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Pavlos Pavlidis - Publications

Affiliations: 
IMBB, FORTH 
Area:
Population Genetics
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41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2025 Bettisworth B, Psonis N, Poulakakis N, Pavlidis P, Stamatakis A. Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads. Molecular Biology and Evolution. PMID 39823473 DOI: 10.1093/molbev/msaf006  0.57
2024 Charamis J, Balaska S, Ioannidis P, Dvořák V, Mavridis K, Ann McDowell M, Pavlidis P, Feyereisen R, Volf P, Vontas J. Comparative genomics uncovers the evolutionary dynamics of detoxification and insecticide target genes across 11 phlebotomine sand flies. Genome Biology and Evolution. PMID 39224065 DOI: 10.1093/gbe/evae186  0.315
2024 Papadadonakis S, Kioukis A, Karageorgiou C, Pavlidis P. Evolution of gene regulatory networks by means of selection and random genetic drift. Peerj. 12: e17918. PMID 39221262 DOI: 10.7717/peerj.17918  0.75
2023 Baumgarten L, Pieper B, Song B, Mane S, Lempe J, Lamb J, Cooke EL, Srivastava R, Strütt S, Žanko D, Casimiro PG, Hallab A, Cartolano M, Tattersall AD, Huettel B, ... ... Pavlidis P, et al. Pan-European study of genotypes and phenotypes in the Arabidopsis relative Cardamine hirsuta reveals how adaptation, demography, and development shape diversity patterns. Plos Biology. 21: e3002191. PMID 37463141 DOI: 10.1371/journal.pbio.3002191  0.71
2023 Zhao H, Souilljee M, Pavlidis P, Alachiotis N. Genome-wide scans for selective sweeps using convolutional neural networks. Bioinformatics (Oxford, England). 39: i194-i203. PMID 37387128 DOI: 10.1093/bioinformatics/btad265  0.32
2023 Aqil A, Speidel L, Pavlidis P, Gokcumen O. Balancing selection on genomic deletion polymorphisms in humans. Elife. 12. PMID 36625544 DOI: 10.7554/eLife.79111  0.375
2022 Koptekin D, Yüncü E, Rodríguez-Varela R, Altınışık NE, Psonis N, Kashuba N, Yorulmaz S, George R, Kazancı DD, Kaptan D, Gürün K, Vural KB, Gemici HC, Vassou D, Daskalaki E, ... ... Pavlidis P, et al. Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean. Current Biology : Cb. PMID 36493775 DOI: 10.1016/j.cub.2022.11.034  0.627
2021 Vasilarou M, Alachiotis N, Garefalaki J, Beloukas A, Pavlidis P. Population Genomics Insights into the First Wave of COVID-19. Life (Basel, Switzerland). 11. PMID 33562321 DOI: 10.3390/life11020129  0.349
2020 Kapopoulou A, Kapun M, Pieper B, Pavlidis P, Wilches R, Duchen P, Stephan W, Laurent S. Demographic analyses of a new sample of haploid genomes from a Swedish population of Drosophila melanogaster. Scientific Reports. 10: 22415. PMID 33376238 DOI: 10.1038/s41598-020-79720-1  0.766
2020 Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki EG, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A. Phylogenetic analysis of SARS-CoV-2 data is difficult. Molecular Biology and Evolution. PMID 33316067 DOI: 10.1093/molbev/msaa314  0.598
2020 Pfeifer B, Alachiotis N, Pavlidis P, Schimek MG. Genome scans for selection and introgression based on k-nearest neighbour techniques. Molecular Ecology Resources. PMID 32639602 DOI: 10.1111/1755-0998.13221  0.342
2020 Taskent O, Lin YL, Patramanis I, Pavlidis P, Gokcumen O. Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage. Genetics. PMID 32234956 DOI: 10.1534/Genetics.120.303167  0.37
2020 Koropoulis A, Alachiotis N, Pavlidis P. Detecting Positive Selection in Populations Using Genetic Data. Methods in Molecular Biology (Clifton, N.J.). 2090: 87-123. PMID 31975165 DOI: 10.1007/978-1-0716-0199-0_5  0.405
2020 Kioukis A, Michalopoulou VA, Briers L, Pirintsos S, Studholme DJ, Pavlidis P, Sarris PF. Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection. Bmc Genomics. 21: 48. PMID 31937246 DOI: 10.1186/s12864-019-6439-x  0.387
2017 Xu D, Pavlidis P, Taskent RO, Alachiotis N, Flanagan C, DeGiorgio M, Blekhman R, Ruhl S, Gokcumen O. Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation. Molecular Biology and Evolution. 34: 2704-2715. PMID 28957509 DOI: 10.1093/Molbev/Msx206  0.318
2017 Pavlidis P, Alachiotis N. A survey of methods and tools to detect recent and strong positive selection. Journal of Biological Research (Thessalonike, Greece). 24: 7. PMID 28405579 DOI: 10.1186/s40709-017-0064-0  0.336
2016 Xu D, Pavlidis P, Thamadilok S, Redwood E, Fox S, Blekhman R, Ruhl S, Gokcumen O. Recent evolution of the salivary mucin MUC7. Scientific Reports. 6: 31791. PMID 27558399 DOI: 10.1038/Srep31791  0.334
2016 Alachiotis N, Pavlidis P. Scalable linkage-disequilibrium-based selective sweep detection: a performance guide. Gigascience. 5: 7. PMID 26862394 DOI: 10.1186/s13742-016-0114-9  0.409
2015 Lin YL, Pavlidis P, Karakoc E, Ajay J, Gokcumen O. The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Molecular Biology and Evolution. 32: 1008-19. PMID 25556237 DOI: 10.1093/Molbev/Msu405  0.346
2015 Eaaswarkhanth M, Pavlidis P, Gokcumen O. Geographic distribution and adaptive significance of genomic structural variants: An anthropological genetics perspective Human Biology. 86: 260-275.  0.301
2014 Eaaswarkhanth M, Pavlidis P, Gokcumen O. Geographic distribution and adaptive significance of genomic structural variants: an anthropological genetics perspective. Human Biology. 86: 260-75. PMID 25959693 DOI: 10.13110/Humanbiology.86.4.0260  0.365
2014 Pybus M, Dall'Olio GM, Luisi P, Uzkudun M, Carreño-Torres A, Pavlidis P, Laayouni H, Bertranpetit J, Engelken J. 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Research. 42: D903-9. PMID 24275494 DOI: 10.1093/nar/gkt1188  0.36
2013 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. Computational and Structural Biotechnology Journal. 6: e201303001. PMID 24688709 DOI: 10.5936/csbj.201303001  0.558
2013 Gokcumen O, Tischler V, Tica J, Zhu Q, Iskow RC, Lee E, Fritz MH, Langdon A, Stütz AM, Pavlidis P, Benes V, Mills RE, Park PJ, Lee C, Korbel JO. Primate genome architecture influences structural variation mechanisms and functional consequences. Proceedings of the National Academy of Sciences of the United States of America. 110: 15764-9. PMID 24014587 DOI: 10.1073/Pnas.1305904110  0.329
2013 Zhang J, Kapli P, Pavlidis P, Stamatakis A. A general species delimitation method with applications to phylogenetic placements. Bioinformatics (Oxford, England). 29: 2869-76. PMID 23990417 DOI: 10.1093/bioinformatics/btt499  0.573
2013 Pavlidis P, Živkovic D, Stamatakis A, Alachiotis N. SweeD: likelihood-based detection of selective sweeps in thousands of genomes. Molecular Biology and Evolution. 30: 2224-34. PMID 23777627 DOI: 10.1093/molbev/mst112  0.643
2013 Werzner A, Pavlidis P, Ometto L, Stephan W, Laurent S. Selective sweep in the Flotillin-2 region of European Drosophila melanogaster. Plos One. 8: e56629. PMID 23437190 DOI: 10.1371/Journal.Pone.0056629  0.774
2012 Alachiotis N, Stamatakis A, Pavlidis P. OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets. Bioinformatics (Oxford, England). 28: 2274-5. PMID 22760304 DOI: 10.1093/bioinformatics/bts419  0.373
2012 Pavlidis P, Metzler D, Stephan W. Selective sweeps in multilocus models of quantitative traits. Genetics. 192: 225-39. PMID 22714406 DOI: 10.1534/genetics.112.142547  0.586
2012 Pavlidis P, Jensen JD, Stephan W, Stamatakis A. A critical assessment of storytelling: gene ontology categories and the importance of validating genomic scans. Molecular Biology and Evolution. 29: 3237-48. PMID 22617950 DOI: 10.1093/Molbev/Mss136  0.735
2012 Saminadin-Peter SS, Kemkemer C, Pavlidis P, Parsch J. Selective sweep of a cis-regulatory sequence in a non-African population of Drosophila melanogaster. Molecular Biology and Evolution. 29: 1167-74. PMID 22101416 DOI: 10.1093/Molbev/Msr284  0.679
2012 Bousios A, Kourmpetis YA, Pavlidis P, Minga E, Tsaftaris A, Darzentas N. The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story. The Plant Journal : For Cell and Molecular Biology. 69: 475-88. PMID 21967390 DOI: 10.1111/j.1365-313X.2011.04806.x  0.301
2011 Tellier A, Laurent SJ, Lainer H, Pavlidis P, Stephan W. Inference of seed bank parameters in two wild tomato species using ecological and genetic data. Proceedings of the National Academy of Sciences of the United States of America. 108: 17052-7. PMID 21949404 DOI: 10.1073/pnas.1111266108  0.736
2011 Svetec N, Werzner A, Wilches R, Pavlidis P, Alvarez-Castro JM, Broman KW, Metzler D, Stephan W. Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine mapping by selective sweep analysis. Molecular Ecology. 20: 530-44. PMID 21199023 DOI: 10.1111/J.1365-294X.2010.04951.X  0.752
2010 Pavlidis P, Laurent S, Stephan W. msABC: a modification of Hudson's ms to facilitate multi-locus ABC analysis. Molecular Ecology Resources. 10: 723-7. PMID 21565078 DOI: 10.1111/J.1755-0998.2010.02832.X  0.736
2010 Pavlidis P, Jensen JD, Stephan W. Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics. 185: 907-22. PMID 20407129 DOI: 10.1534/Genetics.110.116459  0.647
2009 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. Molecular Biology and Evolution. 26: 1549-56. PMID 19349642 DOI: 10.1093/Molbev/Msp065  0.771
2009 Johnsen JM, Teschke M, Pavlidis P, McGee BM, Tautz D, Ginsburg D, Baines JF. Selection on cis-regulatory variation at B4galnt2 and its influence on von Willebrand factor in house mice. Molecular Biology and Evolution. 26: 567-78. PMID 19088380 DOI: 10.1093/molbev/msn284  0.348
2008 Pavlidis P, Hutter S, Stephan W. A population genomic approach to map recent positive selection in model species. Molecular Ecology. 17: 3585-98. PMID 18627454 DOI: 10.1111/j.1365-294X.2008.03852.x  0.658
2006 Pavlidis P, Poirazi P. Individualized markers optimize class prediction of microarray data. Bmc Bioinformatics. 7: 345. PMID 16842618 DOI: 10.1186/1471-2105-7-345  0.347
2003 Yonan AL, Palmer AA, Smith KC, Feldman I, Lee HK, Yonan JM, Fischer SG, Pavlidis P, Gilliam TC. Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network prediction. Genes, Brain, and Behavior. 2: 303-20. PMID 14606695 DOI: 10.1034/J.1601-183X.2003.00041.X  0.323
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