PUBLISHED RESEARCH MANUSCRIPTS

1. D'Anna F, Jareborg N, Jetten M, Ahokas M, Alper P, Andrews R, Bösl K, D'Altri T, Faria D, Fatima N, Fuchs S, Garrard C, Gu W, Heil KF, Kallberg Y, Licciulli F, Lübke NC, Melo AMP, Mičetić I, Oliveira J, Oulas A, Palagi PM, Poterlowicz K, Perez-Sitja X, Ruch P, Sansone SA, Schnitzer H, van Gelder C, Vergoulis T, Wibberg D, Wittig U, Leskošek B, Vondrasek J, Andrabi M. A research data management (RDM) community for ELIXIR. F1000Res. 2024 Sep 30;13:ELIXIR-230. doi: 10.12688/f1000research.146301.2. PMID: 39410979; PMCID: PMC11474151.  

2. Karathanasis N, Papasavva PL, Oulas A, Spyrou GM. Combining clinical and molecular data for personalized treatment in acute myeloid leukemia: A machine learning approach. Comput Methods Programs Biomed. 2024 Dec;257:108432. doi: 10.1016/j.cmpb.2024.108432. Epub 2024 Sep 18. PMID: 39316958.  

3. Baltsavia I, Oulas A, Theodosiou T, Lavigne MD, Andreakos E, Mavrothalassitis G, Iliopoulos I. scRNA-Explorer: An End-user Online Tool for Single Cell RNA-seq Data Analysis Featuring Gene Correlation and Data Filtering. J Mol Biol. 2024 Sep 1;436(17):168654. doi: 10.1016/j.jmb.2024.168654. Epub 2024 Jun 12. PMID: 39237193. 

4. Oulas A, Savva K, Karathanasis N, Spyrou GM. Ranking of cell clusters in a single-cell RNA-sequencing analysis framework using prior knowledge. PLoS Comput Biol. 2024 Apr 18;20(4):e1011550. doi: 10.1371/journal.pcbi.1011550. PMID:38635836; PMCID: PMC11060557.

5. Philippou S, Mastroyiannopoulos NP, Tomazou M, Oulas A, Ackers-Johnson M, Foo RS, Spyrou GM, Phylactou LA. Selective Delivery to Cardiac Muscle Cells Using Cell-Specific Aptamers. Pharmaceuticals (Basel). 2023 Sep 6;16(9):1264. doi: 10.3390/ph16091264. PMID: 37765072; PMCID: PMC10534653.

6. Oulas A, Minadakis G, Zachariou M, Tomazou M, Vlamis-Gardikas A, Spyrou GM. Bacterial Wars-a tool for the prediction of bacterial predominance based on network analysis measures. NAR Genom Bioinform. 2023 May 30;5(2):lqad049. doi: 10.1093/nargab/lqad049. PMID: 37260512; PMCID: PMC10227370.

7. Baltoumas FA, Karatzas E, Paez-Espino D, Venetsianou NK, Aplakidou E, Oulas A, Finn RD, Ovchinnikov S, Pafilis E, Kyrpides NC, Pavlopoulos GA. Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters. Front Bioinform. 2023 Mar 3;3:1157956. doi: 10.3389/fbinf.2023.1157956. PMID: 36959975; PMCID: PMC10029925.

8. Talli I, Dovrolis N, Oulas A, Stavrakaki S, Makedou K, Spyrou GM, Maroulakou I. Novel clinical, molecular and bioinformatics insights into the genetic background of autism. Hum Genomics. 2022 Sep 18;16(1):39. doi:10.1186/s40246-022-00415-x. PMID: 36117207; PMCID: PMC9482726.

9. Koutsoulidou A, Koutalianos D, Georgiou K, Kakouri AC, Oulas A, Tomazou M, Kyriakides TC, Roos A, Papadimas GK, Papadopoulos C, Kararizou E, Spyrou GM, Zamba Papanicolaou E, Lochmüller H, Phylactou LA. Serum miRNAs as biomarkers for the rare types of muscular dystrophy. Neuromuscul Disord. 2022 Mar 11:S0960-8966(22)00067-0. doi: 10.1016/j.nmd.2022.03.003. Epub ahead of print. PMID: 35393236.

10. Kakouri AC, Koutalianos D, Koutsoulidou A, Oulas A, Tomazou M, Nikolenko N, Turner C, Roos A, Lusakowska A, Janiszewska K, Papadimas GK, Papadopoulos C, Kararizou E, Papanicolaou EZ, Gorman G, Lochmüller H, Spyrou GM, Phylactou LA. Circulating small RNA signatures differentiate accurately the subtypes of muscular dystrophies: small-RNA next-generation sequencing analytics and functional insights. RNA Biol. 2022 Jan;19(1):507-518. doi:10.1080/15476286.2022.2058817. PMID: 35388741; PMCID: PMC8993092.

11. Kakouri AC, Votsi C, Oulas A, Nicolaou P, Aureli M, Lunghi G, Samarani M, Compagnoni GM, Salani S, Di Fonzo A, Christophides T, Tanteles GA, Zamba-Papanicolaou E, Pantzaris M, Spyrou GM, Christodoulou K. Transcriptomic characterization of tissues from patients and subsequent pathway analyses reveal biological pathways that are implicated in spastic ataxia. Cell Biosci. 2022 Mar 11;12(1):29. doi: 10.1186/s13578-022-00754-1. PMID: 35277195; PMCID: PMC8917697.]

12. Anastasis Oulas, Margarita Zachariou, Christos T. Chasapis, Marios, Tomazou Umer Z. Ijaz, Georges Pierre Schmartz, George M. Spyrou and Alexios Vlamis-Gardikas. Putative antimicrobial peptides within bacterial proteomes affect bacterial predominance: a network analysis perspective. Front Microbiol. 2021 Nov 12;12:752674.

13. Anastasis Oulas, Jan Richter, Maria Zanti, Marios Tomazou, Kyriaki Michailidou, Kyproula Christodoulou, Christina Christodoulou, George M. Spyrou. In depth analysis of Cyprus-specific mutations of SARS-CoV-2 strains using computational approaches. BMC Genom Data. 2021 Nov 13;22(1):48.

14. Demetris Koutalianos, Andrie Koutsoulidou, Chrystalla Mytidou, Andrea C. Kakouri, Anastasis Oulas et al,  miR-223-3p and miR-24-3p as novel serum-based biomarkers for Myotonic Dystrophy type 1. Mol Ther Methods Clin Dev. 2021 Sep 14;23:169-183.

15. Richter J, Fanis P, Tryfonos C, Koptides D, Krashias G, Bashiardes S, Hadjisavvas A, Loizidou M, Oulas A, Alexandrou D, Kalakouta O, Panayiotidis MI, Spyrou GM, Christodoulou C. Molecular epidemiology of SARS-CoV-2 in Cyprus. PLoS One. 2021 Jul 21;16(7):e0248792. doi: 10.1371/journal.pone.0248792. PMID: 34288921; PMCID: PMC8294526.  

16. Tomazou M, Bourdakou MM, Minadakis G, Zachariou M, Oulas A, Karatzas E, Loizidou E, Kakouri A, Christodoulou C, Savva K, Zanti M, Onisiforou A, Afxenti S, Richter J, Christodoulou CG, Kyprianou T, Kolios G, Dietis N, Spyrou GM. Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19. Brief Bioinform. 2021 May 1:bbab114. doi: 10.1093/bib/bbab114. Epub ahead of print. PMID: 34009288; PMCID: PMC8135326.  

17. Stephanou C, Omirou M, Philippot L, Zissimos AM, Christoforou IC, Trajanoski S, Oulas A, Ioannides IM. Land use in urban areas impacts the composition of soil bacterial communities involved in nitrogen cycling. A case study from Lefkosia (Nicosia) Cyprus. Sci Rep. 2021 Apr 14;11(1):8198. doi: 10.1038/s41598-021-87623-y. PMID: 33854127; PMCID: PMC8047022.  

18. Constantinou A, Polak-Witka K, Tomazou M, Oulas A, Kanti V, Schwarzer R, Helmuth J, Edelmann A, Blume-Peytavi U, Spyrou GM, Vogt A. Dysbiosis and Enhanced Beta-Defensin Production in Hair Follicles of Patients with Lichen Planopilaris and Frontal Fibrosing Alopecia. Biomedicines. 2021 Mar 7;9(3):266. doi: 10.3390/biomedicines9030266. PMID: 33800045; PMCID: PMC7999846.    

19. Anastasis Oulas, Maria Zanti, Marios Tomazou, Margarita Zachariou, George Minadakis, Marilena M Bourdakou1, Pavlos Pavlidis, George M. Spyrou. Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains. PLOS ONE, 2021 Jan 26;16(1):e0238665. doi: 10.1371/journal.pone.0238665. eCollection 2021.

20. Neocleous V, Fanis P, Toumba M, Tanteles GA, Schiza M, Cinarli F, Nicolaides NC, Oulas A, Spyrou GM, Mantzoros CS, Vlachakis D, Skordis N, Phylactou LA. GnRH Deficient Patients With Congenital Hypogonadotropic Hypogonadism: Novel Genetic Findings in ANOS1, RNF216, WDR11, FGFR1, CHD7, and POLR3A Genes in a Case Series and Review of the Literature. Front Endocrinol (Lausanne). 2020 Aug 28;11:626. doi: 10.3389/fendo.2020.00626. eCollection 2020.PMID: 32982993

21. Stefani S, Kousiappa I, Nicolaou N, Papathanasiou ES, Oulas A, Fanis P, Neocleous V, Phylactou LA, Spyrou GM, Papacostas SS. Neurophysiological and Genetic Findings in Patients With Juvenile Myoclonic Epilepsy. Front Integr Neurosci. 2020 Aug 20;14:45. doi: 10.3389/fnint.2020.00045. eCollection 2020.PMID: 32973469 

22. Nicolaou O, Sokratous K, Makowska Z, Morell M, De Groof A, Montigny P, Hadjisavvas A, Michailidou K, Oulas A, Spyrou GM, Demetriou C, Alarcón-Riquelme ME, Psarellis S, Kousios A, Lauwerys B, Kyriacou K. Proteomic analysis in lupus mice identifies Coronin-1A as a potential biomarker for lupus nephritis. Arthritis Res Ther. 2020 Jun 18;22(1):147. doi: 10.1186/s13075-020-02236-6.PMID: 32552896. 

23. Chairta P, Nicolaou P, Sokratous K, Galant C, Houssiau F, Oulas A, Spyrou GM, Alarcon-Riquelme ME, Lauwerys BR, Christodoulou K. Comparative analysis of affected and unaffected areas of systemic sclerosis skin biopsies by high-throughput proteomic approaches. Arthritis Res Ther. 2020 May 7;22(1):107. doi: 10.1186/s13075-020-02196-x.PMID: 32381114.

24. Karatzas E, Zachariou M, Bourdakou MM, Minadakis G, Oulas A, Kolios G, Delis A, Spyrou GM.PathWalks: identifying pathway communities using a disease-related map of integrated information. Bioinformatics. 2020 Jul 1;36(13):4070-4079. doi: 10.1093/bioinformatics/btaa291.PMID: 32369599 . 

25. Tomazou M, Oulas A, Anagnostopoulos AK, Tsangaris GT, Spyrou GM. In Silico Identification of Antimicrobial Peptides in the Proteomes of Goat and Sheep Milk and Feta Cheese. Proteomes. 2019 Sep 21;7(4). pii: E32. doi: 10.3390/proteomes7040032.

26. Neocleous V, Fanis P, Cinarli F, Kokotsis V, Oulas A, Toumba M, Spyrou GM, Phylactou LA, Skordis N. 46,XY complete gonadal dysgenesis in a familial case with a rare mutation in the desert hedgehog (DHH) gene. Hormones (Athens). 2019 Sep;18(3):315-320. doi: 10.1007/s42000-019-00116-6. Epub 2019 Jun 25.

27. Oulas A, Minadakis G, Zachariou M, Spyrou GM. Selecting variants of unknown significance through network-based gene-association significantly improves risk prediction for disease-control cohort. Sci Rep. 2019 Mar 1;9(1):3266. doi: 10.1038/s41598-019-39796-w.

28. Anastopoulos I, Omirou M, Stephanou C, Oulas A, Vasiliades MA, Efstathiou AM, Ioannides IM. Valorization of agricultural wastes could improve soil fertility and mitigate soil direct N2O emissions. J Environ Manage. 2019 Nov 15;250:109389. doi: 10.1016/j.jenvman.2019.109389. Epub 2019 Sep 6.

29. Katsarou K, Mitta E, Bardani E, Oulas A, Dadami E, Kalantidis K. DCL-suppressed Nicotiana benthamiana plants: valuable tools in research and biotechnology. Mol Plant Pathol. 2019 Mar;20(3):432-446. doi: 10.1111/mpp.12761. Epub 2018 Dec 19.

30. Kakouri AC, Christodoulou CC, Zachariou M, Oulas A, Minadakis G, Demetriou CA, Votsi C, Zamba-Papanicolaou E, Christodoulou K, Spyrou GM. Revealing Clusters of Connected Pathways Through Multisource Data Integration in Huntington's Disease and Spastic Ataxia. IEEE J Biomed Health Inform. 2019 Jan;23(1):26-37. doi: 10.1109/JBHI.2018.2865569. Epub 2018 Aug 30.

31. Minadakis G, Zachariou M, Oulas A, Spyrou GM. PathwayConnector: finding complementary pathways to enhance functional analysis. Bioinformatics. 2019 Mar 1;35(5):889-891. doi: 10.1093/bioinformatics/bty693.

32. Jantsch M, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A et al. Positioning Europe for the EPITRANSCRIPTOMICS challenge. RNA Biol. 2018 Apr 19:1-8. doi: 10.1080/15476286.2018.1460996. [Epub ahead of print]

33. Zachariou M, Minadakis G, Oulas A, Afxenti S, Spyrou GM. Integrating multi-source information on a single network to detect disease-related clusters of molecular mechanisms. J Proteomics. 2018 Mar 13. pii: S1874-3919(18)30104-0. doi: 10.1016/j.jprot.2018.03.009. [Epub ahead of print]

34. Anastasis Oulas, George Minadakis, Margarita Zachariou, Kleitos Sokratous, Marilena M Bourdakou, George M Spyrou – “Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches” – Brief Bioinform. 2017 Nov 27. doi: 10.1093/bib/bbx15. 

35. Christina Pavloudi, Jon B Kristoffersen, Anastasis Oulas, Marleen De Troch, Christos Arvanitidis – “Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s "species minimum" concept” – PeerJ. 2017 Oct 13;5:e3687. doi: 10.7717/peerj.3687.

36. Lucas Sinclair, Umer Zeeshan Ijaz, Lars Juhl Jensen, Marco Coolen, Cecile Gubry-Rangin, Simon Berger, Alica Chroňáková, Anastasis Oulas, Christina Pavloudi, Julia Schnetzer, Aaron Weimann, Ali Zeeshan Ijaz, Alexander Eiler, Christopher Quince, Evangelos Pafilis. “Seqenv: linking sequences to environments through text mining” Biodivers Data J. 2016 Nov 1;(4):e8357.

37. Sarah Faulwetter, Evangelos Pafilis, Lucia Fanini, Nicolas Bailly, Donat Agosti, Christos Arvanitidis, Laura Boicenco, Terry Capatano, Simon Claus, Stefanie Dekeyzer, Teodor Georgiev, Aglaia Legaki, Dimitra Mavraki, Anastasis Oulas, Gabriella Papastefanou, Lyubomir Penev, Guido Sautter, Dmitry Schigel, Viktor Senderov, Adrian Teaca, Marilena Tsompanou. “EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases”. Rio Journal - Research Ideas and Outcomes 2: e9774 (06 Jul 2016) doi: 10.3897/rio.2.e9774.

38. Constantinos Varsos, Theodore Patkos, Anastasis Oulas, Christina Pavloudi, Alexandros Gougousis, Umer Ijaz, Irene Filiopoulou, Nikolaos Pattakos, Edward Vanden Berghe, Antonio Fernández-Guerra,      Sarah Faulwetter, Eva Chatzinikolaou, Evangelos Pafilis, Chryssoula Bekiari, Martin Doerr, Christos Arvanitidis. “Optimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab)”. Biodiversity Data J. 2016.

39. Bobrova O, Kristoffersen JB, Oulas A, Ivanytsia V. “Metagenomic 16s rrna investigation of microbial communities in the Black Sea estuaries in South-West of Ukraine”. Acta Biochim Pol. 2016, Feb 29, DOI: 10.18388/abp.2015_1145.

40. Christina Pavloudi, Anastasis Oulas, Katerina Vasileiadou, Elena Sarropoulou, Georgios Kotoulas, Ioannis Karakassis, Christos Arvanitidis. “Salinity is the major factor influencing the sediment bacterial communities in a Mediterranean lagoonal complex (Amvrakikos Gulf, Ionian Sea)” (Marine Genomics, Jan 2016, DOI: 10.1016/j.margen.2016.01.005).

41. Anastasis Oulas, Paraskevi N. Polymenakou, Manolis Mandalakis, Paraskevi Nomikou, Steven Carey, Stephanos Kilias, Christos Christakis, Georgios Kotoulas, Antonios Magoulas,  H.James Tripp, A. David Paez Espino, Natalia N. Ivanova, Nikos C. Kyrpides. “Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology”. Environ Microbiol. 2015 Oct 21. doi: 10.1111/1462-2920.13095.

42. Anastasis Oulas, Christina Pavloudi, Paraskevi Polymenakou, Georgios A. Pavlopoulos, Nikolas Papanikolaou, Georgios Kotoulas, Christos Arvanitidis and Ioannis Iliopoulos, “Metagenomics: tools and insights for analyzing next generation sequencing data derived from biodiversity studies”, Bioinformatics and Biology Insights. 2015 May 5;9:75-88, Libertas Academia.

43. Paraskevi N. Polymenakou, Christos A. Christakis, Manolis Mandalakis, Anastasis Oulas, “Pyrosequencing analysis of microbial communities illuminates the dominance of cosmopolitan species in deep sea sediments of the Eastern Mediterranean Sea”, Res Microbiol. 2015 Apr 20. pii: S0923-2508(15)00057-1.

44. G. A. Pavlopoulos, A. Oulas, E. Iacucci, A. Sifrim, Y. Moreau, R. Schneider, J. Aerts and I. Iliopoulos. “Unraveling genomic variation from next generation sequencing data”, BioData Mining, 6:13, 2013

45. M. Velegraki, E. Papakonstanti, I. Mavroudi, M. Psyllaki, C. Tsatsanis, A. Oulas, I. Iliopoulos, P. Katonis and H. A. Papadaki “Impaired clearance of apoptotic cells leads to HMGB1 release in the bone-marrow of MDS patients and induces TLR4-mediated cytokine production”, Haematologica, 2013

46. A. Oulas, N. Karathanasis, A. Louloupi, I. Iliopoulos, K. Kalantidis and P. Poirazi. “A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2” RNA Biol. 2012 Sep 1;9(9).

47. A. Oulas, N. Karathanasis, A. Louloupi, and P. Poirazi, “Finding Cancer-Associated miRNAs: Methods and Tools” Mol Biotechnol, 2011.

48. A. Oulas, A. Boutla, K. Gkirtzou, M. Reczko, K. Kalantidis, and P. Poirazi, “Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach" Nucleic Acids Res, vol. 37, pp. 3276-87, 2009.

49. A. Oulas, M. Reczko, and P. Poirazi, "MicroRNAs and Cancer – The Search Begins!," IEEE Trans Inf Technol Biomed, vol. 13, pp. 67-77, 2008.

50. L. P. Petalidis, A. Oulas, M. Backlund, M. T. Wayland, L. Liu, K. Plant, L. Happerfield, T. C. Freeman, P. Poirazi, and V. P. Collins, “Improved grading and survival prediction of human astrocytic brain tumors by artificial neural network analysis of gene expression microarray data” Mol Cancer Ther, vol. 7, pp. 1013-24, 2008.

51. M. Reczko, P. Poirazi, A. Oulas, E. Tzamali, M. Manioudaki, V. Tsiaras and I. Tollis. ERCIM News, Special theme: “The Digital Patient” April 2007. 

BOOK CHAPTERS

1. Anastasis Oulas, Nestoras Karathanasis, Annita Louloupi, Georgios A. Pavlopoulos, Panayiota Poirazi, Kriton Kalantidis and Ioannis Iliopoulos, “Prediction of miRNA targets”, Methods in Molecular Biology, 2014.

2. A Oulas, N Karathanasis, P Poirazi - MicroRNA and Cancer, “Computational Identification of miRNAs Involved in Cancer”, Methods in Molecular Biology, 2010.

3. A Oulas, P Poirazi, “Utilization of SSCprofiler to predict a new miRNA gene”, Methods in Molecular Biology 676, 243-252, 2010.