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Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations.
Pavlidis P, Jensen JD, Stephan W. Pavlidis P, et al. Genetics. 2010 Jul;185(3):907-22. doi: 10.1534/genetics.110.116459. Epub 2010 Apr 20. Genetics. 2010. PMID: 20407129 Free PMC article.
Scalable linkage-disequilibrium-based selective sweep detection: a performance guide.
Alachiotis N, Pavlidis P. Alachiotis N, et al. Among authors: pavlidis p. Gigascience. 2016 Feb 8;5:7. doi: 10.1186/s13742-016-0114-9. eCollection 2016. Gigascience. 2016. PMID: 26862394 Free PMC article.
Selective sweep in the Flotillin-2 region of European Drosophila melanogaster.
Werzner A, Pavlidis P, Ometto L, Stephan W, Laurent S. Werzner A, et al. Among authors: pavlidis p. PLoS One. 2013;8(2):e56629. doi: 10.1371/journal.pone.0056629. Epub 2013 Feb 21. PLoS One. 2013. PMID: 23437190 Free PMC article.
Selective sweeps in multilocus models of quantitative traits.
Pavlidis P, Metzler D, Stephan W. Pavlidis P, et al. Genetics. 2012 Sep;192(1):225-39. doi: 10.1534/genetics.112.142547. Epub 2012 Jun 19. Genetics. 2012. PMID: 22714406 Free PMC article.
Selective sweep of a cis-regulatory sequence in a non-African population of Drosophila melanogaster.
Saminadin-Peter SS, Kemkemer C, Pavlidis P, Parsch J. Saminadin-Peter SS, et al. Among authors: pavlidis p. Mol Biol Evol. 2012 Apr;29(4):1167-74. doi: 10.1093/molbev/msr284. Epub 2011 Nov 18. Mol Biol Evol. 2012. PMID: 22101416
Inference of seed bank parameters in two wild tomato species using ecological and genetic data.
Tellier A, Laurent SJ, Lainer H, Pavlidis P, Stephan W. Tellier A, et al. Among authors: pavlidis p. Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):17052-7. doi: 10.1073/pnas.1111266108. Epub 2011 Sep 26. Proc Natl Acad Sci U S A. 2011. PMID: 21949404 Free PMC article.
Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine mapping by selective sweep analysis.
Svetec N, Werzner A, Wilches R, Pavlidis P, Alvarez-Castro JM, Broman KW, Metzler D, Stephan W. Svetec N, et al. Among authors: pavlidis p. Mol Ecol. 2011 Feb;20(3):530-44. doi: 10.1111/j.1365-294X.2010.04951.x. Epub 2010 Dec 24. Mol Ecol. 2011. PMID: 21199023 Free PMC article.
Recent strong positive selection on Drosophila melanogaster HDAC6, a gene encoding a stress surveillance factor, as revealed by population genomic analysis.
Svetec N, Pavlidis P, Stephan W. Svetec N, et al. Among authors: pavlidis p. Mol Biol Evol. 2009 Jul;26(7):1549-56. doi: 10.1093/molbev/msp065. Epub 2009 Apr 6. Mol Biol Evol. 2009. PMID: 19349642
OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets.
Alachiotis N, Stamatakis A, Pavlidis P. Alachiotis N, et al. Among authors: pavlidis p. Bioinformatics. 2012 Sep 1;28(17):2274-5. doi: 10.1093/bioinformatics/bts419. Epub 2012 Jul 3. Bioinformatics. 2012. PMID: 22760304
A population genomic approach to map recent positive selection in model species.
Pavlidis P, Hutter S, Stephan W. Pavlidis P, et al. Mol Ecol. 2008 Aug;17(16):3585-98. doi: 10.1111/j.1365-294X.2008.03852.x. Mol Ecol. 2008. PMID: 18627454 Review.
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