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), 1796–1804. PDF
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, 1–10. https://doi.org/10.1016/j.jcyt.2021.07.010 PDF
Theodoris, C., Low, T. M., Pavlidis, P., & Alachiotis, N. (2021). quickLD: An efficient software for linkage disequilibrium analyses. Molecular Ecology Resources, 21(7), 2580–2587. https://doi.org/10.1111/1755-0998.13438 PDF
Vasilarou, M., Alachiotis, N., Garefalaki, J., Beloukas, A., & Pavlidis, P. (2021). Population genomics insights into the first wave of covid-19. Life, 11(2), 1–19. https://doi.org/10.3390/life11020129 PDF
Morel, B., Barbera, P., Czech, L., Bettisworth, B., Hübner, 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), 1777–1791. https://doi.org/10.1093/molbev/msaa314 PDF
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), 1–17. https://doi.org/10.1371/journal.pone.0238665 PDF
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, 1–12. https://doi.org/10.1002/prot.26178 PDF
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), 1328–1332. https://doi.org/10.23919/Eusipco47968.2020.9287619 PDF
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), 242–253. PDF
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, 65–72. https://doi.org/10.1109/BIBE50027.2020.00019 PDF
Pavlidis, P., & Somel, M. (2020). Of dogs and men. Science, 370(6516), 522–523. https://doi.org/10.1126/science.abe7823 PDF
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), 1–14. https://doi.org/10.1186/s12864-019-6439-x PDF
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), 1597–1609. https://doi.org/10.1111/1755-0998.13221 PDF
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), 1328–1332. PDF
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), 1–8. https://doi.org/10.1038/s41598-020-79720-1 PDF
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), 497–509. https://doi.org/10.1534/genetics.120.303167 PDF
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), 1–10. PDF
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, 1145–1158 (2019). PDF
Pajic, P. et al. Independent amylase gene copy number bursts correlate with dietary preferences in mammals. Elife 1–22 (2019). PDF
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 PDF
Pavlidis, P. & Alachiotis, N. A survey of methods and tools to detect recent and strong positive selection. J. Biol. Res. 24, 7 (2017). PDF
Xu, D. et al. Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation. Mol. Biol. Evol. 34, 2704–2715 (2017). PDF
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) 1–8 (IEEE, 2017). doi:10.23919/FPL.2017.8056814 PDF
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). PDF
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). PDF
Papadantonakis, S., Poirazi, P. & Pavlidis, P. CoMuS: simulating coalescent histories and polymorphic data from multiple species. Mol. Ecol. Resour. 16, 1435–1448 (2016). PDF
Xu, D. et al. Recent evolution of the salivary mucin MUC7. Sci. Rep. 6, 31791 (2016). PDF
Alachiotis, N. & Pavlidis, P. Scalable linkage-disequilibrium-based selective sweep detection: A performance guide. Gigascience 5, (2016). PDF
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). PDF
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). PDF
Eaaswarkhanth, M., Pavlidis, P. & Gokcumen, O. Geographic Distribution and Adaptive Significance of Genomic Structural Variants : An Anthropological Genetics Perspective. Hum. Biol. 86, 260–275 (2014). PDF
Zhang, J., Kapli, P., Pavlidis, P. & Stamatakis, A. A General Species Delimitation Method with Applications to Phylogenetic Placements. Bioinformatics 29, 2869–2876 (2013). PDF
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, 1–16 (2013). PDF
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 PDF
Gokcumen, O. et al. Primate genome architecture in fl uences structural variation mechanisms and functional consequences. Proc. Natl. Acad. Sci. 10, 15764–15769 (2013). PDF
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). PDF
Pavlidis P., Zivkovic D, Stamatakis A. & Alachiotis N. SweeD : Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes. Mol. Biol. Evol. 30, 2224–2234 (2013). PDF
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, 3237–48 (2012). PDF
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). PDF
Alachiotis, N., Stamatakis, A. & Pavlidis, P. OmegaPlus: A Scalable Tool for Rapid Detection of Selective Sweeps in Whole-Genome Datasets. Bioinformatics 28, 2274–2275 (2012). PDF
Pavlidis, P., Metzler, D. & Stephan, W. Selective sweeps in multilocus models of quantitative traits. Genetics 192, 225–39 (2012). PDF
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, 475–88 (2012). PDF
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, 530–44 (2011). PDF
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, 17052–7 (2011). PDF
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, 1167–74 (2011). PDF
Tsuchimatsu, T. et al. Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene. Nature 464, 1342–6 (2010). PDF
Pavlidis, P., Laurent, S. & Stephan, W. msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis. Mol. Ecol. Resour. 10, 723–7 (2010). PDF
Pavlidis, P., Jensen, J. D. & Stephan, W. Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics 185, 907–22 (2010). PDF
Aid-Pavlidis, T., Pavlidis, P. & Timmusk, T. Meta-coexpression conservation analysis of microarray data: a ‘subset’ approach provides insight into brain-derived neurotrophic factor regulation. BMC Genomics 10, 420 (2009). PDF
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, 1549–56 (2009). PDF
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, 567–78 (2009). PDF
Pavlidis, P., Hutter, S. & Stephan, W. A population genomic approach to map recent positive selection in model species. Mol. Ecol. 17, 3585–98 (2008). PDF
Pavlidis, P. & Poirazi, P. Individualized markers optimize class prediction of microarray data. BMC Bioinformatics 7, 345 (2006). PDF
