By Mr Andrew Ranald Francis

Book Chapters

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, http://dx.doi.org/10.1201/9781003292357-3

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

Egri-Nagy A; Francis AR; Gebhardt V, 2014, 'Bacterial genomics and computational group theory: The BioGAP package for GAP', in , pp. 67 - 74, http://dx.doi.org/10.1007/978-3-662-44199-2_12

Journal articles

Francis A; Marchei D; Steel M, 2024, 'Phylogenetic network classes through the lens of expanding covers', Journal of Mathematical Biology, 88, pp. 58, http://dx.doi.org/10.1007/s00285-024-02075-y

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, http://dx.doi.org/10.1007/s00285-023-01965-x

Francis A; Steel M, 2023, 'Labellable Phylogenetic Networks', Bulletin of Mathematical Biology, 85, http://dx.doi.org/10.1007/s11538-023-01157-0

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, http://dx.doi.org/10.1093/sysbio/syac030

Pons JC; Coronado TM; Hendriksen M; Francis A, 2022, 'A polynomial invariant for a new class of phylogenetic networks', PLoS ONE, 17, http://dx.doi.org/10.1371/journal.pone.0268181

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, http://dx.doi.org/10.1098/rspa.2022.0044

Francis A; Huber KT; Moulton V; Wu T, 2022, 'Encoding and ordering X-cactuses', Advances in Applied Mathematics, 142, http://dx.doi.org/10.1016/j.aam.2022.102414

Francis A; Huson DH; Steel M, 2021, 'Normalising phylogenetic networks', Molecular Phylogenetics and Evolution, 163, http://dx.doi.org/10.1016/j.ympev.2021.107215

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, http://dx.doi.org/10.1016/j.dam.2021.02.016

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, http://dx.doi.org/10.3389/fgene.2020.01035

Fischer M; Francis A, 2020, 'How tree-based is my network? Proximity measures for unrooted phylogenetic networks', Discrete Applied Mathematics, 283, pp. 98 - 114, http://dx.doi.org/10.1016/j.dam.2019.12.019

Fischer M; Francis A, 2020, 'The Space of Tree-Based Phylogenetic Networks', Bulletin of Mathematical Biology, 82, http://dx.doi.org/10.1007/s11538-020-00744-9

Francis AR; Wynn HP, 2020, 'A mean first passage time genome rearrangement distance', Journal of Mathematical Biology, 80, pp. 1971 - 1992, http://dx.doi.org/10.1007/s00285-020-01487-w

Hendriksen M; Francis A, 2020, 'A partial order and cluster-similarity metric on rooted phylogenetic trees', Journal of Mathematical Biology, 80, pp. 1265 - 1290, http://dx.doi.org/10.1007/s00285-019-01461-1

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, http://dx.doi.org/10.1016/j.meegid.2019.104043

Hendriksen M; Francis A, 2019, 'Tree-metrizable HGT networks', Mathematical Biosciences, 318, http://dx.doi.org/10.1016/j.mbs.2019.108283

Clark C; Egri-Nagy A; Francis A; Gebhardt V, 2019, 'Bacterial phylogeny in the Cayley graph', Discrete Mathematics, Algorithms and Applications, 11, http://dx.doi.org/10.1142/S1793830919500599

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, http://dx.doi.org/10.1007/s11538-018-0530-3

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, http://dx.doi.org/10.1007/s11538-018-0514-3

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, http://dx.doi.org/10.1016/j.jtbi.2018.03.011

Francis A; Huber KT; Moulton V; Wu T, 2018, 'Bounds for phylogenetic network space metrics', Journal of Mathematical Biology, 76, pp. 1229 - 1248, http://dx.doi.org/10.1007/s00285-017-1171-0

Francis A; Semple C; Steel M, 2018, 'New characterisations of tree-based networks and proximity measures', Advances in Applied Mathematics, 93, pp. 93 - 107, http://dx.doi.org/10.1016/j.aam.2017.08.003

Francis A; Huber KT; Moulton V, 2018, 'Tree-Based Unrooted Phylogenetic Networks', Bulletin of Mathematical Biology, 80, pp. 404 - 416, http://dx.doi.org/10.1007/s11538-017-0381-3

Francis AF; Stehlík M; Wynn HP, 2017, '"building" exact confidence nets', Bernoulli, 23, pp. 3145 - 3165, http://dx.doi.org/10.3150/16-BEJ839

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, http://dx.doi.org/10.1088/1751-8121/aa7d60

Bryant D; Francis A; Steel M, 2017, 'Can We "future-Proof" Consensus Trees?', Systematic Biology, 66, pp. 611 - 619, http://dx.doi.org/10.1093/sysbio/syx030

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, http://dx.doi.org/10.1016/j.jtbi.2017.04.015

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, http://dx.doi.org/10.1007/s00285-014-0852-1

Francis AR; Steel M, 2015, 'Which phylogenetic networks are merely trees with additional arcs?', Systematic Biology, 64, pp. 768 - 777, http://dx.doi.org/10.1093/sysbio/syv037

Francis AR; Steel M, 2015, 'Tree-like reticulation networks-When do tree-like distances also support reticulate evolution?', Mathematical Biosciences, 259, pp. 12 - 19, http://dx.doi.org/10.1016/j.mbs.2014.10.008

Francis AR, 2014, 'An algebraic view of bacterial genome evolution', Journal of Mathematical Biology, 69, pp. 1693 - 1718, http://dx.doi.org/10.1007/s00285-013-0747-6

Francis AR; Wynn HP, 2014, 'Subgroup majorization', Linear Algebra and Its Applications, 444, pp. 53 - 66, http://dx.doi.org/10.1016/j.laa.2013.11.042

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, http://dx.doi.org/10.1016/j.cattod.2013.11.039

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, http://dx.doi.org/10.1007/s00285-013-0702-6

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, http://dx.doi.org/10.1016/j.cattod.2013.11.039

Francis AR; Tanaka M, 2012, 'Evolution of variation in presence and absence of genes in bacterial pathways', BMC Evolutionary Biology, 12, pp. 1 - 11, http://dx.doi.org/10.1186/1471-2148-12-55

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

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, http://dx.doi.org/10.1002/jssc.200900779

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, http://dx.doi.org/10.1371/journal.pcbi.1000672

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, http://dx.doi.org/10.1016/j.jalgebra.2008.10.018

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, http://dx.doi.org/10.1073/pnas.0902437106

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, http://dx.doi.org/10.1016/j.meegid.2007.12.004

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

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, http://dx.doi.org/10.1093/bioinformatics/btn434

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, http://dx.doi.org/10.1017/s1446788700016037

Francis AR; Graham JJ, 2006, 'Centres of Hecke algebras: The Dipper-James conjecture', Journal of Algebra, 306, pp. 244 - 267, http://dx.doi.org/10.1016/j.jalgebra.2006.05.010

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

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