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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.
RESULTS: Examination of sensitivity [TP/(TP+FN)], specificity [TN/(TN+FP)], and accuracy [(TP+TN)/(TP+TN+FP+FN)] across a broad parameter range showed that cRBH was the most accurate and specific algorithm, whereas OrthoMCL was the most sensitive. Evaluation of the algorit …
RESULTS: Examination of sensitivity [TP/(TP+FN)], specificity [TN/(TN+FP)], and accuracy [(TP+TN)/(TP+TN+FP+FN)] across a broad param …
Transcriptional rewiring: the proof is in the eating.
Rokas A, Hittinger CT. Rokas A, et al. Curr Biol. 2007 Aug 21;17(16):R626-8. doi: 10.1016/j.cub.2007.06.025. Curr Biol. 2007. PMID: 17714646
Genomics. Lining up to avoid bias.
Rokas A. Rokas A. Science. 2008 Jan 25;319(5862):416-7. doi: 10.1126/science.1153156. Science. 2008. PMID: 18218881 No abstract available.
Frequent and widespread parallel evolution of protein sequences.
Rokas A, Carroll SB. Rokas A, et al. Mol Biol Evol. 2008 Sep;25(9):1943-53. doi: 10.1093/molbev/msn143. Epub 2008 Jun 25. Mol Biol Evol. 2008. PMID: 18583353
Understanding the patterns and causes of protein sequence evolution is a major challenge in evolutionary biology. One of the critical unresolved issues is the relative contribution of selection and genetic drift to the fixation of amino acid sequence differences between sp …
Understanding the patterns and causes of protein sequence evolution is a major challenge in evolutionary biology. One of the critical …
From gene-scale to genome-scale phylogenetics: the data flood in, but the challenges remain.
Rokas A, Chatzimanolis S. Rokas A, et al. Methods Mol Biol. 2008;422:1-12. doi: 10.1007/978-1-59745-581-7_1. Methods Mol Biol. 2008. PMID: 18629657
Here, we argue that a vast increase in data size alone--although necessary--may not be sufficient to achieve the desired accuracy for three reasons: (i) the existence of short stems in the tree of life, (ii) the saturation of phylogenetic signal in molecular sequences, and …
Here, we argue that a vast increase in data size alone--although necessary--may not be sufficient to achieve the desired accuracy for …
The molecular origins of multicellular transitions.
Rokas A. Rokas A. Curr Opin Genet Dev. 2008 Dec;18(6):472-8. doi: 10.1016/j.gde.2008.09.004. Epub 2008 Oct 14. Curr Opin Genet Dev. 2008. PMID: 18926910 Review.
Multicellularity has evolved multiple times independently from a variety of ancestral unicellular lineages. Past research on multicellularity was focused more on explaining why it was repeatedly invented and less so on the molecular foundations associated with each transit …
Multicellularity has evolved multiple times independently from a variety of ancestral unicellular lineages. Past research on multicel …
Comparative and functional characterization of intragenic tandem repeats in 10 Aspergillus genomes.
Gibbons JG, Rokas A. Gibbons JG, et al. Mol Biol Evol. 2009 Mar;26(3):591-602. doi: 10.1093/molbev/msn277. Epub 2008 Dec 4. Mol Biol Evol. 2009. PMID: 19056904
We have examined the evolution and functional role of ITRs in 10 genomes spanning the fungal genus Aspergillus, a clade of relevance to medicine, agriculture, and industry. ...Fungal ITRs likely participate in a variety of developmental processes and cell-surface-as …
We have examined the evolution and functional role of ITRs in 10 genomes spanning the fungal genus Aspergillus, a clade of relevance …
The effect of domestication on the fungal proteome.
Rokas A. Rokas A. Trends Genet. 2009 Feb;25(2):60-3. doi: 10.1016/j.tig.2008.11.003. Epub 2008 Dec 10. Trends Genet. 2009. PMID: 19081651
I examined the molecular signature of domestication on Aspergillus oryzae, a fungus used to ferment several Japanese food products. The ratio of nonsynonymous to synonymous substitutions and the percentage of estimated deleterious substitutions along the A. oryzae l …
I examined the molecular signature of domestication on Aspergillus oryzae, a fungus used to ferment several Japanese food products. T …
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
A notable exception is the 10 FRQ-like proteins in Fusarium oxysporum, which resulted from nine duplication events. Our results suggest that the machinery required for FWO oscillator function is taxonomically restricted within Ascomycetes. Although the WC proteins are wide
A notable exception is the 10 FRQ-like proteins in Fusarium oxysporum, which resulted from nine duplication events. Our results sugge
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