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A novel algorithm and web-based tool for comparing two alternative phylogenetic trees.
Nye TM, Liò P, Gilks WR. Nye TM, et al. Bioinformatics. 2006 Jan 1;22(1):117-9. doi: 10.1093/bioinformatics/bti720. Epub 2005 Oct 18. Bioinformatics. 2006. PMID: 16234319
Statistical analysis of domains in interacting protein pairs.
Nye TM, Berzuini C, Gilks WR, Babu MM, Teichmann SA. Nye TM, et al. Bioinformatics. 2005 Apr 1;21(7):993-1001. doi: 10.1093/bioinformatics/bti086. Epub 2004 Oct 27. Bioinformatics. 2005. PMID: 15509600
New substitution models for rooting phylogenetic trees.
Williams TA, Heaps SE, Cherlin S, Nye TM, Boys RJ, Embley TM. Williams TA, et al. Among authors: nye tm. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140336. doi: 10.1098/rstb.2014.0336. Philos Trans R Soc Lond B Biol Sci. 2015. PMID: 26323766 Free PMC article.
Trees of trees: an approach to comparing multiple alternative phylogenies.
Nye TM. Nye TM. Syst Biol. 2008 Oct;57(5):785-94. doi: 10.1080/10635150802424072. Syst Biol. 2008. PMID: 18853364
An Algorithm for Constructing Principal Geodesics in Phylogenetic Treespace.
Nye TM. Nye TM. IEEE/ACM Trans Comput Biol Bioinform. 2014 Mar-Apr;11(2):304-15. doi: 10.1109/TCBB.2014.2309599. IEEE/ACM Trans Comput Biol Bioinform. 2014. PMID: 26355778
Predicting the strongest domain-domain contact in interacting protein pairs.
Nye TM, Berzuini C, Gilks WR, Babu MM, Teichmann S. Nye TM, et al. Stat Appl Genet Mol Biol. 2006;5:Article5. doi: 10.2202/1544-6115.1195. Epub 2006 Feb 24. Stat Appl Genet Mol Biol. 2006. PMID: 16646869
Modelling the evolution of multi-gene families.
Nye TM. Nye TM. Stat Methods Med Res. 2009 Oct;18(5):487-504. doi: 10.1177/0962280208099450. Epub 2009 Jan 19. Stat Methods Med Res. 2009. PMID: 19153166
Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees.
Nye TMW, Tang X, Weyenberg G, Yoshida R. Nye TMW, et al. Biometrika. 2017 Dec;104(4):901-922. doi: 10.1093/biomet/asx047. Epub 2017 Sep 27. Biometrika. 2017. PMID: 29422694 Free PMC article.
A congruent phylogenomic signal places eukaryotes within the Archaea.
Williams TA, Foster PG, Nye TM, Cox CJ, Embley TM. Williams TA, et al. Among authors: nye tm. Proc Biol Sci. 2012 Dec 22;279(1749):4870-9. doi: 10.1098/rspb.2012.1795. Epub 2012 Oct 24. Proc Biol Sci. 2012. PMID: 23097517 Free PMC article.
Probabilistic Distances Between Trees.
Garba MK, Nye TMW, Boys RJ. Garba MK, et al. Among authors: nye tmw. Syst Biol. 2018 Mar 1;67(2):320-327. doi: 10.1093/sysbio/syx080. Syst Biol. 2018. PMID: 29029295 Free PMC article.
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