Dimitrios V. Vavoulis - Post Doctoral Researcher
Department of Computer Science
University of Bristol
The Merchant Venturers Building
Woodland Road
Bristol BS8 1UB, United Kingdom

Phone: +44 (0)117 331573
Email: Dimitris.Vavoulis@bristol.ac.uk

Background


Research interests

Bayesian approaches to data modelling in the following research domains:
  • Computational Molecular Biology (Cellular Expression)
  • Computational Neuroscience
  • Systems Biology
  • Bioinformatics

Academic awards and honors

  • Finalist for an EPSRC Postdoctoral Research Fellowship (Life Sciences Interface), 2008
  • PhD Scholarship - BBSRC (BBS/S/K/2003/10144), 2003-2006
  • MSc Scholarship - EPSRC, 2002-2003
  • MSc Award - Hellenic State Scholarships Foundation, 2002

Professional societies

  • International Society for Computational Biology - San Diego, USA
  • Society for Neuroscience - Washinghton DC, USA

Invited talks

  • Bayesian modelling of un-replicated digital gene expression data. Mathematical Biology Unit, NIMR, UK, Oct 2012
  • Bayesian inference and parameter estimation in single-neuron models. Neural Dynamics Forum, University of Bristol, May 2012
  • Parameter estimation in single-neuron models using particle filters. University of York, Sep 2011
  • A model of voltage-dependent gating in the K2P9.1 potassium channel. Warwick Systems Biology Centre, Jun 2010
  • Modelling non-synaptic plasticity in an invertebrate inter-neuron. MPI Biological Cybernetics, Tubingen, Oct 2009
  • Computational models of neurons and small neural networks. Warwick Complexity Science Centre, Mar 2008
  • Mathematical modelling of central pattern generating networks. Warwick Mathematics Institute, Apr 2007

Publications

Peer-reviewed

  1. Vavoulis DV and Gough J. Non-parametric Bayesian modelling of digital gene expression data. http://arxiv.org/abs/1301.4144, 2013
  2. Vavoulis DV, Straub VA, Aston JAD and Feng JF. A self-organizing state-space-model approach for parameter estimation in Hodgkin-Huxley-type models of single neurons PLoS Comput Biol 8(3): e1002401, 2012 COVER IMAGE
  3. Erokhin V, Berzina T, Camorani P, Smerireri A, Vavoulis DV, Feng JF and Fontana MP. Material memristive device circuits with synaptic plasticity: learning and memory Bionanoscience 1(1-2): 24-30, 2011
  4. Marra V, Kemenes I, Vavoulis DV, Feng J, O'Shea M and Benjamin PR. Role of tonic inhibition in associative reward conditioning in Lymnaea Front Behav Neurosci 4:161 doi:10.3389/fnbeh.2010.00161, 2010 SPECIAL ISSUE
  5. Vavoulis DV, Nikitin ES, Kemenes I, Marra V, Feng J, Benjamin PR and Kemenes G. Balanced plasticity and stability of the electrical properties of a molluscan modulatory interneuron after classical conditioning: a computational study Front Behav Neurosci 4:19 doi:10.3389/fnbeh.2010.00019, 2010 SPECIAL ISSUE
  6. Ashmole I, Vavoulis DV, Stansfeld PJ, Mehta PR, Feng JF, Sutcliffe MJ and Stanfield PR. The response of the tandem pore potassium channel TASK-3 (K(2P)9.1) to voltage: gating at the cytoplasmic mouth J Physiol 587(20):4769-4783, 2009 COVER IMAGE
  7. Nikitin ES, Vavoulis DV, Kemenes I, Marra V, Pirger Z, Michel M, Feng J, O'Shea M, Benjamin PR, Kemenes G. Persistent sodium current is a nonsynaptic substrate for long-term associative memory Curr Biol 18(16):1221-1226, 2008 FACULTY OF 1000
  8. Vavoulis DV, Nikitin ES, Feng JF, Benjamin PR & Kemenes G. Computational model of a modulatory cell type in the feeding network of the snail, Lymnaea stagnalis BMC Neurosci 8(Suppl 2): P113, 2007
  9. Vavoulis DV, Straub VA, Kemenes I, Kemenes G, Feng J and Benjamin PR. Dynamic control of a central pattern generator circuit: a computational model of the snail feeding network. Eur J Neurosci 25: 2805-2818, doi: 10.1111/j.1460-9568.2007.05517.x, 2007

Conference proceedings

  1. Vavoulis DV, Pardo L, Heutink P, Gough J. Bayesian inference of differential gene expression based on RNA-seq data, ECCB'12, Switzerland, 2012
  2. Vavoulis DV, Straub VA & Feng JF. Bayesian inference and parameter estimation through stochastic simulation in Hodgkin-Huxley-type models of single neurones. Soc Neurosci Abstract, Washington DC, 2010
  3. Vavoulis DV, Nikitin ES, Kemenes G, Feng JF & Benjamin PR. Neuronal plasticity in a molluscan feeding CPG: computational modelling of the Cerebral Giant Cells in Lymnaea. Soc Neurosci Abstract, Washington DC, 2006
  4. Vavoulis DV, Straub VA, Kemenes G, Feng JF & Benjamin PR. Pattern generation and modulation in a molluscan feeding system: a computational study. Soc Neurosci Abstract, Washington DC, 2005
  5. Vavoulis DV, Straub VA, Dunn SJ, Feng JF & Benjamin PR. Modelling plateau potentials in a molluscan Central Pattern Generator. Soc Neurosci Abstract. Washington DC, 2004

Monographs

  1. Vavoulis DV. Computational modelling of the feeding Central Pattern Generator in the pond snail, Lymnaea stagnalis. PhD Thesis, University of Sussex, United Kingdom, 2007
  2. Vavoulis DV. An individual-based model of chemical synaptic transmission MSc Dissertation, University of Sussex, United Kingdom, 2003
  3. Vavoulis DV. A mathematical model for the seasonal migrations of juvenile sole (Solea solea L.) in a coastal area in the Bay of Biscay. MSc Dissertation, University of Patra, Greece, 2002
  4. Vavoulis DV. Analysis of fundamental ecological models. BSc Dissertation, University of Patra, Greece, 1999

Various Essays

  1. Vavoulis DV. Are living cells ultra-stable systems?. EASy MSc, University of Sussex, Brighton, 2003
  2. Vavoulis DV. Artificial neural networks as a tool for biological inquiry. EASy MSc, University of Sussex, Brighton, 2002
  3. Vavoulis DV. Is klinotaxis a sufficient mechanism for generating chemical trail-following behaviour in ants? EASy MSc, University of Sussex, Brighton, 2002