2020

20 articles in 2020

140. 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, (3) 10; e1700495, DOI: 10.1126/sciadv.1700495

139. Platis M, Vlachakis D, Foudah AI, Muharram MM, Alqarni MH, Papageorgiou AC, Labrou NE. The interaction of Schistosoma japonicum glutathione transferase with Cibacron blue 3GA and its fragments. Med Chem. 2020, 16:1, doi: 10.2174/1573406416666200403074742

138. Vlachakis D. Antibody clustering and 3D modelling for neurodegenerative diseases. Springer - Nature: Computational Neurodegeneration. 2020, In Press

137. Bacopoulou F, Landisa GN, Efthymiou V, Pałasz A, Tsitsika A, Darviri C, Vlachakis D, Chrousos GP. Body composition in adolescent abdominal obesity / metabolic syndrome. European Journal of Clinical Investigation. 2020, In Press

136. Vlachakis D, Papakonstantinou E, Efthimiadou A, Bacopoulou F, Goulielmos G, Chrousos GP, Eliopoulos E. Ancestral cancer genes shaping evo-devo; an integrated biochemical and computational study. World Academy of Sciences Journal. 2020, 2(7), 1-8. doi:10.3892/wasj.2020.48

135. Raftopoulou S, Nicolaides NC, Papageorgiou L, Amfilochiou A, Zakinthinos SG, Potamitis G, Eliopoulos E, Chrousos GP, Vlachakis D. Structural study of the DNA – Clock/Bmal1 complex provides insights for the role of cortisol, hGR and HPA axis in stress management and sleep disorders. Adv Exp Med Biol. 2020;1195:59-71. doi:10.1007/978-3-030-32633-3_10.

134. Papageorgiou L, Maroulis D, Chrousos GP, Eliopoulos E, Vlachakis D. Antibody clustering using a machine learning pipeline that fuses genetic, structural and physicochemical properties. Adv Exp Med Biol. 2020;1194:41-58. doi:10.1007/978-3-030-32622-7_4

133. Papageorgiou L, Papakostantinou E, Salis C, Polychronidou E, Hagidimitriou M, Maroulis D, Eliopoulos E, Vlachakis D. Drugena: A fully automated immunoinformatics platform for the design of antibody drug conjugates against neurodegenerative diseases. Adv Exp Med Biol. 2020;1194:203-215. doi:10.1007/978-3-030-32622-7_18.

132. Koumandou VL, Papageorgiou L, Tsaniras SC, Papathanassopoulou A, Hagidimitriou M, Cosmidis N, Vlachakis D. Microbiome hijacking towards an integrative pest management pipeline. Adv Exp Med Biol. 2020;1195:21-32. doi:10.1007/978-3-030-32633-3_4

131. Salis C, Papageorgiou L, Papakostantinou E, Hagidimitriou M, Vlachakis D. Olive Oil Polyphenols in Neurodegenerative Pathologies. Adv Exp Med Biol. 2020;1195:77-91. doi:10.1007/978-3-030-32633-3_12.

130. Papakonstantinou E, Megalooikonomou V, Vlachakis D. Dark Suite; a comprehensive toolbox for computer-aided drug design. EMBnet Journal. 2020;25:e928. doi:10.14806/ej.25.0.928

129. Papakonstantinou E, Bacopoulou F, Megalooikonomou V, Efthimiadou A, Vlachakis D. An in silico and in vitro pipeline for the rapid screening of helicase modulators. EMBnet Journal. 2020;25:e927. doi:10.14806/ej.25.0.927

128. Mitsis A, Papageorgiou L, Efthimiadou A, Bacopoulou F, Vlachakis D, Chrousos GP, Eliopoulos E. A comprehensive structural and functional analysis of the Ligand Binding Domain of the Nuclear Receptor Superfamily shows highly conserved signaling motifs and two distinct canonical forms through evolution. World Academy of Sciences Journal. 2020; 1(6), 264-274 https://doi.org/10.3892/wasj.2020.30

127. Mitsis A, Papageorgiou L, Efthimiadou A, Bacopoulou F, Vlachakis D, Chrousos GP, Eliopoulos E. Transcription Factors and Evolution: An integral part of gene expression. World Academy of Sciences Journal. 2020, 2(1), 3-8 https://doi.org/10.3892/wasj.2020.32

126. Tsekouras V, Mavrikou S, Vlachakis D, Makridakis M, Stroggilos R, Zoidakis J, Termentzi A, Moschopoulou G, Kintzios S. Proteome analysis of leaf, stem and callus in Viscum album and identification of lectins and viscotoxins with bioactive properties. Plant Cell Tiss Organ Cult 2020, https://doi.org/10.1007/s11240-020-01777-7

125. Papakonstantinou E, Zagorščak M, Duarte-López A, Temitayo O, Kaisaridi P, Diakou I, Eliopoulos E, Megalooikonomou V, Kossida S, Bonavides-Martinez C, Klucar L, Villiers E, Korpelainen E, Barreto-Hernández E, Magklaras G, Eriksson N, Efthimiadou A, Vlachakis D, Bongcam-Rudloff E, D'Elia D. EMBnet 30th Anniversary: something to be proud of. EMBnet Journal. 2020, In Press

124. Charalampopoulou M, Syrigos K, Filopoulos E, Megalooikonomou V, Vlachakis D, Chrousos GP, Darviri C. Reliability and validity of the instrument Newly Diagnosed Breast Cancer Stress Scale in the Greek population. Journal of Molecular Biochemistry. 2020, In Press

123. Sioula EK, Tigani X, Artemiadis A, Vlachakis D, Chrousos GP, Darviri C, Alexopoulos EC. An 8-week stress management program in information technology professionals and the role of a new cognitive behavioral method: A pilot randomized controlled trial. Journal of Molecular Biochemistry. 2020, In Press

122. Zigkiri E, Nicolaides N, Bacopoulou F, Simos D, Vlachakis D, Chrousos GP, Darviri C. Τhe Effect of the Pythagorean Self-Awareness Intervention on Psychological, Lifestyle and Cognitive Measures of a Community Sample. Journal of Molecular Biochemistry. 2020, In Press

121. Kalogiratou DS, Bacopoulou F, Kanaka-Gantenbein C, Tigani X, Gerakini O, Vlachakis D, Chrousos GP, Darviri C. Effects of a cognitive stress management program-Pythagorean Self Awareness-on childhood emotional eating and psychological wellbeing. A pragmatic trial. Journal of Molecular Biochemistry. 2020, In Press

2019

12 articles in 2019

120. Tsaniras SC, Delinasios GJ, Petropoulos M, Panagopoulos A, Anagnostopoulos AK, Villiou M, Vlachakis D, Bravou V, Stathopoulos GT, Taraviras S. DNA Replication Inhibitor Geminin and Retinoic Acid Signaling Participate in Complex Interactions Associated With Pluripotency. Cancer Genomics Proteomics. 2019, 16(6):593-601.

119. Vlamos P, Kotsireas I, Vlachakis D. Complexity in Medical Informatics. 2019, Complexity, 8658124

118. Kalogiratou DS, Bacopoulou F, Kanaka-Gantenbein C, Vlachakis D, Gerakini O, Chrousos GP, Darviri C. Greek Validation of Emotional Eating Scale for Children and Adolescents. JMolBiochem. 2019 (8): 26-32

117. Markomanolaki ZS, Tigani X, Siamatras T, Bacopoulou F, Tsartsalis A, Artemiadis A, Megalooikonomou V, Vlachakis D, Chrousos GP, Darviri C. Stress Management in Women with Hashimoto’s thyroiditis: A Randomized Controlled Trial. JMolBiochem. 2019 (8): 3-12

116. Papakonstantinou E, Pierouli K, Eliopoulos E, Vlachakis D. Systems Biology consolidating state of the art genetics and bioinformatics. IntechOpen Book Series. 2019, Systems Biology

115. Salis C, Papakonstantinou E, Pierouli K, Mitsis A, Basdeki L, Megalooikonomou V, Vlachakis D, Hagidimitriou M. A genomic data mining pipeline for 15 species of the genus Olea. EMBNet J. 2019, e922

114. Papakonstantinou E, Bacopoulou F, Brouzas D, Megalooikonomou V, D’ Elia D, Bongcam-Rudloff E, Vlachakis D. NOTCH3 and CADASIL Syndrome; a genetic and structural overview. EMBNet J. 2019, e921

113. Papakonstantinou E, Vlachakis D. State of the art immunogenetics and immunoinformatics. JMolBiochem 2019 (8): 1-2

112. Chronopoulou E, Vlachakis D, Papageorgiou A, Ataya F, Labrou NE. Structure-based design and application of an engineered glutathione transferase for the development of an optical biosensor for pesticides determination. BBA - General Subjects. 2019, 1863(3):565-576.

111. Theoharaki C, Chronopoulou E, Vlachakis D, Ataya FS, Giannopoulos P, Maurikou S, Skopelitou K, Papageorgiou AC, Labrou NE. Delineation of the functional and structural properties of the glutathione transferase family from the plant pathogen Erwinia carotovora. Funct Integr Genomics. 2019, 19(1):1-12 doi: 10.1007/s10142-018-0618-8

110. Pierouli K., Mitsis A., Papakonstantinou E. and Vlachakis D. Gene Profiling in cancer in the era of metagenomics and precision medicine. IntechOpen Book Series. 2019, Gene Profiling in Cancer

109. Picasi E, Kaisaridi P, Diakou I, Kaliafentakis K, Papageorgiou L, Megalooikonomou V, Vlachakis D. Insights into the mechanism of coccidiosis from Isospora Suis. Online Journal Bioinformatics. 2019, 20(1):1-8

2018

11 articles in 2018

108. 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

107. 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

106. Vlachakis D. Molecular Docking - Overview, Background, Application and What the Future Holds. IntechOpen Book Series. 2018, Molecular Docking

105. Picasi E, Tartas A, Megalooikonomou V, Vlachakis D. Introducing Thetis: a comprehensive suite for event detection in molecular dynamics. Journal of Molecular Biochemistry. 2018, 7:71-77.

104. Boulaki V, Vlachakis D, Sotiraki S, Kossida S.An up-to-date review of piglet isosporosis: New insights and therapeutic perspectives. Veterinary Science: Breakthroughs in Research and Practice. 2018, Pages 116-131 ISBN: 978-152255641-1;1522556400;978-152255640-4 DOI:10.4018/978-1-5225-5640-4.ch006

103. Amidi A, Amidi S, Vlachakis D, Megalooikonomou V, Paragios N, Zacharaki EI. EnzyNet: enzyme classification using 3D convolutional neural networks on spatial representation. PeerJ. 2018, 6:e4750

102. Papageorgiou L, Picasi E, Raftopoulou S, Mantaiou M, Megalooikonomou V, Vlachakis D. Genomic Big Data Hitting The Storage Bottleneck. EMBnet Journal. 2018;24. pii: e910.

101. 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

100. 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

099. Marinou M, Platis D, Ataya FS, Chronopoulou E, Vlachakis D, Labrou NE. Structure-based design and application of a nucleotide coenzyme mimetic ligand: Application to the affinity purification of nucleotide dependent enzymes. Journal of Chromatography A. 2018 (1535):88-100

098. Bakopoulos M, Papageorgiou L, Megalooikonomou V, Vlachakis D. State of the art sensor-based wearables and nanorobotics for life sciences. Online Journal Bioinformatics. 2018, 1(19): 35-40

2017

9 articles in 2017

097. 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

096. Papageorgiou L, Megalooikonomou V, Vlachakis D. Antisoma Application: A Fully Integrated V-Like Antibodies Platform. AIMS Medical Science, 2017, 4(4): 382-394

095. Vlachakis D. On Novel Anti-viral HIV Gene Editing Platforms. J Genet DNA Res. 2017, Editorial Article, v1:pp1

094. Vlachakis D, Zacharaki EI, Tsiamaki E, Koulouri M, Raftopoulou S, Papageorgiou L, Chrousos GP, Ellul J, Megalooikonomou V. Insights into the molecular mechanisms of stress and inflammation in ageing and frailty of the elderly. Journal of Molecular Biochemistry. 2017, 6, 41-44

093. Papageorgiou L, Vlachakis C, Dragoumani K, Raftopoulou S, Brouzas D, Nicolaides NC, Chrousos GP, Charmandari E, Megalooikonomou V, Vlachakis D. HCV genetics and genotypes dictate future antiviral strategies. Journal of Molecular Biochemistry. 2017, 6, 33-40

092. 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

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

090. Tagkalakis F, Vlachakis D, Megalooikonomou V, Skordas A. A Novel Approach to Finger Vein Authentication. ISBI. 2017:16968681

089. 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

2016

10 articles in 2016

088. 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, 55(5):749–757

087. 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, 86(6):845-851

086. 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.

085. 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.

084. 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

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

082. 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.

081. 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.

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

079. 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.

2015

10 articles in 2015

078. 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.

077. 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.

076. 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.

075. 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.

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

073. 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.

072. 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.

071. 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.

070. 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.

069. 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.

2014

12 articles in 2014

068. 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.

067. 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.

066. 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.

065. 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.

064. 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.

063. 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.

062. 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.

061. 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.

060. Tsiliki G, Vlachakis D, Kossida S, On integrating multi-platform microarray data, Philos Trans A Math Phys Eng Sci 2014 20130136

059. 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

058. 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

057. 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

2013

26 articles in 2013

056. 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

055. 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

054. 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

053. 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

052. 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

051. 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

050. 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

049. 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

048. 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

047. 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

046. 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

045. 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

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

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

042. 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

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

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

039. 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

038. 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

037. 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

036. 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

035. 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

034. 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

033. D Vlachakis, Tsiliki G, Kossida S, 3D Molecular Modelling of the Helicase Enzyme of the Endemic, Zoonotic Greek Goat Encephalitis Virus, ISBN: 978-3-642-41012-3. 2013. Engineering Applications of Neural Networks, Communications in Computer and Information Science 383: 165-171pp.

032. D Vlachakis, Tsiliki G, Kondos D, Kontopoulos DG. Feidakis C, Kossida S, Applied bioinformatics in the structural, post-genomic era. COST Farm animal proteomics, ISBN: 978-90-8686-222-1. April 2013. pp 23-25.

2012

9 articles in 2012

031. 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

030. 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

029. 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

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

027. 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

026. 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

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

024. 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

023. 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

2011

1 article in 2011

022. 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

2010

3 articles in 2010

021. 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

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

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

2009

7 articles in 2009

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

017. 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

016. 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

015. 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

014. 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

013. D Vlachakis, M Vlassi. Molecular modelling of a novel series of Dengue virus (typeII) helicase potential inhibitors, by a de novo structure-based drug design approach. FEBS JOURNAL 276, 171-171, Prague, Czech-Republic, July 2009

012. Y Vangelatos, M Billini, D Vlachakis, V Sophianopoulou. Molecular modelling study of PrnB, the major proline transporter of Aspergillus nidulans. FEBS JOURNAL 276, 123-124, Prague, Czech-Republic, July 2009

2008

4 articles in 2008

011. 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

010. 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

009. Brancale A, D Vlachakis, Kandil S, Biondaro S, Berry C, Neyts J, Discovery of a Novel HCV Helicase Inhibitor by a De Novo Drug Design Approach. Antiviral Research. 2008, 78(2):22. [doi:10.1016/j.antiviral.2008.01.030, ISSN: 0166-3542]

008. Yalcintepe J, D Vlachakis, Prasse A, Gaede K, Müller-Quernheim J, Zissel G, Expression und Bedeutung des TLR9 auf BAL Zellen von Patienten mit Sarkoidose und EAA. Pneumologie. 2008, 68:288. [doi:10.1055/s-2008-1074351,ISSN:0934-8387]

2007

2 articles in 2007

007. 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

006. Yalcintepe J, D Vlachakis, Prasse A, Müller-Quernheim J, Zissel G, Expression und Bedeutung des TLR9 auf BAL Zellen von Patienten mit Sarkoidose und EAA. Pneumologie. 2007, 61(1):27. [doi:10.1055/s-2007-967248,ISSN:0934-8387]

2006

3 articles in 2006

005. Brancale A, D Vlachakis, Barbera MC, Silvestri R, Berry C, Netys J. Synthesis and evaluation of novel potential HCV Helicase inhibitors. Antiviral Research. 2006, 70(1):53. [doi:10.1016/j.antiviral.2006.02.001,ISSN:0166-3542]

004. Meek KM, Knupp C, D Vlachakis, Boulton ME and Kamma CS. Homology-based molecular modelling of the bovine corneal biglycan core protein: implications for structure and function. Journal of Investigative Ophthalmology & Vision Sciences. 2006; 47(1):3000 [ISSN: 0146-0404]

003. D Vlachakis, Oldfield S and Brancale A. The three-dimensional structures of the Dengue virus, West Nile Virus, Japanese Encephalitis and Yellow Fever Polymerase proteins predicted by homology-based molecular modelling. Antiviral Research. 2005, 65(3):69. [doi:10.1016/j.antiviral.2005.01.001,ISSN: 0166-3542]

2005

2 articles in 2005

002. D Vlachakis, Muller-Quernheim J, Zissel G. CXCR3 ligands and BAL cytology in ILD. Eur Respir J. 2005; 26(49):101[ISSN: 0903-1936]

001. D Vlachakis, Berry C, Jones GW and Brancale A. An Assay for the biological testing of potential inhibitors for the HCV helicase, Dengue virus helicase and Dengue virus helicase/protease complex (NS3 domain). Antiviral Research. 2005, 65(3):60. [doi:10.1016/j.antiviral.2005.01.001,ISSN: 0166-3542]

*** D Vlachakis Computer-Aided Drug Design and Biological Evaluation of Novel Anti-Viral Agents. PhD Thesis Welsh School of Pharmacy & School of Life Sciences of Cardiff University in collaboration with ROSCHE pharma, Palo Alto, California. Completed on June 2005 (just before my 25th BDay). Defended in 2006.







INTERNATIONAL SCIENTIFIC PATENTS

01. WO/2009/125191 – 15.10.2009 (Pub) – PCT/GB2009/000936 – 09.04.2009


Brancale A, Vlachakis D, Berry C, Neyts J.

HCV ANTIVIRAL DRUG DESIGN (BENZENE DERIVATIVES): Compounds, which according to the invention can display potent inhibition against Hepatitis C Virus (HCV) helicase & potent anti-viral activity against HCV.

Hepatitis C is a liver infection caused by a flavivirus (HCV) that affects over 170 million people worldwide. In most cases the infection becomes chronic and 20% of the carriers develop cirrhosis. Currently the infection is treated with interferon, but this therapy does not completely eliminate the virus and more efficacious treatments are needed.

A new assay for the measurement of helicase enzyme activity was developed for the evaluation of the potency of potential inhibitors. This assay involves the use of a DNA or RNA duplex substrate and recombinant purified helicase. The DNA duplex consisted of a pair of oligonucleotides, one biotinylated and the other one DIG-labelled, at their respective 5' termini. This DNA duplex was immobilised, via the biotin molecule, on the surface of a neutravidin-coated 96 well plate. Helicase will initiate its unwinding activity upon activation with ATP, leading eventually in the release of the DIG labelled oligonucleotides, which translates in signal (luminescence) reduction with respect to control wells. This signal can be produced and quantified with the aid of a chemiluminescence antibody.

Other assay methods for this type of enzyme may analyse ATPase activity but assessment of the effects on helicase unwinding activity has been identified as the best way to evaluate inhibitors of this class of enzyme (1). Helicase activity assays rely on the ability of the enzyme to displace one strand (release strand) of DNA or RNA from another (template) strand. Many reports use displacement of radio-labelled release strands, detected either after gel electrophoresis (eg (2)), thin layer chromatography (eg (3)) or scintillation counting (eg (4)). The latter method may be amenable to high-throughput screening but carries the practical disadvantages of the use of radioactive materials. Further methods have incorporated DIG labelled release strands to allow detection by ELISA (5). We propose a new combined method that uses chemiluminescent antibody detection of residual release strand to give a robust helicase assay, that does not employ radiolabeled compounds and gives a stable read-out that is highly suited to high-throughput screening.

As proof of concept, the HCV helicase was expressed and isolated using recombinant protein techniques and then used in our assay. We found this assay to be highly reproducible since only slight variation was observed when a total of 96 helicase reactions (including controls) were performed on one plate. Therefore, our suggested rapid helicase assay is fast, convenient and highly reproducible while obviating the need to employ radiochemicals. These criteria make it suitable for high throughput screening of potential helicase inhibitors.

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02. GR/2012/0100266 – 21.05.2012 (Pub) – 201201605 – 21.05.2012


Kossida S, Vlachakis D, Tsiliki G, Pavlopoulou A.

3D PHARMACOPHORE FOR THE DESIGN OF HUMAN POLYADENOSINE RIBONUCLEASE(PARN) INHIBITORS. This invention is about a highly specific, custom-made three dimensional Pharmacophore model for the catalytic site of the human poly-adenosine ribonuclease (PARN).

The present invention relates to means and methods for the design of highly specific anti-PARN agent using our 3D pharmacophore model. Using a library of previously published modified nucleoside analog substrates acting in the proximity of the scissile bond of PARN, we conducted structure – activity relationship (SAR) analysis, structural characterization and complex (receptor-ligand) based molecular dynamics simulations that led to the design of a PARN-specific pharmacophore model. Our full pharmacophore model consists of five pharmacophoric annotation points, which include two hydrogen donating PAPs, one hydrophobic PAP, one aromatic PAP and a hydrogen accepting PAP, in the vicinity of human poly-Adenosine ribonuclease catalytic site.

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ISBN SCIENTIFIC BOOKS

Molecular Docking

Book Editor: DIMITRIOS VLACHAKIS
Published: July 11th 2018
DOI: 10.5772/intechopen.69830
ISBN: 978-1-78923-355-1
Print ISBN: 978-1-78923-354-4
Publisher: InTech Publishing

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Gene Expression Profiling in Cancer

Book Editor: DIMITRIOS VLACHAKIS
Published: June 19th 2019
ISBN: 978-1-83880-176-2
Print ISBN: 978-1-83880-175-5
eBook (PDF) ISBN: 978-1-78985-383-4
Publisher: InTech Publishing

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Systems Biology

Book Editor: DIMITRIOS VLACHAKIS
Published: June 19th 2019
ISBN: 9978-1-83880-804-4
Print ISBN: 978-1-83880-803-7
eBook (PDF) ISBN: 978-1-83880-805-1
Publisher: InTech Publishing

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ANTIVIRAL COMPUTER-AIDED DRUG DESIGN

By DIMITRIOS VLACHAKIS [Monograph] 2012
Printed: 112 pages – Paperback book
ISBN-13:978-1-300-22974-2
Publisher:University of Cardiff, Wales, UK
Reseller: AMAZON $45.00

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COMPUTER-AIDED DRUG DESIGN. THE HCV FAMILY EXAMPLE

By DIMITRIOS VLACHAKIS [Monograph] 2011
Printed: 222 pages – Hardcover book
ISBN-10: 0-557-77243-5, ISBN-13: 978-0-557-77243-8
Publisher:University of Cardiff, Wales, UK
Reseller: AMAZON $28.97

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THE FLAVIVIRIDAE VIRAL FAMILY: PROPERTIES AND GENOME BANK

By DIMITRIOS VLACHAKIS [Monograph] 2008
Printed: Printed: 345 pages – Paperback book
SBN-10: 0-615-24327-4, ISBN-13: 978-0-615-24327-6
Publisher:University of Cardiff, Wales, UK
Reseller: AMAZON $22.64

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AN INTRODUCTION TO MOLECULAR MODELLING, FROM THEORY TO APPLICATION

By DIMITRIOS VLACHAKIS [Monograph] 2007
Printed: 158 pages – Paperback book
SBN-10: 0-615-17606-2, ISBN-13: 978-0-615-17606-2
Publisher:University of Cardiff, Wales, UK
Reseller: AMAZON $12.50

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ADIPOCYTE VIABILITY AND LDH

By DIMITRIOS VLACHAKIS [Monograph] 2007
Printed: 40 pages – Hardcover book
ISBN-10: 0-615-15238-4, ISBN-13: 978-0-615-15238-7
Publisher:University of Cardiff, Wales, UK
Reseller: AMAZON $16.90

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A BIOINFORMATICS METHOD FOR THE PRODUCTION OF ANTIBODY-DRUG CONJUGATES THROUGH SITE- SPECIFIC CYSTEINE CONJUGATION

By ARIANNA FILNTISI, DIMITRIOS VLACHAKIS AND GEORGE K. MATSOPOULOS
FULL BOOK: Bioinformatics - Updated Features And Applications,
Prof. Ibrokhim Abdurakhmonov (Ed.) – Chapter 2 – 22 Pages DOI: 10.5772/62747
ISBN 978-953-51-2547-1
SBN Print 978-953-51-2546-4
Publisher: InTech Publishing

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Genetic and geo-epidemiological analysis of the Zika virus pandemic; learning lessons from the recent Ebola outbreak

By DIMITRIOS VLACHAKIS, LOUIS PAPAGEORGIOU AND VASILIS MEGALOOIKONOMOU
FULL BOOK: Current Topics in Zika
Prof. Alfonso J. Rodriguez-Morales (Ed.) – Chapter 3 – 15 Pages DOI: 10.5772/65145.
ISBN: 978-1-78923-271-4
Print ISBN: 978-1-78923-270-7
Publisher: InTech Publishing

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Dimitrios P. Vlachakis