Staff Profile
Dr Tom Nye
Senior Lecturer in Statistics
- Email: tom.nye@ncl.ac.uk
- Telephone: +44 (0) 191 208 5369
- Personal Website: https://tomnye.github.io/
- Address: School of Mathematics, Statistics and Physics
Newcastle University
Newcastle upon Tyne
NE1 7RU
Background
I am a Senior Lecturer in Statistics in the School of Mathematics, Statistics and Physics. I joined the School in 2006; prior to that I was a PDRA at the Medical Research Council Biostatistics Unit in Cambridge, and I also worked in industry for a few years. My PhD was in global analysis and gauge theory.
Research
Research interests:-
- Bayesian inference of phylogenetic trees
- Non-Euclidean geometric statistics for data sets of trees and graphs
- Tree-valued stochastic processes
- Statistical modelling in computational neuroscience
See my Google Scholar pages for more information.
Teaching
Undergraduate Teaching
MAS1604 Introduction to Probability
Publications
- Garba MK, Nye TMW, Lueg J, Huckemann SF. Information geometry for phylogenetic trees. Journal of Mathematical Biology 2021, 82(3), 19.
- Heaps SE, Nye TMW, Boys RJ, Williams TA, Cherlin S, Embley TM. Generalizing rate heterogeneity across sites in statistical phylogenetics. Statistical Modelling 2020, 20(4), 410-436.
- Hannaford NE, Heaps SE, Nye TMW, Williams TA, Embley TM. Incorporating compositional heterogeneity into Lie Markov models for phylogenetic inference. The Annals of Applied Statistics 2020, 14(4), 1964-1983.
- Nye TMW. Random walks and Brownian motion on cubical complexes. Stochastic Processes and their Applications 2020, 130(4), 2185-2199.
- Garba MK, Nye TMW, Boys RJ. Probabilistic Distances Between Trees. Systematic Biology 2018, 67(2), 320-327.
- Cherlin S, Heaps SE, Nye TMW, Boys RJ, Williams TA, Embley TM. The effect of nonreversibility on inferring rooted phylogenies. Molecular Biology and Evolution 2018, 35(4), 984-1002.
- Nye TMW, Tang X, Weyenberg G, Yoshida R. Principal Component Analysis and the Locus of the Fréchet Mean in the Space of Phylogenetic Trees. Biometrika 2017, 104(4), 901-922.
- Williams TA, Heaps SE, Cherlin S, Nye TMW, Boys RJ, Embley TM. New substitution models for rooting phylogenetic trees. Philosophical Transactions of the Royal Society B: Biological Sciences 2015, 370(1678), 20140336.
- Nye TMW. An Algorithm for Constructing Principal Geodesics in Phylogenetic Treespace. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2014, 11(2), 304-315.
- Heaps SE, Nye TMW, Boys RJ, Williams TA, Embley TM. Bayesian modelling of compositional heterogeneity in molecular phylogenetics. Statistical Applications in Genetics and Molecular Biology 2014, 13(5), 589-609.
- Nye TMW, White MC. Diffusion on some simple stratified spaces. Journal of Mathematical Imaging and Vision 2013, n/a, n/a.
- Williams TA, Foster PG, Nye TMW, Cox CJ, Embley TM. A congruent phylogenomic signal places eukaryotes within the Archaea. Proceedings of the Royal Society B: Biological Sciences 2012, 279(1749), 4870-4879.
- Nye TMW. Principal components analysis in the space of phylogenetic trees. Annals of Statistics 2011, 39(5), 2716-2739.
- Nye TMW. Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies. Systematic Biology 2008, 57(5), 785-794.
- Nye TMW, Liò P, Gilks WR. A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics 2006, 22(1), 117-119.
- Nye TMW, Berzuini C, Gilks WR, Babu MM, Teichmann S. Predicting the Strongest Domain-Domain Contact in Interacting Protein Pairs. Statistical Applications in Genetics and Molecular Biology 2006, 5(1), Article 5.
- Nye TMW, Berzuini C, Gilks WR, Babu MM, Teichmann SA. Statistical analysis of domains in interacting protein pairs. Bioinformatics 2005, 21(7), 993-1001.