Journal "Peer-Reviewed" Articles



6 articles in 2017

85. Papageorgiou L, Megalooikonomou V, Vlachakis D. Genetic and structural study of DNA-directed RNA polymerase II of Trypanosoma brucei, towards the designing of novel antiparasitic agents. PeerJ. 2017, 5:e3061

84. 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. NPG Scientific Reports. 2017. In Press

83. Chatzikonstantinou M, Vlachakis D, Papageorgiou L, Papageorgiou AC, Labrou NE. The Glutathione Transferase Family of Chlamydomonas reinhardtii: Identification and Characterization of Novel Sigma Class-like Enzymes. Algal Research. 2017, 24 (A): 237-250

82. Amidi S, Amidi A, Vlachakis D, Paragios N, Zacharaki EI. Automatic single- and multilabel enzymatic function prediction by machine learning. PeerJ. 2017, 5:e3095

81. Tagkalakis F, Vlachakis D, Megalooikonomou V, Skordas A. A Novel Approach to Finger Vein Authentication. ISBI. 2017

80. Vlachakis D, Armaos A, Kossida S. Advanced Protein Alignments Based on Sequence,Structure and Hydropathy Profiles; The Paradigm of the Viral Polymerase Enzyme. Math. Comput. Sci. 2017, pp. 1-12



11 articles in 2016

79. Champeris TS, Patmanidi AL, Giannou AD, Villiou M, Vlachakis D, Stathopoulos GT, Taraviras S. Pluripotency, Geminin and Retinoic Acid Signaling. Critical Reviews In Biochemistry & Molecular Biology. 2016. In Press.

78. Schnerch J, Prasse A, Vlachakis D, Schuchardt KL, Pechkovsky DV, Goldmann T, Gaede KI, Müller-Quernheim J, Zissel G. Functional TLR9 Expression and CXCR3 Ligand Release in Pulmonary Sarcoidosis. Am J Respir Cell Mol Biol. 2016 Jul 8. [Epub ahead of print].

77. Sertedaki A, Markou A, Vlachakis D, Kossida S, Campanac E, Hoffman DA, Sierra ML, Xekouki P, Stratakis CA, Kaltsas G, Piaditis GP, Chrousos GP, Charmandari E. Functional characterization of two novel germline mutations of the KCNJ5 gene in hypertensive patients without primary aldosteronism but with ACTH‐dependent aldosterone hypersecretion. Clin Endocrinol (Oxf). 2016 Jun 13. [Epub ahead of print].

76. Amidi A, Amidi S, Vlachakis D, Paragios N, Zacharaki EI. A Machine Learning Methodology for Enzyme Functional Classification Combining Structural and Protein Sequence Descriptors. Bioinformatics and Biomedical Engineering. Volume 9656 of the series Lecture Notes in Computer Science pp 728-738.

75. Tsaniras SC, Vlachakis D. HCV, Dengue, West Nile and now Zika; What’s next? The threat of endemic TBE relatives in Southern Europe. J Mol Biochem. 2016, 5(1):20.

74. Mavromati J, Hamzaraj E, Gjeta Z, Mavromati E, Vlachakis D, Kossida S, Shabani E. First Results of Proteomics Analyses in Blood Serum of Sheep in Albania. Anglisticum Journal. 2016, 2 (4): 235-240

73. Tsaniras SC, Vlachakis D. Diet, obesity and cancer. J Mol Biochem. 2015, 4(2):20.

72. 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.

71. 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. √ [Corresponding Author]

70. Papageorgiou L, Cuong NT, Vlachakis D. Antibodies as stratagems against cancer. Royal Society Chemistry: Molecular Biosystems. 2016, 12(7):2047-55

69. Axarli I, Muleta AW, Vlachakis D, Kossida S, Kotzia G, Maltezos A, Dhavala P, Papageorgiou AC, Labrou NE. Directed Evolution of Tau Class Glutathione Transferases Reveals A Site That Regulates Catalytic Efficiency And Masks Cooperativity. Biochemical Journal. 2016, 473(5):559-70.



10 articles in 2015

68. Nicolaides NC, Skyrla E, Vlachakis D, Psarra AG, Moutsatsou P, Sertedaki A, Kossida S, Charmandari E. Functional Characterization of the hGRαT556I Causing Chrousos Syndrome. European Journal of Clinical Investigation. 2015, 46(1):42-49.

67. Nicolaides NC, Geer EB, Vlachakis D, Roberts ML, Psarra AM, Moutsatsou P, Sertedaki A, Kossida S, Charmandari E. A Novel Mutation of the hGR Gene Causing Chrousos Syndrome. European Journal of Clinical Investigation. 2015, 45(8):782-791.

66. Tsaniras SC, Vlachakis D, Taraviras S: The Nucleophosmin-Pin1 interaction links the cell cycle, cancer and pluripotency. J Mol Biochem. 2015, 4(3):50-51.

65. Vlachakis D, Bencurova E, Papageorgiou L, Bhide M, Kossida S. Protein phosphorylation prediction: limitations, merits and pitfalls. J Mol Biochem. 2015, 4(2):36-41.

64. Loukatou S, Papageorgiou L, Vlachakis D. Optimisation of a potent series of HCV helicase drug candidates. J Mol Biochem. 2015, 4(1):1-4.

63. Loukatou S, Chatzinikolaou P, Vlachakis D, Kossida S. Genome-wide copy number variation from next generation sequencing data. Online Journal of bioinformatics. 2015, 16(2):254-262.

62. Bencurova E, Kovac A, Pulzova L, Gyuranecz M, Mlynarcik P, Mucha R, Vlachakis D, Kossida S, Flachbartova Z, Bhide M. Deciphering the protein interaction in adhesion of Francisella tularensis subsp. holarctica to the endothelial cells. Microbial Pathogenesis. 2015, 81:6-15.

61. Konstantara K, Danelakis A, Tzogogianni D, Polychronidou E, Venieris G, Papageorgiou L, Vlachakis D. Respiratory gating in lung cancer radiotherapy. Online Journal of bioinformatics. 2015, 16(2):194-201.

60. Polychronidou E, Vlachakis D, Papageorgiou L, Vlamos P. Biological databases as key for data integration, analysis and visualization. Online Journal of bioinformatics. 2015, 16(1):51-60.

59. Vlachakis D, Fakourelis P, Megalooikonomou V, Makris C, Kossida S. DrugOn: a fully integrated pharmacophore modelling and structure optimization toolkit, PeerJ. 2015, 13;3:e725.



12 articles in 2014

58. Vlachakis D, Armaos, A., Kasampalidis, I., Filntisi, A., Kossida, S. ASSP; The antibody secondary structure profile search tool. CEUR Workshop Proceedings. 2014,(1):69-77.

57. Polychronidou E, Vlachakis D, Vlamos P, Baumann M, Kossida S. Notch Signaling and Ageing, Advances in Experimental Medicine and Biology (AEMB). 2014, 822:25-36.

56. Inturia R, Wäneskoga M, Vlachakis D, Alia Y, Eka P, Pungaa T, Bjerling P. A splice variant of the human phosphohistidine phosphatase 1 (PHPT1) is degraded by the proteasome, The International Journal of Biochemistry & Cell Biology. 2014, 57: 69–75.

55. Filntisi A, Vlachakis D, Matsopoulos G, Kossida S. Computational construction of antibody-drug conjugates using surface lysines as the antibody conjugation site and a non-cleavable linker, Cancer Informatics. 2014, 13: 179–186.

54. Papageorgiou L, Loukatou S, Koumandou VL, Makałowski W, Megalooikonomou V, Vlachakis D, Kossida S. Structural models for the design of novel antiviral agents against Greek Goat Encephalitis, PeerJ. 2014, 2:e664.

53. Vlachakis D, Champeris Tsaniras S, Ioannidou K, Papageorgiou L, Baumann M, Kossida S. A series of Notch3 mutations in CADASIL; insights from 3D molecular modelling and evolutionary analyses, J Mol Biochem. 2014, 3(3):97-105.

52. Loukatou S, Fakourelis P, Papageorgiou L, Megalooikonomou V, Kossida S, Vlachakis D. Ebola virus epidemic: a deliberate accident?, J Mol Biochem. 2014, 3(3):72-76.

51. Loukatou S, Papageorgiou L, Fakourelis P, Filntisi A, Polychronidou E, Bassis I, Megalooikonomou V, Makałowski W, Vlachakis D, Kossida S. Molecular dynamics simulations through GPU video games technologies, J Mol Biochem. 2014, 3(2):64-71.

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

49. Vlachakis D, Champeris Tsaniras S, Tsiliki G, Megalooikonomou V, Kossida S, 3D structural analysis of proteins using electrostatic surfaces based on image segmentation, J Mol Biochem 2014 3(1):27-33

48. Maltezos A, Platis D, Vlachakis D, Kossida S, Marinou M, Labrou NE, Design, Synthesis and Application of Benzyl-sulphonate Biomimetic Affinity Adsorbents for Monoclonal Antibody Purification from Transgenic Corn, J. Mol. Recognit. 2014 27:19-31

47. 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



25 articles in 2013

46. 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

45. Steinhauf D, Rodriguez A, Vlachakis D, Virgo G, Maksimov V, Kristell C, Olsson I, Linder T, Kossida S, Bongcam-Rudloff E, Bjerling P, Silencing motifs in the Clr2 protein from fission yeast, Schizosaccharomyces pombe, Plos One 2013 9(1):e86948

44. Chatzinikolaou P, Makris C, Vlachakis D, Kossida S, A benchmark of structural variant analysis tools for next generation sequencing data, International Journal of Systems Biology and Biomedical Technologies (IJSBBT) 2013 2(4):86-98

43. Filntisi A, Bencurova E, Papangelopoulos N, Vlachakis D, Kossida S, State-of-the-Art Neural Networks Applications in Biology, International Journal of Systems Biology and Biomedical Technologies (IJSBBT) 2013 2(4):63-85

42. Vlachakis D, Tsiliki G, Kossida S. 3D Molecular Modelling of the Helicase Enzyme of the Endemic, Zoonotic Greek Goat Encephalitis Virus, Communications in Computer and Information Science 2013 383: 165-171

41. Boulaki V, Vlachakis D, Sotiraki S, Kossida S, An up-to-date review of piglet isosporosis; new insights and therapeutic perspectives, International Journal of Systems Biology and Biomedical Technologies (IJSBBT) 2013 2(4):49-62

40. Papangelopoulos N, Vlachakis D, Filntisi A, Fakourelis P, Papageorgiou L, Megalooikonomou V, Kossida S, State of the art GPGPU applications in bioinformatics, International Journal of Systems Biology and Biomedical Technologies (IJSBBT) 2013 2(4):24-48

39. Ioannidou K, Vlachakis D, Matsopoulos G, Kastania A, Kossida S, Neuroscience and symptoms related to the CADASIL disease, International Journal of Systems Biology and Biomedical Technologies (IJSBBT) 2013 2(4):17-23

38. Papageorgiou L, Vlachakis D, Koumandou VL, Papangelopoulos N, Kossida S, Computer-aided drug design and biological evaluation of novel anti-Greek goat encephalitis agents, International Journal of Systems Biology and Biomedical Technologies (IJSBBT) 2013 2(4):1-16

37.Vlachakis D, Karozou A, Kossida S,3D molecular modelling study of the H7N9 RNA-dependent RNA polymerase as an emerging pharmacological target, Influenza Res Treat 2013 2013:645348, 9pages

36. Filntisi A, Vlachakis D, Matsopoulos G, Kossida S, 3D structural bioinformatics of proteins and antibodies; state of the art, perspectives and challenges, International Journal of Systems Biology and Biomedical Technologies (IJSBBT) 2013 2(3):67-74

35. Vlachakis D, Champeris Tsaniras S, Kossida S, Insights into the structure and 3D spatial arrangement of the b-ketoacyl carrier protein synthases, J Mol Biochem 2013 2(3):150-158

34. Vlachakis D, Karozou A, Champeris Tsaniras S, Kossida S, An update on the virology of the H7N9 strain of the influenza A virus, International Journal of Systems Biology and Biomedical Technologies (IJSBBT) 2013 2(3):59-66

33. Pavlopoulou A, Vlachakis D*, Balatsos N, Kossida S, A comprehensive phylogenetic analysis of deadenylases, Evolutionary Bioinformatics 2013 9:491-497

32. Carvalho CS, Vlachakis D, Tsiliki G, Megalooikonomou V, Kossida S, Protein signatures using electrostatic molecular surfaces in harmonic space, PeerJ 2013 1:e185

31. Vlachakis D, Kontopoulos DG, Kossida S, Space Constrained Homology Modelling; the paradigm of the RNA-dependent RNA Polymerase of Dengue (Type II) Virus, Comput Math Methods Med 2013 2013:108910, 9 pages

30. Vlachakis D, Kossida S, Antibody Drug Conjugate Bioinformatics: Drug delivery through the letterbox, Comput Math Methods Med 2013 2013:282398, 4 pages

29. Vlachakis D, Pavlopoulou A, Kazazi D, Kossida S, Unravelling microalgal molecular interactions using evolutionary and structural bioinformatics, Gene 2013 528(2):109-119

28. Vlachakis D, Champeris Tsaniras S, Karozou A, Kossida S, An update on virology and emerging viral epidemics, J Mol Biochem 2013, 2(2):80-84

27. Vlachakis D, Kossida S, Molecular modelling and pharmacophore elucidation study of the Classical Swine Fever virus helicase as a promising pharmacological target, PeerJ 2013 1:e85

26. Vlachakis D, Champeris Tsaniras S, Feidakis C, Kossida S, An in silico 3D study of the biglycan core protein, using homology modelling techniques, J Mol Biochem 2013 2(2):85-93

25. Vlachakis D, Koumandou VL, Kossida S, A holistic evolutionary and structural study of flaviviridae provides insights into the function and inhibition of HCV Helicase, PeerJ 2013,1:e74

24. Vlachakis D, Tsiliki G, Roumbelakis MG, Pavlopoulou A, Champeris Tsaniras S, Kossida S, Antiviral stratagems against HIV using RNA interference (RNAi) technology, Evolutionary Bioinformatics 2013, 9:203-213

23. Vlachakis D, Feidakis C, Megalooikonomou V, Kossida S, IMGT/Collier-de-Perles: A two-dimensional visualization tool for amino acid domain sequences, Theor Biol Med Model 2013 21;10(1):14

22. 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



9 articles in 2012

21. Vlachakis D, Pavlopoulou A, Tsiliki G, Komiotis D, Stathopoulos C, Balatsos N, Kossida S, An intergraded in silico approach to design specific inhibitors targeting human poly(A)-specific ribonuclease, Plos One 2012 7(12):e51113

20. Vlachakis D, Champeris Tsaniras S, Kossida S, Current viral infections and epidemics of flaviviridae; lots of grief but also some hope, J Mol Biochem 2012 1(3):144-149

19. Vlachakis D, Tsiliki G, Tsagkrasoulis D, Carvalho CS, Megalooikonomou V, Kossida S, Speeding up the drug discovery process: structural similarity searches using molecular surfaces, EMBnet Journal. 2012, 18(1), 6-9

18. Vlachakis D, Champeris Tsaniras S, An introduction to M-theory and its application in biology, J Mol Biochem 2012 1(2):65-67

17. Kapasa M, Vlachakis D, Kostadima M, Sotiropoulou G, Kossida S, Towards the elucidation of the regulatory network guiding the insulin producing cells, Genomics. 2012, 1(2), 35-47

16. Vlachakis D, Tsagkrasoulis D, Megalooikonomou V, Kossida S, Introducing Drugster: a comprehensive drug design, lead and structure optimization toolkit, Bioinformatics. 2012, 29(1):126-8

15. Vlachakis D, Champeris Tsaniras S, The shape of science, J Mol Biochem 2012 1(1):4-5

14. Balatsos N, Vlachakis D, Chatzigeorgiou V, Manta S, Komiotis D, Vlassi M, Stathopoulos C, Kinetic and in silico analysis of the slow-binding inhibition of human poly(A)-specific ribonuclease (PARN) by novel nucleoside analogues, Biochimie 2012 94(1):214-21

13. Sellis D, Drosou V, Vlachakis D, Voukkalis N, Giannakouros T, Vlassi M, Phosphorylation of the arginine/serine repeats of lamin B receptor by SRPK1-Insights from molecular dynamics simulations, Biochim Biophys Acta (Gen. Subjects) 2012 1820(1):44-55



1 article in 2011

12. Vlachakis D, Brancale A, Berry C, Kossida S, A rapid assay for the biological evaluation of helicase activity Nature Protocol Exchange. 2011, doi: 10.1038/protex.2011.275



3 articles in 2010

11. Vlachaki C, Skarlos P, Patrozou E, Vlachakis D, Mpikou K, Mperoukas K. Nutritional management of patients before, during and upon radiotherapy for pelvis tumour, H J Nutr Diet 2010 01(2):100-105

10. Vlachaki C, Karageorgou M, Karakozis S, Vlachakis D, Nutritional management after Bariatric Surgery, H J Nutr Diet 2010 01(1):29-36

09. Patrozou E, Vlachaki C, Liolia D, Vlachakis D, The role of the dietician in inflammation prevention, H J Nutr Die 2010 01(1):37-43



5 articles in 2009

08. Sellis D, Vlachakis D, Vlassi M, Gromita: A Fully Integrated Graphical User Interface to Gromacs 4, Bioinformatics and Biology Insights 2009 3:99-102

07. Vangelatos I, Vlachakis D, Sophianopoulou V, Diallinas G,Modelling and mutational evidence identify the substrate binding site and functional elements in APC amino acid transporters, Mol Membr Biol 2009 26(5):356-70

06. Vlachakis D, Theoretical study of the Usutu virus helicase 3D structure, by means of computer-aided homology modelling, Theor Biol Med Model 2009 25;6:9,1-9

05. Balatsos NA, Vlachakis D, Maragozidis P, Manta S, Anastasakis D, Kyritsis A, Vlassi M, Komiotis D,Stathopoulos C, Competitive inhibition of human poly(A)-specific ribonuclease (PARN) by synthetic fluoro-pyranosyl nucleosides, Biochemistry 2009 7;48(26):6044-6051

04. Kandil S, Biondaro S, Vlachakis D, Cummins AC, Coluccia A, Berry C, Leyssen P, Neyts J, Brancale A, Discovery of a novel HCV helicase inhibitor by a de novo drug design approach, Bioorg Med Chem Lett 2009 1;19(11):2935-7



2 articles in 2008

03. Brancale A, Vlachaki C, Vlachakis D, Molecular modelling study of the 3D structure of the Bovine Viral Diarrhea Virus (BVDV) helicase, In Silico Biol 2008, 35:461-469

02. Palaiomylitou M, Tartas A, Vlachakis D, Tzamarias D, Vlassi M, Investigating the structural stability of the Tup1-interaction domain of Ssn6: evidence for a conformational change on the complex, Proteins 2008 70(1):72-82



1 article in 2007

01. Vlachakis D, Brancale A, The 3D structure of the Japanese Encephalitis helicase, using homology based molecular modelling technique, Online Journal of bioinformatics 2007 8(2):154-164