{"id":114,"date":"2025-03-08T19:39:01","date_gmt":"2025-03-08T16:39:01","guid":{"rendered":"https:\/\/gomedprecision.gr\/?page_id=114"},"modified":"2026-05-12T10:57:32","modified_gmt":"2026-05-12T07:57:32","slug":"%ce%b5%cf%80%ce%b9%cf%83%cf%84%ce%b7%ce%bc%ce%bf%ce%bd%ce%b9%ce%ba%ce%ad%cf%82-%ce%b4%ce%b7%ce%bc%ce%bf%cf%83%ce%b9%ce%b5%cf%8d%cf%83%ce%b5%ce%b9%cf%82-%cf%83%ce%b5-%cf%80%ce%b5%cf%81%ce%b9%ce%bf","status":"publish","type":"page","link":"https:\/\/gomedprecision.gr\/en\/%ce%b5%cf%80%ce%b9%cf%83%cf%84%ce%b7%ce%bc%ce%bf%ce%bd%ce%b9%ce%ba%ce%ad%cf%82-%ce%b4%ce%b7%ce%bc%ce%bf%cf%83%ce%b9%ce%b5%cf%8d%cf%83%ce%b5%ce%b9%cf%82-%cf%83%ce%b5-%cf%80%ce%b5%cf%81%ce%b9%ce%bf\/","title":{"rendered":"Scientific publications in Journals"},"content":{"rendered":"<ul class=\"wp-block-list\">\n<li>Aplakidou, E., Vergoulidis, N., Chasapi, M., Venetsianou, N. K., Kokoli, M., Panagiotopoulou, E., . . . Georgakopoulos-Soares, I. (2024). Visualizing metagenomic and metatranscriptomic data: A comprehensive review. Computational and Structural Biotechnology Journal, 23, 2011. (doi:&nbsp;<a href=\"https:\/\/doi.org\/10.1016\/j.csbj.2024.04.060\" target=\"_blank\" rel=\"noreferrer noopener\">10.1016\/j.csbj.2024.04.060<\/a>)<\/li>\n\n\n\n<li>Arbi, M., Skamnelou, M., Koufoudaki, L., Bakali, V., Bournaka, S., Zitouni, S., . . . Tsika, A. C. (2026). McIdas localizes to centrioles and controls centriole numbers through PLK4-dependent phosphorylation. <em>EMBO reports<\/em>, 1-32. (DOI: <a href=\"https:\/\/doi.org\/10.1038\/s44319-026-00697-5\">https:\/\/doi.org\/10.1038\/s44319-026-00697-5<\/a>)<\/li>\n\n\n\n<li>Badra-Fajardo, N., Karydi, E., Bayona-Feliu, A., G\u00f3mez-Gonz\u00e1lez, B., Preza, O., Arbi, M., . . . Aguilera, A. (2026). FANCD2 restrains fork progression and prevents fragility at early origins upon re-replication. <em>Nature Communications<\/em>.(DOI: <a href=\"https:\/\/doi.org\/10.5281\/zenodo.18000043\">https:\/\/doi.org\/10.5281\/zenodo.18000043<\/a>)<\/li>\n\n\n\n<li>Baltoumas, F. A., Karatzas, E., Venetsianou, N. K., Aplakidou, E., Giatras, K., Chasapi, M. N., . . . Trougakos, I. P. (2025). Darling (v2. 0): Mining disease-related databases for the detection of biomedical entity associations. Computational and Structural Biotechnology Journal. (DOI: <a href=\"https:\/\/doi.org\/10.1016\/j.csbj.2025.06.025\" target=\"_blank\" rel=\"noreferrer noopener\">10.1016\/j.csbj.2025.06.025<\/a>)<\/li>\n\n\n\n<li>Bampos, C., Megalooikonomou, V. (2025). Network motif detection using hidden markov models. Scientific Reports, 15(1), 41954. (DOI: <a href=\"https:\/\/doi.org\/10.1038\/s41598-025-25936-y\"> https:\/\/doi.org\/10.1038\/s41598-025-25936-y<\/a>)<\/li>\n\n\n\n<li>Bampos, C., Megalooikonomou, V. (in press). Integer Linear Programming for Contrasting State Interventions in Boolean Networks. PeerJ. Accepted for publication.<\/li>\n\n\n\n<li>Bampos, C., Megalooikonomou, V. (under review). Structure-Informed Machine Learning and Deep Learning for High-Confidence BRCA1\/2 Missense Variant Classification. Bioinformatics.<\/li>\n\n\n\n<li>Bampos, C., Megalooikonomou, V. (under review). Exploration of Schizophrenia-Associated Gene Modules Using Graph Theory, Co-Expression Networks, and Dimensionality Reduction. Plos One.<\/li>\n\n\n\n<li>Chantzi, N., Nayak, A., Baltoumas, F. A., Aplakidou, E., Liew, S. W., Galuh, J. E., . . . Sazed, S. A. (2024). Quadrupia: Derivation of G-quadruplexes for organismal genomes across the tree of life. bioRxiv, 2024.2007. 2009.602008. (DOI: <a href=\"https:\/\/doi.org\/10.1101\/2024.07.09.602008\" target=\"_blank\" rel=\"noreferrer noopener\">10.1101\/2024.07.09.602008<\/a> )<\/li>\n\n\n\n<li>Chantzi, N., Nayak, A., Baltoumas, F. A., Aplakidou, E., Liew, S. W., Galuh, J. E., . . . Mouratidis, I. (2025). Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life. Genome research, gr. 279790.279124. (DOI: <a href=\"https:\/\/doi.org\/10.1101\/gr.279790.124\" target=\"_blank\" rel=\"noreferrer noopener\">10.1101\/gr.279790.124<\/a>)<\/li>\n\n\n\n<li>Chasapi, M. N., Chasapi, I. N., Aplakidou, E., Baltoumas, F. A., Karatzas, E., Iliopoulos, I., . . . Pavlopoulos, G. A. (2025). metagRoot: a comprehensive database of protein families associated with plant root microbiomes. Nucleic Acids Research. Advance online publication (gkaf862). (DOI: <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkaf862\" target=\"_blank\" rel=\"noreferrer noopener\">10.1093\/nar\/gkaf862<\/a>)<\/li>\n\n\n\n<li>Giannoukakos, S., Miliotis, M., Zacharopoulou, E., &amp; Hatzigeorgiou, A. (2025). Tissue-Specific MicroRNA Function: Integrating Target Prediction with Expression Data. Physiology, 40(S1), 1642.(DOI: <a href=\"https:\/\/doi.org\/10.1152\/physiol.2025.40.S1.1642\">https:\/\/doi.org\/10.1152\/physiol.2025.40.S1.1642<\/a>)<\/li>\n\n\n\n<li>Grigoriadis, D., Tsifintaris, M., Giannakakis, A., Pavlopoulos, G. A., &amp; Perdikopanis, N. (2025). Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications. Computational and Structural Biotechnology Journal. (DOI: <a href=\"https:\/\/doi.org\/10.1016\/j.csbj.2025.11.004\" target=\"_blank\" rel=\"noreferrer noopener\">10.1016\/j.csbj.2025.11.004<\/a>)<\/li>\n\n\n\n<li>Karatzas, E., Beracochea, M., Baltoumas, F. A., Aplakidou, E., Richardson, L., Fellows Yates, J. A., . . . Kyrpides, N. C. (2025). nf-core\/proteinfamilies: A scalable pipeline for the generation of protein families. bioRxiv, 2025.2008. 2012.670010. (DOI: <a href=\"https:\/\/doi.org\/10.1101\/2025.08.12.670010\" target=\"_blank\" rel=\"noreferrer noopener\">10.1101\/2025.08.12.670010<\/a>)<\/li>\n\n\n\n<li>Kontou, P. I., &amp; Bagos, P. G. (2024). The goldmine of GWAS summary statistics: a systematic review of methods and tools. BioData Mining, 17(1), 31. (DOI: <a href=\"https:\/\/doi.org\/10.1186\/s13040-024-00385-x\">https:\/\/doi.org\/10.1186\/s13040-024-00385-x<\/a>)<\/li>\n\n\n\n<li>Kosicki, M., Baltoumas, F. A., Kelman, G., Boverhof, J., Ong, Y., Cook, L. E., . . . Visel, A. (2025). VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers. Nucleic Acids Research, 53(D1), D324-D330. (DOI : <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkae940\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1093\/nar\/gkae940<\/a>)<\/li>\n\n\n\n<li>Manios, G. A., Michailidi, A., Kontou, P. I., &amp; Bagos, P. G. (2025). PRED-LD: efficient imputation of GWAS summary statistics. BMC bioinformatics, 26(1), 107. (DOI: <a href=\"https:\/\/doi.org\/10.1186\/s12859-025-06119-y\">https:\/\/doi.org\/10.1186\/s12859-025-06119-y<\/a>)<\/li>\n\n\n\n<li>Manios, G. A., Kandylas, D., Kylonis, A., Bagos, P. G., &amp; Kontou, P. I. (2025). fastMETA: a fast and efficient tool for multivariate meta-analysis of GWAS. <em>Frontiers in Genetics, 16<\/em>, 1718626. (DOI: <a href=\"https:\/\/doi.org\/10.3389\/fgene.2025.1718626\">https:\/\/doi.org\/10.3389\/fgene.2025.1718626<\/a>)<\/li>\n\n\n\n<li>Mouratidis, I., Baltoumas, F. A., Chantzi, N., Patsakis, M., Chan, C. S., Montgomery, A., . . . Das, A. (2024). kmerDB: a database encompassing the set of genomic and proteomic sequence information for each species. Computational and Structural Biotechnology Journal, 23, 1919-1928. (DOI: <a href=\"https:\/\/doi.org\/10.1016\/j.csbj.2024.04.050\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1016\/j.csbj.2024.04.050<\/a>)<\/li>\n\n\n\n<li>Mouratidis, I., Konnaris, M. A., Chantzi, N., Chan, C. S., Patsakis, M., Provatas, K., . . . Mareboina, M. (2025). Identification of the shortest species-specific oligonucleotide sequences. Genome research, 35(2), 279-295. (DOI: <a href=\"https:\/\/doi.org\/10.1101\/gr.280070.124\" target=\"_blank\" rel=\"noreferrer noopener\">10.1101\/gr.280070.124<\/a>) <\/li>\n\n\n\n<li>Nikolitsa, E. K., Kontou, P. I., &amp; Bagos, P. G. (2025). metacp: a versatile software package for combining dependent or independent p-values. BMC bioinformatics, 26(1), 109. (DOI: <a href=\"https:\/\/doi.org\/10.1186\/s12859-025-06126-z\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1186\/s12859-025-06126-z<\/a>)<\/li>\n\n\n\n<li>Patsakis, M., Provatas, K., Baltoumas, F. A., Chantzi, N., Mouratidis, I., Pavlopoulos, G. A., &amp; Georgakopoulos-Soares, I. (2025). MAFin: motif detection in multiple alignment files. Bioinformatics, 41(4), btaf125. (DOI: <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf125\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1093\/bioinformatics\/btaf125<\/a>)<\/li>\n\n\n\n<li>Perdikopanis, N., Giannakakis, A., Kavakiotis, I., &amp; Hatzigeorgiou, A. G. (2024). D-sORF: Accurate Ab Initio Classification of Experimentally Detected Small Open Reading Frames (sORFs) Associated with Translational Machinery. Biology, 13(8), 563. (DOI: <a href=\"https:\/\/doi.org\/10.3390\/biology13080563\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.3390\/biology13080563<\/a>)<\/li>\n\n\n\n<li>Provatas, K., Chan, C. S., Kerasiotis, I., Bochalis, E., Nayak, A., Zacharia, B. E., . . . Georgakopoulos-Soares, I. (2026). neomerDB: a comprehensive database of neomer biomarkers in cancer. Database, 2026, baag006. (DOI: <a href=\"https:\/\/doi.org\/10.1093\/database\/baag006\">https:\/\/doi.org\/10.1093\/database\/baag006<\/a>)<\/li>\n\n\n\n<li>Provatas, K., Chantzi, N., Amptazi, N., Patsakis, M., Nayak, A., Mouratidis, I., . . . Georgakopoulos-Soares, I. (2025). invertiaDB: a database of inverted repeats across organismal genomes. Nucleic Acids Research, 53(8), gkaf329. (DOI: <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkaf329\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1093\/nar\/gkaf329<\/a>)<\/li>\n\n\n\n<li>Spiliopoulos, K. C., Veltsista, D., Veltsou, E., Tzimogianni, V., Seo, G. H., Kim, J., . . . Chroni, E. (2025). Hereditary, non HINT1 related, axonal neuropathy with neuromyotonia. Neurological Sciences, 1-4. (DOI : <a href=\"https:\/\/doi.org\/10.1007\/s10072-025-08022-z\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1007\/s10072-025-08022-z<\/a>)<\/li>\n\n\n\n<li>Theocharopoulos, P. C., Anagnostou, P., Georgakopoulos, S. V., Tasoulis, S. K., &amp; Plagianakos, V. P. (2025). Large language models for efficient topic modeling. Neural Computing and Applications, 1-19. (DOI: <a href=\"https:\/\/doi.org\/10.1007\/s00521-025-11593-9\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1007\/s00521-025-11593-9<\/a>)<\/li>\n\n\n\n<li>Theodosiou, T., Vrettos, K., Baltsavia, I., Baltoumas, F., Papanikolaou, N., Antonakis, A. \u039d., . . . Karaglani, M. (2024). BioTextQuest v2. 0: An evolved tool for biomedical literature mining and concept discovery. Computational and Structural Biotechnology Journal, 23, 3247-3253. (DOI: <a href=\"https:\/\/doi.org\/10.1016\/j.csbj.2024.08.016\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/doi.org\/10.1016\/j.csbj.2024.08.016<\/a>)<\/li>\n\n\n\n<li>Tsifintaris, M., Grigoriadis, D., Sitmalidis, M., Repanas, P., Lazarashvili, E. K., Anastasiadi, C., . . . Giannakakis, A. (2025). ASTRA: a comprehensive resource of stress-induced transcriptional activity in human cell lines. Nucleic Acids Research, gkaf1174. (DOI: <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkaf1174\" target=\"_blank\" rel=\"noreferrer noopener\">10.1093\/nar\/gkaf1174<\/a>)<\/li>\n\n\n\n<li>Vogiatzoglou, A. V., Kontou, P. I., Bagos, P. G., &amp; Braliou, G. G. (2024). Genetic association of SLC6A3 (dopamine transporter) gene polymorphisms with personality disorders and substance abuse disorders: a systematic review and meta-analysis. Psychiatric genetics, 34(5), 93-105. (DOI: <a href=\"https:\/\/doi.org\/10.1097\/YPG.0000000000000375\" target=\"_blank\" rel=\"noreferrer noopener\">10.1097\/YPG.0000000000000375<\/a>)<\/li>\n\n\n\n<li>Zacharopoulou, E., Paraskevopoulou, M. D., Tastsoglou, S., Alexiou, A., Karavangeli, A., Pierros, V., . . . Karagkouni, D. (2025). microT-CNN: an avant-garde deep convolutional neural network unravels functional miRNA targets beyond canonical sites. Briefings in Bioinformatics, 26(1), bbae678. (DOI: <a href=\"https:\/\/doi.org\/10.1093\/bib\/bbae678\">https:\/\/doi.org\/10.1093\/bib\/bbae678<\/a>)<\/li>\n\n\n\n<li>Zhao, J., Baltoumas, F. A., Konnaris, M. A., Mouratidis, I., Liu, Z., Sims, J., . . . Ahituv, N. (2025). MPRAbase a Massively Parallel Reporter Assay database. Genome research, gr. 280387.280124. (DOI: <a href=\"https:\/\/doi.org\/10.1101\/gr.280387.124\" target=\"_blank\" rel=\"noreferrer noopener\">10.1101\/gr.280387.124<\/a>)<\/li>\n<\/ul>","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"pgc_sgb_lightbox_settings":"","footnotes":""},"class_list":["post-114","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/gomedprecision.gr\/en\/wp-json\/wp\/v2\/pages\/114","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/gomedprecision.gr\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/gomedprecision.gr\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/gomedprecision.gr\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/gomedprecision.gr\/en\/wp-json\/wp\/v2\/comments?post=114"}],"version-history":[{"count":30,"href":"https:\/\/gomedprecision.gr\/en\/wp-json\/wp\/v2\/pages\/114\/revisions"}],"predecessor-version":[{"id":208,"href":"https:\/\/gomedprecision.gr\/en\/wp-json\/wp\/v2\/pages\/114\/revisions\/208"}],"wp:attachment":[{"href":"https:\/\/gomedprecision.gr\/en\/wp-json\/wp\/v2\/media?parent=114"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}