Dimitrios Vlachakis

MSc, MPhil, PhD, MRSC, MRSB, FGS
Asst Professor - AUA

He leads the Dark DNA group at the Genetics Laboratory, Biotechnology Department, School of Applied Biology and Biotechnology of the Agricultural University of Athens.

His biological, medical, PhD and PostDoctoral studies in the USA & the UK led to a series of publications and international patents on antiviral drugs. Prof Vlachakis is also appointed as an Affiliated Researcher at the Faculty of Natural and Mathematical Sciences at the King’s College London and as an Adjunct Investigator of the Qatar Genome Programme (QGP) at the Qatar Foundation, Sidra Medicine, Doha, Qatar.

Since 2012 he has been serving as the Editor in Chief of the Journal of Molecular Biochemistry and as the Deputy Editor in Chief for the EMBnet journal. He was recently elected as an Executive Board member and P & PR PC member of EMBnet. To date, he has published more than 130 original peer-reviewed articles, 8 ISBN books, 3 scientific patents and has been on the receiving end of numerous grants and awards.

Our research interests revolve around three distinct, yet intersecting, areas: i) The functional role of long non-coding RNAs, ii) Stress mechanisms and homeostasis via nuclear receptors & iii) Computational and molecular virology. We develop and apply our research to a repertoire of scientific domains. Namely, we have been investigating the role of nuclear receptors in gene expression and regulation and in particular the role of the glucocorticoid receptor in stress. Then, we look into the realm of viruses and in particular into the ssRNA family of flaviviridae and ebola virus for the investigation of the genetic elasticity of viral genomes (antigenic drift/shift) and how epigenetics could annihilate current vaccination protocols. In our lab we use a wide spectrum of methodologies ranging from state-of-the-art bioinformatics, molecular modelling and hypercomputing pipelines to traditional genetic and biochemistry in vitro and in vivo techniques. On one hand, we have developed our own software for machine learning, deep learning and data mining for multimodal fusion of information from genetic, structural and physicochemical analyses. On the other hand, we use DNA engineering, SDM, cloning, expression and protein purification techniques to biologically test and evaluate the validity and reliability of our models.

Selected Publications

Guerra J , Valadao AL, Vlachakis D, Polak K, Vila IK, Taffoni C, Prabakaran T, Marriott AS, Kaczmarek R, Houel A, Auzemery B, Déjardin S, Boudinot P, Nawrot B, Jones NJ, Paludan SR, Kossida S, Langevin C, Laguette N. Lysyl-tRNA synthetase produces diadenosine tetraphosphate to curb STING-dependent inflammation. Science Advances. 2020, In Press

Antoniou N, Vlachakis D, Memou A, Leandrou E, Valkimadi PE, Melachroinou K, Re DB, Przedborski S, Dauer WT, Stefanis L, Rideout HJ. A motif within the armadillo repeat of Parkinson’s-linked LRRK2 interacts with FADD to hijack the extrinsic death pathway. Scientific Reports (NPG). 2018 (8):3455

Vlachakis D, Labrou NE, Iliopoulos C, Hardy J, Lewis PA, Rideout H, Trabzuni D. Insights into the Influence of Specific Splicing Events on the Structural Organization of LRRK2. Int. J. Mol. Sci. 2018, 19(9), 2784; https://doi.org/10.3390/ijms19092784

Kostaropoulos T, Papageorgiou L, Champeris TS, Vlachakis D, Eliopoulos E. Carcinogenic Pesticide Control via Hijacking Endosymbiosis; The Paradigm of DSB-A from Wolbachia pipientis for the Management of Otiorhynchus singularis In Vivo. 2018; 32(5):1051-1062. doi: 10.21873/invivo.11346

Vlachakis C, Dragoumani K, Raftopoulou S, Mantaiou M, Papageorgiou L, Champeris TS, Megalooikonomou V, Vlachakis D. Human Emotions on the Onset of Cardiovascular and Small Vessel Related Diseases. In Vivo. 2018;32(4):859-870. doi: 10.21873/invivo.11320

Papageorgiou L, Loukatou S, Kossida S, Maroulis D, Vlachakis D. An updated evolutionary study of Flaviviridae NS3 helicase and NS5 RNA-dependent RNA polymerase, reveals novel invariable motifs as potential pharmacological targets. Royal Society Chemistry: Molecular Biosystems. 2016, 12(7):2080-93.

Kontopoulos DG, Vlachakis D, Tsiliki G, Kossida S. Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces. BMC Structural Biology. 2016. 16:4. Papageorgiou L, Cuong NT, Vlachakis D. Antibodies as stratagems against cancer. Royal Society Chemistry: Molecular Biosystems. 2016, 12(7):2047-55

Tsiliki G, Vlachakis D, Kossida S, On integrating multi-platform microarray data, Phyl Trans R Soc A 2014 20130136

Vlachakis D, Pavlopoulou A, Roumbelakis M, Feidakis C, Anagnou N, Kossida S, Emerging pharmacological targets: An in silico study of Trypanosoma brucei DNA Topoisomerase IB, Genomics 2014 103(1):107-113

Dalkas G, Vlachakis D, Tsagkrasoulis D, Kastania A, Kossida S, State of the art technology in modern computer-aided drug design, Briefings in Bioinformatics 2013 14(6):745-752

Vlachakis D, Tsagkrasoulis D, Megalooikonomou V, Kossida S, Introducing Drugster: a comprehensive drug design, lead and structure optimization toolkit, Bioinformatics 2013 29(1):126-128

PubMed Link

“...not all those who wander are lost...” J.R.R.Tolkien