Dimitrios V. Vavoulis

I am a computational biologist at the Oxford Molecular Diagnostics Centre (OMDC, Department of Oncology) and the Centre for Human Genetics (CHG) at the University of Oxford. I hold a BSc and an MRes with distinction in Biology from the University of Patras (Greece), as well as an MSc in Evolutionary and Adaptive Systems with distinction and a DPhil in Computational Neurobiology from the University of Sussex. Before joining Oxford, I held research positions at the Universities of Warwick and Bristol.

A central theme throughout my career has been the application of computational methodologies for data modeling and analysis in the Life Sciences. My primary interest lies in the use of probabilistic machine learning to analyze large-scale genomic data, typically generated by next-generation sequencing technologies, with a particular focus on Cancer Genomics. Recent work includes the development of statistical methods for tracking clonal dynamics in liquid cancers, such as leukemias (Vavoulis et al., Bioinformatics 2020), uncovering genomic and transcriptomic correlates of Richter’s syndrome—a complication of Chronic Lymphocytic Leukaemia with a poor prognosis (Klintman et al., Blood 2020)—non-invasive prenatal diagnosis of sickle-cell disease (Cutts, Vavoulis, et al., Blood 2019), and the joint analysis of genotypic and gene expression data for the discovery of eQTLs (Vavoulis et al., Bioinformatics 2017).

Currently, I am exploring an exciting avenue of research in collaboration with experimental and clinical scientists at OMDC, CHG, and other institutions. This research focuses on identifying cell-free DNA signals in blood, detected through whole genome and targeted sequencing assays, which hold promise as biomarkers for early cancer detection and for monitoring minimal residual disease (Vavoulis et al., 2023).

You can find me online on Twitter and/or Github.

1. Vavoulis DV. "Exploring Bayesian approaches to eQTL mapping through probabilistic programming", in Methods in Molecular Biology (vol. 2082), Springer, 2019

For a full list of publications, check pubmed 

*equal contribution, co-first or co-senior authors

1. Vavoulis DV, Cutts A, ..., Schuh A. "Multimodal cell-free DNA whole-genome analysis combined with TET-Assisted Pyridine Borane Sequencing is sensitive and reveals specific cancer signals", medRxiv, 2023
2. Robbe P, Ridout KE, Vavoulis DV, ..., Schuh A. "Whole-genome sequencing of CLL identifies subgroups with distinct biological and clinical features", Nature Genetics, 2022 
3. Vavoulis DV, Cutts A, Taylor JC, Schuh A. "A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data", Bioinformatics, 2020
4. Klintman J, Appleby N, ..., Taylor JC*, Vavoulis DV*, Schuh A*. "Differential genomic and transcriptomic events associated with high-grade transformation of Chronic Lymphocytic Leukemia", Blood, 2020
5. Cutts A*, Vavoulis DV*, Petrou M, Smith F, Clark B, Henderson S, Schuh A. "A method for non-invasive prenatal diagnosis of monogenic autosomal recessive disorders", Blood, 2019
6. Vavoulis DV, Pagnamenta AT, Knight SJL, Pentony MM, ..., Taylor JC. "Whole genome sequencing identifies putative associations between genomic polymorphisms and clinical response to the anti-epileptic drug levetiracetam", medRxiv, 2019
7. Vavoulis DV, Taylor J & Schuh A. "Hierarchical probabilistic models for multiple gene-variant associations based on next-generation sequencing data”, Bioinformatics, 2017
8. Vavoulis DV, Frascescatto M, Heutink P & Gough J. “DGEclust: Differential expression analysis of clustered count data”, Genome Biology, 2015
9. Oates M, Stahlhacke J, Vavoulis DV, …, Gough J. “The SUPERFAMILY 1.75 database in 2014: a doubling of data”, Nucleic Acids Research, 2014
10. Vavoulis DV, Straub VA, Aston JAD & Feng JF. “A self-organising state-space-model approach for parameter estimation in Hodgkin-Huxley-type models of single neurones”, PLoS Computational Biology, 2012
11. Vavoulis DV, Nikitin ES, Kemenes I, Feng JF, Benjamin PR & Kemenes G. “Balanced plasticity and stability of the electrical properties of a molluscan modulatory interneuron after conditioning: a computational study”, Front Behav Neurosci, 2010
12. Ashmole I, Vavoulis DV, Stansfeld PJ, Mehta PR, Feng JF, Sutcliffe MJ & Stanfield PR. “The response of the tandem pore potassium channel TASK-3 (K_2P9.1) to voltage: gating at the cytoplasmic mouth”, J Physiol, 587(20):4769-4783, 2009
13. Nikitin ES, Vavoulis DV, Kemenes I, Marra V, Pirger Z, Michel M, Feng JF, O’Shea M, Benjamin PR & Kemenes G. “Persistent sodium current is a non-synaptic substrate for long-term associative memory”, Curr Biol 18(16): 1221-1226, 2008
14. Vavoulis DV, Straub VA, Kemenes I, Kemenes G, Feng JF & Benjamin PR. “Dynamic control of a Central Pattern Generator circuit: a computational model of the snail feeding network”, Eur J Neurosci, 2007