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Evaluating ortholog prediction algorithms in a yeast model clade.
Salichos L, Rokas A. Salichos L, et al. PLoS One. 2011 Apr 13;6(4):e18755. doi: 10.1371/journal.pone.0018755. PLoS One. 2011. PMID: 21533202 Free PMC article.
Inferring ancient divergences requires genes with strong phylogenetic signals.
Salichos L, Rokas A. Salichos L, et al. Nature. 2013 May 16;497(7449):327-31. doi: 10.1038/nature12130. Epub 2013 May 8. Nature. 2013. PMID: 23657258
The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae.
Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, Rokas A. Gibbons JG, et al. Curr Biol. 2012 Aug 7;22(15):1403-9. doi: 10.1016/j.cub.2012.05.033. Epub 2012 Jul 12. Curr Biol. 2012. PMID: 22795693 Free PMC article.
Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture.
Kent BN, Salichos L, Gibbons JG, Rokas A, Newton IL, Clark ME, Bordenstein SR. Kent BN, et al. Genome Biol Evol. 2011;3:209-18. doi: 10.1093/gbe/evr007. Epub 2011 Feb 2. Genome Biol Evol. 2011. PMID: 21292630 Free PMC article.
The diversity and evolution of circadian clock proteins in fungi.
Salichos L, Rokas A. Salichos L, et al. Mycologia. 2010 Mar-Apr;102(2):269-78. doi: 10.3852/09-073. Mycologia. 2010. PMID: 20361495
Transcriptome-wide analysis of small RNA expression in early zebrafish development.
Wei C, Salichos L, Wittgrove CM, Rokas A, Patton JG. Wei C, et al. RNA. 2012 May;18(5):915-29. doi: 10.1261/rna.029090.111. Epub 2012 Mar 8. RNA. 2012. PMID: 22408181 Free PMC article.
Computing the Internode Certainty and Related Measures from Partial Gene Trees.
Kobert K, Salichos L, Rokas A, Stamatakis A. Kobert K, et al. Mol Biol Evol. 2016 Jun;33(6):1606-17. doi: 10.1093/molbev/msw040. Epub 2016 Feb 25. Mol Biol Evol. 2016. PMID: 26915959 Free PMC article.
The real cost of sequencing: scaling computation to keep pace with data generation.
Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M. Muir P, et al. Genome Biol. 2016 Mar 23;17:53. doi: 10.1186/s13059-016-0917-0. Genome Biol. 2016. PMID: 27009100 Free PMC article.
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