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Dimitrios V. Vavoulis

BSc, MRes, MSc, PhD

Statistical Machine Learning, Computational Genomics

Short Biography

I am a computational biologist at the Department of Oncology and at the Wellcome Centre for Human Genetics (WCHG), University of Oxford. I hold a BSc in Biology and an MRes in Environmental Biology with Distinction from the University of Patras (Greece), as well as an MSc in Evolutionary and Adaptive Systems with Distinction, and a Ph.D. in Computational Neurobiology from the University of Sussex. Before moving to Oxford, I held research positions at the Universities of Warwick and Bristol. 

The unifying thread underlying my research has always been a keen interest in applying computational methodologies for data modelling and analysis in the Life Sciences. I find fascinating the applications of probabilistic machine learning for the analysis of big genomic data, typically generated by next-generation sequencing technologies, especially in the context of Cancer Genomics. Recent work includes the development of statistical methodologies for tracking clonal dynamics in liquid cancers (i.e. leukaemias; Vavoulis et al., Bioinformatics 2020), for discovering the genomic and transcriptomic correlates of Richter’s syndrome (a complication of Chronic Lymphocytic Leukaemia with dismal prognosis; Klintman et al., Blood 2020), for the non-invasive prenatal diagnosis of sickle-cell disease (Cutts, Vavoulis, et al., Blood 2019), and for the joint analysis of genotypic and gene expression data for the discovery of eQTLs (Vavoulis et al., Bioinformatics 2017). An exciting avenue of research currently pursued in collaboration with experimental and clinical scientists at the OMDC, WCHG, and elsewhere focuses on the discovery of cell-free DNA signals in the blood (as revealed by whole genome and targeted sequencing assays via appropriate data analysis), which could be used as biomarkers for early cancer detection and for monitoring minimal residual disease.

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

Book chapter

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

SELECTED PUBLICATIONS

For a full list of publications, check pubmed 

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

  1. Robbe P, Ridout KE, Vavoulis DV, ..., Schuh A. "Whole-genome sequencing of CLL identifies subgroups with distinct biological and clinical features", Nature Genetics, 2022 
  2. 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
  3. 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 

  4. 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

  5. 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

  6. Vavoulis DV, Taylor J & Schuh A. "Hierarchical probabilistic models for multiple gene-variant associations based on next-generation sequencing data”, Bioinformatics, 2017

  7. Vavoulis DV, Frascescatto M, Heutink P & Gough J. “DGEclust: Differential expression analysis of clustered count data”, Genome Biology, 2015

  8. Oates M, Stahlhacke J, Vavoulis DV, …, Gough J. “The SUPERFAMILY 1.75 database in 2014: a doubling of data”, Nucleic Acids Research, 2014

  9. 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

  10. 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

  11. Ashmole I, Vavoulis DV, Stansfeld PJ, Mehta PR, Feng JF, Sutcliffe MJ & Stanfield PR. “The response of the tandem pore potassium channel TASK-3 (K2P9.1) to voltage: gating at the cytoplasmic mouth”. J Physiol, 587(20):4769-4783, 2009

  12. 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

  13. 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