Publications

Preprints

  1. Kapopoulou, A, Kapun, M, Pavlidis, P, Pieper, B, & … 2018, ‘Early split between African and European populations of Drosophila melanogaster’, bioRxiv    
  2. Kioukis, A, & Pavlidis, P 2018, ‘Evolution of gene regulatory networks by means of selection and random genetic drift’, bioRxiv
  3. Primetis, E, Chavlis, S, & Pavlidis, P 2018, ‘Evolutionary Models of Amino Acid Substitutions Based on the Tertiary Structure of their Neighborhoods’, bioRxiv
  4. Antonis Kioukis, Vassiliki A. Michalopoulou, Laura Briers, Stergios Pirintsos, David J. Studholme, Pavlos Pavlidis, Panagiotis F. Sarris 2019 Draft Genome Sequence and intraspecific diversification of the wild crop relative Brassica cretica Lam. using demographic model selection bioRxiv

Peer Reviewed Publications

  1. 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).
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  2. Pajic, P. et al. Independent amylase gene copy number bursts correlate with dietary preferences in mammals. Elife 1–22 (2019).
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  3. 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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  4. 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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  5. Xu, D. et al. Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation. Mol. Biol. Evol. 34, 2704–2715 (2017).
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  6. 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
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  7. 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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  8. 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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  9. Papadantonakis, S., Poirazi, P. & Pavlidis, P. CoMuS: simulating coalescent histories and polymorphic data from multiple species. Mol. Ecol. Resour. 16, 1435–1448 (2016).
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  10. Xu, D. et al. Recent evolution of the salivary mucin MUC7. Sci. Rep. 6, 31791 (2016).
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  11. Alachiotis, N. & Pavlidis, P. Scalable linkage-disequilibrium-based selective sweep detection: A performance guide. Gigascience 5, (2016).
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  12. 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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  13. 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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  14. 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).
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  15. Zhang, J., Kapli, P., Pavlidis, P. & Stamatakis, A. A General Species Delimitation Method with Applications to Phylogenetic Placements. Bioinformatics 29, 2869–2876 (2013).
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  16. 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).
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  17. 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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  18. Gokcumen, O. et al. Primate genome architecture in fl uences structural variation mechanisms and functional consequences. Proc. Natl. Acad. Sci. 10, 15764–15769 (2013).
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  19. 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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  20. 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).
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  21. 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).
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  22. 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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  23. 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).
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  24. Pavlidis, P., Metzler, D. & Stephan, W. Selective sweeps in multilocus models of quantitative traits. Genetics 192, 225–39 (2012).
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  25. 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).
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  26. 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).
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  27. 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).
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  28. 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).
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  29. Tsuchimatsu, T. et al. Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene. Nature 464, 1342–6 (2010).
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  30. 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).
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  31. 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).
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  32. 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).
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  33. 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).
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  34. 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).
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  35. Pavlidis, P., Hutter, S. & Stephan, W. A population genomic approach to map recent positive selection in model species. Mol. Ecol. 17, 3585–98 (2008).
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  36. Pavlidis, P. & Poirazi, P. Individualized markers optimize class prediction of microarray data. BMC Bioinformatics 7, 345 (2006).
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