{"id":736,"date":"2019-07-26T10:21:15","date_gmt":"2019-07-26T10:21:15","guid":{"rendered":"http:\/\/pop-gen.eu\/wordpress\/?page_id=736"},"modified":"2024-07-01T20:06:38","modified_gmt":"2024-07-01T20:06:38","slug":"publications","status":"publish","type":"page","link":"https:\/\/pop-gen.eu\/wordpress\/publications","title":{"rendered":"Publications"},"content":{"rendered":"\n

Preprints<\/h2>\n\n\n\n
  1. Kioukis, A, & Pavlidis, P 2018, ‘Evolution of gene regulatory networks by means of selection and random genetic drift’, bioRxiv<\/a><\/em>
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  2. Chatzinikolaou, G., Stratigi, K., Agathangelou, K., Tsekrekou, M., Goulielmaki, E., Chatzidoukaki, O., Gkirtzimanaki, K., Aid-Pavlidis, T., Aivaliotis, M., Pavlidis, P., & others. (2020). ERCC1-XPF Interacts with Topoisomerase II$\u03b2$ to Facilitate the Repair of Activity-induced DNA Breaks. BioRxiv.
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    Peer Reviewed Publications<\/h2>\n\n\n\n
    1. Zervou, M. A., Doutsi, E., Pavlidis, P., & Tsakalides, P. (2021). Structural classification of proteins based on the computationally efficient recurrence quantification analysis and horizontal visibility graphs. Bioinformatics, 37(13), 1796\u20131804.
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    2. Latsoudis, H., Stylianakis, E., Mavroudi, I., Kanterakis, A., Pavlidis, P., Georgopoulou, A., Batsali, A., Gontika, I., Fragiadaki, I., Zamanakou, M., Germenis, A. E., & Papadaki, H. A. (2021). Significance of regional population HLA immunogenetic datasets in the efficacy of umbilical cord blood banks and marrow donor registries: a study of Cretan HLA genetic diversity. Cytotherapy, 000, 1\u201310. https:\/\/doi.org\/10.1016\/j.jcyt.2021.07.010
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    3. Theodoris, C., Low, T. M., Pavlidis, P., & Alachiotis, N. (2021). quickLD: An efficient software for linkage disequilibrium analyses. Molecular Ecology Resources, 21(7), 2580\u20132587. https:\/\/doi.org\/10.1111\/1755-0998.13438
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    4. Vasilarou, M., Alachiotis, N., Garefalaki, J., Beloukas, A., & Pavlidis, P. (2021). Population genomics insights into the first wave of covid-19. Life, 11(2), 1\u201319. https:\/\/doi.org\/10.3390\/life11020129
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    5. Morel, B., Barbera, P., Czech, L., Bettisworth, B., H\u00fcbner, L., Lutteropp, S., Serdari, D., Kostaki, E. G., Mamais, I., Kozlov, A. M., Pavlidis, P., Paraskevis, D., & Stamatakis, A. (2021). Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult. Molecular Biology and Evolution, 38(5), 1777\u20131791. https:\/\/doi.org\/10.1093\/molbev\/msaa314
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    6. Oulas, A., Zanti, M., Tomazou, M., Zachariou, M., Minadakis, G., Bourdakou, M. M., Pavlidis, P., & Spyrou, G. M. (2021). Generalized linear models provide a measure of virulence for specific mutations in SARS-cov-2 strains. PLoS ONE, 16(1 1), 1\u201317. https:\/\/doi.org\/10.1371\/journal.pone.0238665
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    7. Primetis, E., Chavlis, S., & Pavlidis, P. (2021). Evolutionary models of amino acid substitutions based on the tertiary structure of their neighborhoods. Proteins: Structure, Function and Bioinformatics, September 2020, 1\u201312. https:\/\/doi.org\/10.1002\/prot.26178
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    8. Zervou, M. A., Doutsi, E., Pavlidis, P., & Tsakalides, P. (2021). Efficient dynamic analysis of low-similarity proteins for structural class prediction. European Signal Processing Conference, 2021-Janua(ii), 1328\u20131332. https:\/\/doi.org\/10.23919\/Eusipco47968.2020.9287619
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    9. Grigoriou, M., Banos, A., Filia, A., Pavlidis, P., Giannouli, S., Karali, V., Nikolopoulos, D., Pieta, A., Bertsias, G., Verginis, P., & others. (2020). Transcriptome reprogramming and myeloid skewing in haematopoietic stem and progenitor cells in systemic lupus erythematosus. Annals of the Rheumatic Diseases, 79(2), 242\u2013253.
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    10. Theodoris, C., Alachiotis, N., Low, T. M., & Pavlidis, P. (2020). QLD: High-performance Computation of Linkage Disequilibrium on CPU and GPU. Proceedings – IEEE 20th International Conference on Bioinformatics and Bioengineering, BIBE 2020, 65\u201372. https:\/\/doi.org\/10.1109\/BIBE50027.2020.00019
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    11. Pavlidis, P., & Somel, M. (2020). Of dogs and men. Science, 370(6516), 522\u2013523. https:\/\/doi.org\/10.1126\/science.abe7823
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    12. Kioukis, A., Michalopoulou, V. A., Briers, L., Pirintsos, S., Studholme, D. J., Pavlidis, P., & Sarris, P. F. (2020). Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection. BMC Genomics, 21(1), 1\u201314. https:\/\/doi.org\/10.1186\/s12864-019-6439-x
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    13. Pfeifer, B., Alachiotis, N., Pavlidis, P., & Schimek, M. G. (2020). Genome scans for selection and introgression based on k-nearest neighbour techniques. Molecular Ecology Resources, 20(6), 1597\u20131609. https:\/\/doi.org\/10.1111\/1755-0998.13221
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    14. Zervou, M. A., Doutsi, E., Pavlidis, P., & Tsakalides, P. (2020). Efficient Dynamic Analysis of Low-similarity Proteins for Structural Class Prediction. 2020 28th European Signal Processing Conference (EUSIPCO), 1328\u20131332.
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    15. Kapopoulou, A., Kapun, M., Pieper, B., Pavlidis, P., Wilches, R., Duchen, P., Stephan, W., & Laurent, S. (2020). Demographic analyses of a new sample of haploid genomes from a Swedish population of Drosophila melanogaster. Scientific Reports, 10(1), 1\u20138. https:\/\/doi.org\/10.1038\/s41598-020-79720-1
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    16. Taskent, O., Lin, Y. L., Patramanis, I., Pavlidis, P., & Gokcumen, O. (2020). Analysis of haplotypic variation and deletion polymorphisms point to multiple archaic introgression events, including from altai neanderthal lineage. Genetics, 215(2), 497\u2013509. https:\/\/doi.org\/10.1534\/genetics.120.303167
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    17. Natsidis, P., Tsakogiannis, A., Pavlidis, P., Tsigenopoulos, C. S., & Manousaki, T. (2019). Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling. Communications Biology, 2(1), 1\u201310.
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    18. Noelle, M. et al. Comparisons of molecular diversity indices , selective sweeps and population structure of African rice with its wild progenitor and Asian rice. Theor. Appl. Genet. 132, 1145\u20131158 (2019).
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    19. Pajic, P. et al. Independent amylase gene copy number bursts correlate with dietary preferences in mammals. Elife 1\u201322 (2019).
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    20. Alachiotis, N. & Pavlidis, P. RAiSD detects positive selection based on multiple signatures of a selective sweep and SNP vectors. Commun. Biol. (2018). doi:10.1038\/s42003-018-0085-8
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    21. Pavlidis, P. & Alachiotis, N. A survey of methods and tools to detect recent and strong positive selection. J. Biol. Res. 24, 7 (2017).
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    22. Xu, D. et al. Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation. Mol. Biol. Evol. 34, 2704\u20132715 (2017).
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    23. Bozikas, D., Alachiotis, N., Pavlidis, P., Sotiriades, E. & Dollas, A. Deploying FPGAs to future-proof genome-wide analyses based on linkage disequilibrium. in 2017 27th International Conference on Field Programmable Logic and Applications (FPL) 1\u20138 (IEEE, 2017). doi:10.23919\/FPL.2017.8056814
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    24. Kapli, P. et al. Multi-rate Poisson Tree Processes for single-locus species delimitation under Maximum Likelihood and Markov Chain Monte Carlo. Bioinformatics 33, btx025 (2017).
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    25. Xu, D., Jaber, Y., Pavlidis, P. & Gokcumen, O. VCFtoTree: A user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. BMC Bioinformatics 18, (2017).
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    26. Papadantonakis, S., Poirazi, P. & Pavlidis, P. CoMuS: simulating coalescent histories and polymorphic data from multiple species. Mol. Ecol. Resour. 16, 1435\u20131448 (2016).
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    27. Xu, D. et al. Recent evolution of the salivary mucin MUC7. Sci. Rep. 6, 31791 (2016).
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    28. Alachiotis, N. & Pavlidis, P. Scalable linkage-disequilibrium-based selective sweep detection: A performance guide. Gigascience 5, (2016).
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    29. Lin, Y.-L., Pavlidis, P., Karakoc, E., Ajay, J. & Gokcumen, O. The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Mol. Biol. Evol. 32, (2015).
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    30. Pybus, M. et al. 1000 Genomes Selection Browser 1.0: A genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Res. 42, (2014).
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    31. Eaaswarkhanth, M., Pavlidis, P. & Gokcumen, O. Geographic Distribution and Adaptive Significance of Genomic Structural Variants : An Anthropological Genetics Perspective. Hum. Biol. 86, 260\u2013275 (2014).
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    32. Zhang, J., Kapli, P., Pavlidis, P. & Stamatakis, A. A General Species Delimitation Method with Applications to Phylogenetic Placements. Bioinformatics 29, 2869\u20132876 (2013).
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    33. Alachiotis, N., Vogiatzi, E., Pavlidis, P. & Stamatakis, A. ChromatoGate : A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection. Comput. Struct. Biotechnol. J. 6, 1\u201316 (2013).
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    34. Pissis, S. P., Stamatakis, A. & Pavlidis, P. MoTeX: A word-based HPC tool for MoTif extraction. in 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 (2013). doi:10.1145\/2506583.2506587
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    35. Gokcumen, O. et al. Primate genome architecture in fl uences structural variation mechanisms and functional consequences. Proc. Natl. Acad. Sci. 10, 15764\u201315769 (2013).
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    36. Werzner, A., Pavlidis, P., Ometto, L., Stephan, W. & Laurent, S. Selective Sweep in the Flotillin-2 Region of European Drosophila melanogaster. PLoS One 8, (2013).
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    37. Pavlidis P., Zivkovic D, Stamatakis A. & Alachiotis N. SweeD : Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes. Mol. Biol. Evol. 30, 2224\u20132234 (2013).
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    38. Pavlidis, P., Jensen, J. D., Stephan, W. & Stamatakis, A. A critical assessment of storytelling: gene ontology categories and the importance of validating genomic scans. Mol. Biol. Evol. 29, 3237\u201348 (2012).
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    39. Alachiotis, N., Pavlidis, P. & Stamatakis, A. Exploiting multi-grain parallelism for efficient selective sweep detection. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 7439 LNCS, (2012).
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    40. Alachiotis, N., Stamatakis, A. & Pavlidis, P. OmegaPlus: A Scalable Tool for Rapid Detection of Selective Sweeps in Whole-Genome Datasets. Bioinformatics 28, 2274\u20132275 (2012).
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    41. Pavlidis, P., Metzler, D. & Stephan, W. Selective sweeps in multilocus models of quantitative traits. Genetics 192, 225\u201339 (2012).
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    42. Bousios, A. et al. The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story. Plant J. 69, 475\u201388 (2012).
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    43. Svetec, N. et al. Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine mapping by selective sweep analysis. Mol. Ecol. 20, 530\u201344 (2011).
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    44. Tellier, A., Laurent, S. J. Y., Lainer, H., Pavlidis, P. & Stephan, W. Inference of seed bank parameters in two wild tomato species using ecological and genetic data. Proc. Natl. Acad. Sci. U. S. A. 108, 17052\u20137 (2011).
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    45. Saminadin-Peter, S. S., Kemkemer, C., Pavlidis, P. & Parsch, J. Selective Sweep of a cis-Regulatory Sequence in a Non-African Population of Drosophila melanogaster. Mol. Biol. Evol. 29, 1167\u201374 (2011).
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    46. Tsuchimatsu, T. et al. Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene. Nature 464, 1342\u20136 (2010).
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    47. Pavlidis, P., Laurent, S. & Stephan, W. msABC: a modification of Hudson\u2019s ms to facilitate multi-locus ABC analysis. Mol. Ecol. Resour. 10, 723\u20137 (2010).
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    48. Pavlidis, P., Jensen, J. D. & Stephan, W. Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics 185, 907\u201322 (2010).
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    49. Aid-Pavlidis, T., Pavlidis, P. & Timmusk, T. Meta-coexpression conservation analysis of microarray data: a \u2018subset\u2019 approach provides insight into brain-derived neurotrophic factor regulation. BMC Genomics 10, 420 (2009).
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    50. Svetec, N., Pavlidis, P. & Stephan, W. Recent strong positive selection on Drosophila melanogaster HDAC6, a gene encoding a stress surveillance factor, as revealed by population genomic analysis. Mol. Biol. Evol. 26, 1549\u201356 (2009).
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    51. Johnsen, J. M. et al. Selection on cis-regulatory variation at B4galnt2 and its influence on von Willebrand factor in house mice. Mol. Biol. Evol. 26, 567\u201378 (2009).
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    52. Pavlidis, P., Hutter, S. & Stephan, W. A population genomic approach to map recent positive selection in model species. Mol. Ecol. 17, 3585\u201398 (2008).
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    53. Pavlidis, P. & Poirazi, P. Individualized markers optimize class prediction of microarray data. BMC Bioinformatics 7, 345 (2006).
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      Preprints Kioukis, A, & Pavlidis, P 2018, ‘Evolution of gene regulatory networks by means of selection and random genetic drift’, bioRxiv Chatzinikolaou, G., Stratigi, K., Agathangelou, K., Tsekrekou, M., Goulielmaki, E., Chatzidoukaki, O., Gkirtzimanaki, K., Aid-Pavlidis, T., Aivaliotis, M., Pavlidis, P., & others. (2020). ERCC1-XPF Interacts with Topoisomerase II$\u03b2$ to Facilitate the Repair of Activity-induced … <\/p>\n

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