres of the group algebra and iwahori-hecke algebra of the symmetric group', Far East Journal of Mathematical Sciences, 58, pp. 119 - 143

Journal articles | 2010

Ballouz S; Lan R; Francis AR; Tanaka M, 2010, 'Conditions for the evolution of gene clusters in bacterial genomes.', PLoS Computational Biology, 6, pp. e1000672 - e1000672,

Journal articles | 2010

Stevenson PG; Mnatsakanyan M; Francis AR; Shalliker RA, 2010, 'A discussion on the process of defining 2-D separation selectivity', Journal of Separation Science, 33, pp. 1405 - 1413,

Journal articles | 2009

Francis A; Jones L, 2009, 'A new integral basis for the centre of the Iwahori-Hecke algebra of type A', Journal of Algebra, 321, pp. 866 - 878,

Journal articles | 2009

Luciani F; Sisson SA; Jiang H; Francis AR; 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, 106, pp. 14711 - 14715,

Journal articles | 2008

Luciani F; Francis AR; Tanaka M, 2008, 'Interpreting genotype cluster sizes of Mycobacterium tuberculosis isolates typed with IS6110 and spoligotyping', Infection Genetics and Evolution, 8, pp. 182 - 190,

Journal articles | 2008

Reyes JF; Francis AR; Tanaka M, 2008, 'Models of deletion for visualizing bacterial variation: an application to tuberculosis spoligotypes', BMC bioinformatics, 9, pp. 496 - 511

Journal articles | 2008

Tang C; Reyes JF; Luciani F; Francis AR; Tanaka M, 2008, 'spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex', Bioinformatics, 24, pp. 2414 - 2415,

Journal articles | 2007

Francis A; Jones L, 2007, 'On the square root of the centre of the Hecke algebra of type a', Journal of the Australian Mathematical Society, 82, pp. 209 - 220,

Journal articles | 2006

Francis AR; Graham JJ, 2006, 'Centres of Hecke algebras: The Dipper-James conjecture', Journal of Algebra, 306, pp. 244 - 267,

Journal articles | 2006

Tanaka M; Francis AR; Luciani F; Sisson SA, 2006, 'Using approximate Bayesian computation to estimate tuberculosis transmission parameters from genotype data', Genetics, 173, pp. 1511 - 1520,

Journal articles | 2006

Tanaka M; Francis AR, 2006, 'Detecting emerging strains of tuberculosis by using spoligotypes', Proceedings of the National Academy of Sciences of the United States of America, 103, pp. 15266 - 15271

Journal articles | 2006

Tanaka M; Phong R; Francis AR, 2006, 'An evaluation of indices for quantifying tuberculosis transmission using genotypes of pathogen isolates', BMC Infectious Diseases, 6

Journal articles | 2005

Francis A; Jones L, 2005, 'On bases of centres of Iwahori-Hecke algebras of the symmetric group', Journal of Algebra, 289, pp. 42 - 69,

Journal articles | 2005

Tanaka M; Francis AR, 2005, 'Methods of quantifying and visualising outbreaks of tuberculosis using genotypic information', Infection Genetics and Evolution, 5, pp. 35 - 43

Journal articles | 2003

Francis A, 2003, 'Centralizers of Iwahori-Hecke algebras II: The general case', Algebra Colloquium, 10, pp. 95 - 100,

Journal articles | 2001

Francis A, 2001, 'Centralizers of Iwahori-Hecke algebras', Transactions of the American Mathematical Society, pp. 2725 - 2739

Journal articles | 2001

Francis A, 2001, 'The Brauer homomorphism and the minimal basis for centers of Iwahori-Hecke algebras of type A', Communications in Algebra, pp. 85 - 97

Journal articles | 1999

Francis A, 1999, 'The minimal basis for the centre of an Iwahori-Hecke algebra', Journal of Algebra, pp. 1 - 28
Preprints | 2024

Marchei D; Merelli E; Francis A, 2024, Factorizing the Brauer monoid in polynomial time,

Preprints | 2023

Francis A; Marchei D; Steel M, 2023, Phylogenetic network classes through the lens of expanding covers,

Preprints | 2022

Clark C; Jonušas J; Mitchell JD; Francis A, 2022, An algebraic model for inversion and deletion in bacterial genome rearrangement,

Preprints | 2021

Fischer M; Francis A; Wicke K, 2021, Phylogenetic Diversity Rankings in the Face of Extinctions: the Robustness of the Fair Proportion Index,

Preprints | 2021

Francis A; Huber KT; Moulton V; Wu T, 2021, Encoding and ordering X-cactuses,

Preprints | 2021

Francis A; Jarvis PD, 2021, Brauer and partition diagram models for phylogenetic trees and forests,

Preprints | 2021

Francis A, 2021, "Normal" phylogenetic networks may be emerging as the leading class,

Preprints | 2021

Pons JC; Coronado TM; Hendriksen M; Francis A, 2021, A polynomial invariant for a new class of phylogenetic networks,

Preprints | 2020

Bhatia S; Egri-Nagy A; Serdoz S; Praeger CE; Gebhardt V; Francis A, 2020, A path-deformation framework for determining weighted genome rearrangement distance,

Preprints | 2020

Erdős PL; Francis A; Mezei TR, 2020, Rooted NNI moves on tree-based phylogenetic networks,

Preprints | 2020

Francis A; Guo Y; Hurley P; Obst O; Park L; Tanaka M; Thomson R; Wang XR, 2020, Projected ICU and Mortuary load due to COVID-19 in Sydney,

Preprints | 2019

Fischer M; Francis A, 2019, How tree-based is my network? Proximity measures for unrooted phylogenetic networks,

Preprints | 2019

Fischer M; Francis A, 2019, The space of tree-based phylogenetic networks,

Preprints | 2019

Francis A; Wynn H, 2019, A mean first passage time genome rearrangement distance,

Preprints | 2019

Hendriksen M; Francis A, 2019, A partial order and cluster-similarity metric on rooted phylogenetic trees,

Preprints | 2019

Hendriksen M; Francis A, 2019, Tree-metrizable HGT networks,

Preprints | 2018

Hendriksen M; Francis A, 2018, Lattice consensus: A partial order on phylogenetic trees that induces an associatively stable consensus method,

Preprints | 2017

Francis A; Huber K; Moulton V; Wu T, 2017, Bounds for phylogenetic network space metrics,

Preprints | 2017

Francis A; Huber K; Moulton V, 2017, Tree-based unrooted phylogenetic networks,

Preprints | 2017

Francis A; Moulton V, 2017, Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution,

Preprints | 2017

Rodrigues GS; Francis AR; Sisson SA; Tanaka MM, 2017, Inferences on the acquisition of multidrug resistance in \emph{Mycobacterium tuberculosis} using molecular epidemiological data,

Preprints | 2016

Bhatia S; Feijão P; Francis AR, 2016, Position and content paradigms in genome rearrangements: the wild and crazy world of permutations in genomics,

Preprints | 2016

Bryant D; Francis A; Steel M, 2016, Can we 'future-proof' consensus trees?,

Preprints | 2016

Clark C; Egri-Nagy A; Francis AR; Gebhardt V, 2016, Bacterial phylogeny in the Cayley graph,

Preprints | 2016

Francis A; Semple C; Steel M, 2016, New Characterisations of Tree-Based Networks and Proximity Measures,

Preprints | 2016

Serdoz S; Egri-Nagy A; Sumner J; Holland BR; Jarvis PD; Tanaka MM; Francis AR, 2016, Maximum likelihood estimates of pairwise rearrangement distances,

Preprints | 2016

Sumner JG; Jarvis PD; Francis AR, 2016, A representation-theoretic approach to the calculation of evolutionary distance in bacteria,

Preprints | 2015

East J; Egri-Nagy A; Francis AR; Mitchell JD, 2015, Finite Diagram Semigroups: Extending the Computational Horizon,

Preprints | 2015

Francis AR; Steel M, 2015, Which phylogenetic networks are merely trees with additional arcs?,

Preprints | 2014

Bhatia S; Egri-Nagy A; Francis AR, 2014, Algebraic double cut and join -- A group-theoretic approach to the operator on multichromosomal genomes,

Preprints | 2014

Egri-Nagy A; Gebhardt V; Tanaka MM; Francis AR, 2014, Group-theoretic models of the inversion process in bacterial genomes,

Preprints | 2014

Francis AR; Steel M, 2014, Tree-like Reticulation Networks - When Do Tree-like Distances Also Support Reticulate Evolution?,

Preprints | 2014

Francis AR; Stehlik M; Wynn HP, 2014, "Building" exact confidence nets,

Preprints | 2013

Francis AR; Wynn HP, 2013, Subgroup Majorization,

Preprints | 2013

Francis AR, 2013, An algebraic view of bacterial genome evolution,

Preprints | 2012

Francis A; Jones L, 2012, Multiplicative Bases for the Centres of the Group Algebra and Iwahori-Hecke Algebra of the Symmetric Group,

Preprints | 2008

Francis A; Wang W, 2008, The centers of Iwahori-Hecke algebras are filtered,

Preprints | 2007

Francis A; Jones L, 2007, A new integral basis for the centre of the Hecke algebra of type A,

Preprints | 2007

Francis A; Jones L, 2007, Monomial bases for the centres of the group algebra and Iwahori--Hecke algebra of S_4,

Preprints | 2007

Francis A; Jones L, 2007, On the square root of the centre of the Hecke algebra of type A,

Conference Papers | 2007

Francis A; Wang W, 2007,

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