TurboTree: a fast algorithm for minimal trees. - David Penny; Michael D. Hendy (Comput. Appl. Biosci., 1987)

On the Distribution of Lengths of Evolutionary Trees. - M. Carter; Michael D. Hendy; David Penny; László A. Székely; Nicholas C. Wormald (SIAM J. Discret. Math., 1990)

A combinatorial description of the closest tree algorithm for finding evolutionary trees. - Michael D. Hendy (Discret. Math., 1991)

The path sets of weighted partially labelled trees. - Michael D. Hendy (Australas. J Comb., 1992)

The Effects of Sequence Length, Tree Topology, and Number of Taxa on the Performance of Phylogenetic Methods. - Michael A. Charleston; Michael D. Hendy; David Penny (J. Comput. Biol., 1994)

Reconstructing Trees When Sequence Sites Evolve at Variable Rates. - Mike A. Steel; László A. Székely; Michael D. Hendy (J. Comput. Biol., 1994)

Complete Families of Linear Invariants for Some Stochastic Models of Sequence Evolution, with and without Molecular Clock Assumption. - Michael D. Hendy; David Penny (J. Comput. Biol., 1996)

Reconstructing Phylogenies From Nucleotide Pattern Probabilities: A Survey and some New Results. - Mike A. Steel; Michael D. Hendy; David Penny (Discret. Appl. Math., 1998)

Multiple maxima of likelihood in phylogenetic trees: an analytic approach. - Benny Chor; Michael D. Hendy; Barbara R. Holland; David Penny (RECOMB, 2000)

Chromatically unique bipartite graphs with low 3-independent partition numbers. - Feng Ming Dong; Khee Meng Koh; Kee L. Teo; Charles H. C. Little; Michael D. Hendy (Discret. Math., 2000)

An attempt to classify bipartite graphs by chromatic polynomials. - Feng Ming Dong; Khee Meng Koh; Kee L. Teo; Charles H. C. Little; Michael D. Hendy (Discret. Math., 2000)

Analytic Solutions for Three-Taxon MLMC Trees with Variable Rates Across Sites. - Benny Chor; Michael D. Hendy; David Penny (WABI, 2001)

Sharp bounds for the number of 3-independent partitions and the chromaticity of bipartite graphs. - Feng Ming Dong; Khee Meng Koh; Kee L. Teo; C. H. C. Little; Michael D. Hendy (J. Graph Theory, 2001)

Two invariants for adjointly equivalent graphs. - Feng Ming Dong; Kee L. Teo; Charles H. C. Little; Michael D. Hendy (Australas. J Comb., 2002)

Zeros of adjoint polynomials of paths and cycles. - Feng Ming Dong; Kee L. Teo; Charles H. C. Little; Michael D. Hendy (Australas. J Comb., 2002)

The vertex-cover polynomial of a graph. - Feng Ming Dong; Michael D. Hendy; Kee L. Teo; Charles H. C. Little (Discret. Math., 2002)

Non-chordal graphs having integral-root chromatic polynomials II. - Feng Ming Dong; Kee L. Teo; Khee Meng Koh; Michael D. Hendy (Discret. Math., 2002)

Chromaticity of some families of dense graphs. - Feng Ming Dong; Kee L. Teo; Charles H. C. Little; Michael D. Hendy (Discret. Math., 2002)

Upper bounds on maximum likelihood for phylogenetic trees. - Michael D. Hendy; Barbara R. Holland (ECCB, 2003)

A Search for H/ACA SnoRNAs in Yeast Using MFE Secondary Structure Prediction. - Sverker Edvardsson; Paul P. Gardner; Anthony M. Poole; Michael D. Hendy; David Penny; Vincent Moulton (Bioinform., 2003)

Reconstructing phylogeny by Quadratically Approximated Maximum Likelihood. - M. D. Woodhams; Michael D. Hendy (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Graph-functions associated with an edge-property. - Feng Ming Dong; Michael D. Hendy; Kee L. Teo; Charles H. C. Little (Australas. J Comb., 2004)

Chromatically Unique Multibridge Graphs. - Feng Ming Dong; Kee L. Teo; Charles H. C. Little; Michael D. Hendy; Khee Meng Koh (Electron. J. Comb., 2004)

Hadamard conjugation: an analytic tool for phylogenetics. - Michael D. Hendy (Mathematics of Evolution and Phylogeny, 2007)

Analytic solutions for three taxon ML trees with variable rates across sites. - Benny Chor; Michael D. Hendy; David Penny (Discret. Appl. Math., 2007)

Compressing DNA sequence databases with coil. - W. Timothy J. White; Michael D. Hendy (BMC Bioinform., 2008)

Hadamard Conjugation for the Kimura 3ST Model: Combinatorial Proof Using Path Sets. - Michael D. Hendy; Sagi Snir (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

An Algorithm to Solve the Motif Alignment Problem for Approximate Nested Tandem Repeats. - Atheer A. Matroud; Michael D. Hendy; Christopher P. Tuffley (RECOMB-CG, 2010)

An Algorithm to Solve the Motif Alignment Problem for Approximate Nested Tandem Repeats in Biological Sequences. - Atheer A. Matroud; Christopher P. Tuffley; Michael D. Hendy (J. Comput. Biol., 2011)

A Comparison of Three Heuristic Methods for Solving the Parsing Problem for Tandem Repeats. - Atheer A. Matroud; Christopher P. Tuffley; David Bryant; Michael D. Hendy (BSB, 2012)

An Asymmetric Alignment Algorithm for Estimating Ancestor-Descendant Edit Distance for Tandem Repeats. - Atheer A. Matroud; Christopher P. Tuffley; Michael D. Hendy (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)