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Optimal alphabets for an RNA world.
Gardner PP, Holland BR, Moulton V, Hendy M, Penny D. Gardner PP, et al. Proc Biol Sci. 2003 Jun 7;270(1520):1177-82. doi: 10.1098/rspb.2003.2355. Proc Biol Sci. 2003. PMID: 12816657 Free PMC article.
Estimating the reliability of evolutionary trees.
Penny D, Hendy M. Penny D, et al. Mol Biol Evol. 1986 Sep;3(5):403-17. doi: 10.1093/oxfordjournals.molbev.a040407. Mol Biol Evol. 1986. PMID: 2832694
Distribution of the number of matches between nucleotide sequences.
Rinsma I, Hendy M, Penny D. Rinsma I, et al. Bull Math Biol. 1990;52(3):349-58. doi: 10.1007/BF02458576. Bull Math Biol. 1990. PMID: 2379020
A bias in ML estimates of branch lengths in the presence of multiple signals.
Penny D, White WT, Hendy MD, Phillips MJ. Penny D, et al. Mol Biol Evol. 2008 Feb;25(2):239-42. doi: 10.1093/molbev/msm263. Epub 2007 Nov 28. Mol Biol Evol. 2008. PMID: 18048399
LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites.
Shavit Grievink L, Penny D, Hendy MD, Holland BR. Shavit Grievink L, et al. Among authors: hendy md. BMC Evol Biol. 2008 Nov 21;8:317. doi: 10.1186/1471-2148-8-317. BMC Evol Biol. 2008. PMID: 19021917 Free PMC article.
Compressing DNA sequence databases with coil.
White WT, Hendy MD. White WT, et al. BMC Bioinformatics. 2008 May 20;9:242. doi: 10.1186/1471-2105-9-242. BMC Bioinformatics. 2008. PMID: 18489794 Free PMC article.
Hadamard conjugation for the Kimura 3ST model: combinatorial proof using path sets.
Hendy MD, Snir S. Hendy MD, et al. IEEE/ACM Trans Comput Biol Bioinform. 2008 Jul-Sep;5(3):461-71. doi: 10.1109/TCBB.2007.70227. IEEE/ACM Trans Comput Biol Bioinform. 2008. PMID: 18670048
Upper bounds on maximum likelihood for phylogenetic trees.
Hendy MD, Holland BR. Hendy MD, et al. Bioinformatics. 2003 Oct;19 Suppl 2:ii66-72. doi: 10.1093/bioinformatics/btg1062. Bioinformatics. 2003. PMID: 14534174
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