Staff Profile
Dr Tom Nye
Senior Lecturer in Statistics
 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
I am a Senior Lecturer in Statistics in the School of Mathematics, Statistics and Physics. My research focuses on inference problems for phylogenetic trees and statistics in nonEuclidean spaces. I have taught a wide variety of modules at Newcastle, but most often I teach modules on probability to stage 1 students and nonEuclidean statistics to stage 4 students.
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.
I am part of the Applied Probability Group. My research interests include:
 Bayesian inference of phylogenetic trees
 NonEuclidean geometric statistics for data sets of trees and graphs
 Treevalued stochastic processes
 Statistical modelling in computational neuroscience
See my Google Scholar pages for more information.
If you are interested in pursuing a PhD under my supervision, look at the suggested PhD projects in statistics, and contact me via email.
Current students should access materials for my modules on canvas.

Articles
 Hannaford NE, Heaps SE, Nye TMW, Curtis TP, Allen B, Golightly A, Wilkinson DJ. A sparse Bayesian hierarchical vector autoregressive model for microbial dynamics in a wastewater treatment plant. Computational Statistics and Data Analysis 2023, 179, 107659.
 Garba MK, Nye TMW, Lueg J, Huckemann SF. Information geometry for phylogenetic trees. Journal of Mathematical Biology 2021, 82(3), 19.
 Nye TMW. Random walks and Brownian motion on cubical complexes. Stochastic Processes and their Applications 2020, 130(4), 21852199.
 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), 19641983.
 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), 410436.
 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), 9841002.
 Garba MK, Nye TMW, Boys RJ. Probabilistic Distances Between Trees. Systematic Biology 2018, 67(2), 320327.
 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), 901922.
 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.
 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), 589609.
 Nye TMW. An Algorithm for Constructing Principal Geodesics in Phylogenetic Treespace. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2014, 11(2), 304315.
 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), 48704879.
 Nye TMW. Principal components analysis in the space of phylogenetic trees. Annals of Statistics 2011, 39(5), 27162739.
 Nye TMW. Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies. Systematic Biology 2008, 57(5), 785794.
 Nye TMW, Berzuini C, Gilks WR, Babu MM, Teichmann S. Predicting the Strongest DomainDomain Contact in Interacting Protein Pairs. Statistical Applications in Genetics and Molecular Biology 2006, 5(1), Article 5.
 Nye TMW, Liò P, Gilks WR. A novel algorithm and webbased tool for comparing two alternative phylogenetic trees. Bioinformatics 2006, 22(1), 117119.
 Nye TMW, Berzuini C, Gilks WR, Babu MM, Teichmann SA. Statistical analysis of domains in interacting protein pairs. Bioinformatics 2005, 21(7), 9931001.