A Probabilistic Algorithm for Gene-Species Reconciliation with Segmental Duplications.

Michael A. Charleston

Yao-ban Chan Céline Scornavacca Michael A. Charleston A Probabilistic Algorithm for Gene-Species Reconciliation with Segmental Duplications. 2026 203-218 33 J. Comput. Biol. 2 https://doi.org/10.1177/15578666251392595 db/journals/jcb/jcb33.html#ChanSC26 streams/journals/jcb

Raima Carol Appaw Nicholas Fountain-Jones Michael A. Charleston What makes a small-world network? Leveraging machine learning for the robust prediction and classification of networks. 2024 abs/2403.13215 CoRR https://doi.org/10.48550/arXiv.2403.13215 db/journals/corr/corr2403.html#abs-2403-13215

K. V. S. N. Rama Rao James Montgomery 0001 Saurabh Kumar Garg 0001 Michael A. Charleston Bioacoustics Data Analysis - A Taxonomy, Survey and Open Challenges. 57684-57708 2020 8 IEEE Access https://doi.org/10.1109/ACCESS.2020.2978547 https://www.wikidata.org/entity/Q133893694 db/journals/access/access8.html#RaoMGC20

Maria Victoria Schneider Philippa C. Griffin Sonika Tyagi Madison Flannery Saravanan Dayalan Simon Gladman Nathan S. Watson-Haigh Philipp E. Bayer Michael A. Charleston Ira Cooke Rob Cook Richard J. Edwards David Edwards Dominique Gorse Malcolm J. McConville David Powell Marc R. Wilkins Andrew Lonie Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. 384-389 2019 20 Briefings Bioinform. 2 https://doi.org/10.1093/bib/bbx071 https://www.wikidata.org/entity/Q47225773 db/journals/bib/bib20.html#SchneiderGTFDGW19

Michael A. Charleston Molecular Phylogenetics. 700-711 2019 Encyclopedia of Bioinformatics and Computational Biology (2) https://doi.org/10.1016/b978-0-12-809633-8.20675-4 reference/bioinf/2019-2 db/reference/bioinf/ebcb2019-2.html#Charleston19

Benjamin Drinkwater Michael A. Charleston Towards sub-quadratic time and space complexity solutions for the dated tree reconciliation problem. 15 2016 11 Algorithms Mol. Biol. https://doi.org/10.1186/s13015-016-0077-5 https://www.wikidata.org/entity/Q39744708 db/journals/almob/almob11.html#DrinkwaterC16

Benjamin Drinkwater Michael A. Charleston RASCAL: A Randomized Approach for Coevolutionary Analysis. 218-227 2016 23 J. Comput. Biol. 3 https://doi.org/10.1089/cmb.2015.0111 https://www.wikidata.org/entity/Q40038842 db/journals/jcb/jcb23.html#DrinkwaterC16

Martin McGrane Michael A. Charleston Biological Network Edit Distance. 776-788 2016 23 J. Comput. Biol. 9 https://doi.org/10.1089/cmb.2016.0062 https://www.wikidata.org/entity/Q50626261 db/journals/jcb/jcb23.html#McGraneC16

Vincent Gramoli Michael A. Charleston Bryn Jeffries Irena Koprinska Martin McGrane Alex Radu Anastasios Viglas Kalina Yacef Mining autograding data in computer science education. 1 2016 ACSW https://doi.org/10.1145/2843043.2843070 conf/acsc/2016 db/conf/acsc/acsw2016.html#GramoliCJKMRVY16

Cali E. Willet Bianca Haase Michael A. Charleston Claire M. Wade Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker. 599-601 2015 31 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btu691 https://www.wikidata.org/entity/Q42689522 db/journals/bioinformatics/bioinformatics31.html#WilletHCW15

Benjamin Drinkwater Michael A. Charleston A time and space complexity reduction for coevolutionary analysis of trees generated under both a Yule and Uniform model. 61-71 2015 57 Comput. Biol. Chem. https://doi.org/10.1016/j.compbiolchem.2015.02.003 https://www.wikidata.org/entity/Q39019400 db/journals/candc/candc57.html#DrinkwaterC15

Alex Radu Michael A. Charleston Node Handprinting: A Scalable and Accurate Algorithm for Aligning Multiple Biological Networks. 687-697 2015 22 J. Comput. Biol. 7 https://doi.org/10.1089/cmb.2014.0247 https://www.wikidata.org/entity/Q41475330 db/journals/jcb/jcb22.html#RaduC15

Alistair M. Senior Michael A. Charleston Mathieu Lihoreau Jérôme Buhl David Raubenheimer Stephen J. Simpson Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model. 2015 11 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1004111 https://www.wikidata.org/entity/Q35224254 db/journals/ploscb/ploscb11.html#SeniorCLBRS15

Benjamin Drinkwater Michael A. Charleston A Sub-quadratic Time and Space Complexity Solution for the Dated Tree Reconciliation Problem for Select Tree Topologies. 93-107 2015 WABI https://doi.org/10.1007/978-3-662-48221-6_7 conf/wabi/2015 db/conf/wabi/wabi2015.html#DrinkwaterC15

Benjamin Drinkwater Michael A. Charleston Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem. S14 2014 15 BMC Bioinform. S-16 https://doi.org/10.1186/1471-2105-15-S16-S14 https://www.wikidata.org/entity/Q35529523 db/journals/bmcbi/bmcbi15S.html#DrinkwaterC14

Alex Radu Michael A. Charleston Node Fingerprinting: An Efficient Heuristic for Aligning Biological Networks. 760-770 2014 21 J. Comput. Biol. 10 https://doi.org/10.1089/cmb.2014.0114 https://www.wikidata.org/entity/Q51051771 db/journals/jcb/jcb21.html#RaduC14

Ilana Lichtenstein Michael A. Charleston Tibério S. Caetano Jennifer R. Gamble Mathew A. Vadas Active Subnetwork Recovery with a Mechanism-Dependent Scoring Function; with application to Angiogenesis and Organogenesis studies. 59 2013 14 BMC Bioinform. https://doi.org/10.1186/1471-2105-14-59 https://www.wikidata.org/entity/Q34595978 db/journals/bmcbi/bmcbi14.html#LichtensteinCCGV13

Richard Gluga Judy Kay Raymond Lister Simon Michael A. Charleston James Harland Donna Teague A conceptual model for reflecting on expected learning vs. demonstrated student performance. 77-86 2013 ACE http://dl.acm.org/citation.cfm?id=2667208 conf/ace/2013 db/conf/ace/ace2013.html#GlugaKLSCHT13

Md. Shaik Sadi Fei-Ching Kuo Joshua Wing Kei Ho Michael A. Charleston Tsong Yueh Chen Verification of phylogenetic Inference Programs Using Metamorphic Testing. 729-747 2011 9 J. Bioinform. Comput. Biol. 6 https://doi.org/10.1142/S021972001100563X https://www.wikidata.org/entity/Q51498288 db/journals/jbcb/jbcb9.html#SadiKHCC11

Ran Libeskind-Hadas Michael A. Charleston On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem. 105-117 2009 16 J. Comput. Biol. 1 https://doi.org/10.1089/cmb.2008.0084 https://www.wikidata.org/entity/Q46611191 db/journals/jcb/jcb16.html#Libeskind-HadasC09

Joshua Wing Kei Ho Maurizio Stefani Cristobal G. dos Remedios Michael A. Charleston Differential variability analysis of gene expression and its application to human diseases. 390-398 2008 ISMB https://doi.org/10.1093/bioinformatics/btn142 https://www.wikidata.org/entity/Q37283258 conf/ismb/2008 db/conf/ismb/ismb2008.html#HoSRC08

Jeremy G. Sumner Michael A. Charleston Phylogenetic estimation with partial likelihood tensors http://arxiv.org/abs/0807.3387 2008 CoRR abs/0807.3387 db/journals/corr/corr0807.html#abs-0807-3387

Ali Al Mazari Albert Y. Zomaya Michael A. Charleston Roger J. Garsia A Novel Algorithm for Adaptive and Neutral Evolutionary Patterns Associated with HIV Drug Resistance. 285-292 2007 conf/aiccsa/2007 AICCSA https://doi.org/10.1109/AICCSA.2007.370896 https://doi.ieeecomputersociety.org/10.1109/AICCSA.2007.370896 db/conf/aiccsa/aiccsa2007.html#MazariZCG07

Michael A. Charleston Susan L. Perkins Traversing the tangle: Algorithms and applications for cophylogenetic studies. 62-71 2006 39 J. Biomed. Informatics 1 https://doi.org/10.1016/j.jbi.2005.08.006 https://www.wikidata.org/entity/Q36287349 db/journals/jbi/jbi39.html#CharlestonP06

Michael A. Charleston Alison P. Galvani A cophylogenetic perspective on host-pathogen evolution. 145-160 2006 Disease Evolution: Models, Concepts, and Data Analyses conf/dimacs/dimacs71 db/conf/dimacs/dimacs71.html#CharlestonG06 https://doi.org/10.1090/dimacs/071/07

Michael A. Charleston Hitch-Hiking: A Parallel Heuristic Search Strategy, Applied to the Phylogeny Problem. 79-91 2001 8 J. Comput. Biol. 1 db/journals/jcb/jcb8.html#Charleston01 https://doi.org/10.1089/106652701300099137 https://www.wikidata.org/entity/Q52064401

Michael A. Charleston Spectrum: spectral analysis of phylogenetic data. 98-99 1998 14 Bioinform. 1 db/journals/bioinformatics/bioinformatics14.html#Charleston98 https://doi.org/10.1093/bioinformatics/14.1.98 https://www.wikidata.org/entity/Q32081232

Roderic D. M. Page Michael A. Charleston Reconciled trees and incongruent gene and species trees. 57-70 1996 Mathematical Hierarchies and Biology conf/dimacs/dimacs37 db/conf/dimacs/dimacs37.html#PageC96 https://doi.org/10.1090/dimacs/037/04

Michael A. Charleston Toward a Characterization of Landscapes of Combinatorial Optimization Problems, with Special Attention to the Phylogeny Problem. 439-450 1995 2 J. Comput. Biol. 3 db/journals/jcb/jcb2.html#Charleston95 https://doi.org/10.1089/cmb.1995.2.439 https://www.wikidata.org/entity/Q48793645

Michael A. Charleston Michael D. Hendy David Penny The Effects of Sequence Length, Tree Topology, and Number of Taxa on the Performance of Phylogenetic Methods. 133-151 1994 1 J. Comput. Biol. 2 https://doi.org/10.1089/cmb.1994.1.133 https://www.wikidata.org/entity/Q38562246 db/journals/jcb/jcb1.html#CharlestonHP94

Raima Carol Appaw Philipp E. Bayer Jérôme Buhl Tibério S. Caetano Yao-ban Chan Tsong Yueh Chen Rob Cook Ira Cooke Saravanan Dayalan Benjamin Drinkwater David Edwards Richard J. Edwards Madison Flannery Nicholas Fountain-Jones Alison P. Galvani Jennifer R. Gamble Saurabh Kumar Garg 0001 Roger J. Garsia Simon Gladman Richard Gluga Dominique Gorse Vincent Gramoli Philippa C. Griffin Bianca Haase James Harland Michael D. Hendy Joshua W. K. HoJoshua Wing Kei Ho Bryn Jeffries Judy Kay Irena Koprinska Fei-Ching Kuo Ran Libeskind-Hadas Ilana Lichtenstein Mathieu Lihoreau Raymond Lister Andrew Lonie Ali Al Mazari Malcolm J. McConville Martin McGrane James Montgomery 0001 Roderic D. M. Page David Penny Susan L. Perkins David Powell Alex Radu K. V. S. N. Rama Rao David Raubenheimer Cristobal G. dos Remedios Md. Shaik Sadi Maria Victoria Schneider Céline Scornavacca Alistair M. Senior Simon Stephen J. Simpson Maurizio Stefani Jeremy G. Sumner Donna Teague Sonika Tyagi Mathew A. Vadas Anastasios Viglas Claire M. Wade Nathan S. Watson-Haigh Marc R. Wilkins Cali E. Willet Kalina Yacef Albert Y. Zomaya