{"id":34,"date":"2014-02-06T09:22:36","date_gmt":"2014-02-06T15:22:36","guid":{"rendered":"http:\/\/agrilife.org\/casolalab\/?page_id=34"},"modified":"2022-12-05T13:38:12","modified_gmt":"2022-12-05T19:38:12","slug":"publications","status":"publish","type":"page","link":"https:\/\/agrilife.org\/casolalab\/publications\/","title":{"rendered":"Selected Publications"},"content":{"rendered":"

Google Scholar<\/a><\/p>\n

PubMed<\/a><\/p>\n

Selected peer-reviewed articles <\/strong><\/p>\n

(*Graduate student; ^Postdoc; 1co-first author)
\n<\/strong><\/p>\n

Casola C, *Owoyemi A, Pepper AE, Ioerger TR. “Accurate identification of de novo genes in plant genomes using machine learning algorithms<\/strong>“. bioRxiv 2022. (preprint<\/a>)<\/p>\n

Markova DN, Ruma FB, Casola C, Mirsalehi A, Betr\u00e1n E (2022) “Recurrent co-domestication of PIF\/Harbinger transposable element proteins in insects<\/strong>.” Mob DNA 30;13(1):28. (paper<\/a>)<\/p>\n

Casola C, *Li J (2022) “Beyond RuBisCO: Convergent molecular evolution of multiple chloroplast genes in C4 plants<\/strong>“. PeerJ. 2022; 10: e12791. (paper<\/a>).<\/p>\n

*Li J, West JB, Hart A, Wegrzyn JL, Smith MA, Domec JC, Loopstra CA, Casola C (2021) “Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly\u00a0Pine Genotypes<\/strong>“. Front Genet 2021 12:661440. (paper<\/a>)<\/p>\n

Ruckman SN, Jonika M, Casola C, Blackmon H (2020) \u201cChromosome number evolves at equal rates in holocentric and monocentric clades<\/strong>\u201d. PLoS Genet 2020 Oct 13;16(10):e1009076. (paper<\/a>)<\/p>\n

Y Xing, AR Dabney, X Li, Wang G, Gill CA, C Casola (2020) “SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes”<\/strong>. Front Genet Feb 21;11:82. (paper<\/a>)<\/p>\n

Casola C, Lawing AM (2019) \u201cThe nonrandom evolution of gene families<\/strong>\u201d. Am J Bot 106(1):14-17. (paper<\/a>)<\/p>\n

C Casola (2018) “From de novo to” de nono”: most novel protein coding genes identified with phylostratigraphy represent old genes or recent duplicates<\/strong>“. Genome Biol Evol, 22 October (paper<\/a>).<\/p>\n

Casola C, ^Koralewski TE (2018) \u201cPinaceae show elevated rates of gene turnover that are robust to incomplete gene annotation<\/strong>\u201d. Plant J\u00a0 2018. (paper<\/a>)<\/p>\n

Cossu RM1, Casola C1, Giacomello S, Scofield DG, Vidalis A, Zuccolo A. (2017) \u201cLTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes<\/strong>\u201d. Genome Biol Evol 9(12):3449-3462. (paper<\/a>)<\/p>\n

Neale D et al. [Casola C, ^Koralewski TE contributing authors] (2017) \u201cThe Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae<\/strong>\u201d. G3 7(9):3157-3167. (paper<\/a>)<\/p>\n

Casola C, Betr\u00e1n E (2017) “The genomic impact of gene retrocopies: what have we learned from comparative genomics, population genomics and transcriptomic analyses?<\/strong>” Genome Biol Evol 9(6):1351-1373. (paper<\/a>)<\/p>\n

*Lin X, Faridi N, Casola C (2016) “An Ancient Trans-Kingdom Horizontal Transfer of Penelope-like Retroelements from Arthropods to Conifers<\/strong>“.\u00a0Genome Biol Evol 8(4):1252-66. (paper<\/a>) Media: here<\/a>, here<\/a>, here<\/a> and here<\/a> (in Italian)<\/p>\n

Carbone L, et al. (2014) “Gibbon genome and the fast karyotype evolution of small apes<\/strong>“. Nature 513:195\u2013201. (paper<\/a>)<\/p>\n

Marmoset Genome Sequencing and Analysis Consortium; Marmoset Genome Sequencing and Analysis Consortium (2014) “The common marmoset genome provides insight into primate biology and evolution<\/strong>“. Nat Genet 46:850-7. (paper<\/a>)<\/p>\n

Casola C, Conant GC, Hahn MW (2012) “Very low rate of gene conversion in the yeast genome<\/strong>“. Mol Biol Evol 29:3817-26. (paper<\/a>)<\/p>\n

Casola C, Zekonyte U, Phillips AD, Cooper DN, Hahn MW (2012) “Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease<\/strong>“. Genome Res 22:429-35. (paper<\/a>; Nature Review Genetics<\/a> research highlight)<\/p>\n

Emera D, Casola C, Lynch VJ, Wildman D, Agnew D, Wagner GP (2012) “Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements<\/strong>“. Mol Biol Evol 29:239-47. (paper<\/a>)<\/p>\n

Colbourne JK et al. (2011) “The ecoresponsive genome of Daphnia pulex.<\/strong>“. Science 331:555-61. (paper<\/a>)<\/p>\n

Locke DP et al. (2011) “Comparative and demographic analysis of orang-utan genomes<\/strong>“. Nature 469:529-533. (paper<\/a>)<\/p>\n

Casola C, Ganote CL, Hahn MW (2010) “Non-allelic gene conversion in the genus Drosophila<\/strong>“. Genetics 185:95-103. (paper<\/a>)<\/p>\n

Casola C, Hahn MW (2009) “Gene conversion among paralogs results in moderate false detection of positive selection using likelihood methods<\/strong>“. J Mol Evol 68:679-87. (paper<\/a>)<\/p>\n

Han MV, Demuth JP, McGrath CL, Casola C, Hahn MW (2009) “Adaptive evolution of young gene duplicates in mammals<\/strong>“. Genome Res 19:859-67. (paper<\/a>)<\/p>\n

McGrath CL, Casola C, Hahn MW (2009) “Minimal effect of ectopic gene conversion in four mammalian genomes<\/strong>“. Genetics 182:615-22. (paper<\/a>)<\/p>\n

Bai Y, Casola C, Betr\u00e1n E (2009) “Quality of regulatory elements in Drosophila retrogenes<\/strong>“. Genomics 93:83-9. (paper<\/a>)<\/p>\n

Bai Y, Casola C, Betr\u00e1n E (2008) “Evolutionary origin of regulatory regions of retrogenes in Drosophila<\/strong>“. BMC Genomics 9:241. (paper<\/a>)<\/p>\n

Casola C, Hucks D, Feschotte C (2008) “Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals<\/strong>“. Mol Biol Evol 25:29-41. (paper<\/a>)<\/p>\n

Lin R, Ding L, Casola C, Ripoll DR, Feschotte C, Wang H (2007) “Transposase-derived transcription factors regulate light signaling in Arabidopsis<\/strong>“. Science 318:1302-5. (paper<\/a>)<\/p>\n

Casola C, Lawing AM, Betr\u00e1n E, Feschotte C (2007) “PIF-like transposons are common in Drosophila and have been repeatedly domesticated to generate new host genes<\/strong>“. Mol Biol Evol 24:1872-88. (paper<\/a>)<\/p>\n

Bai Y, Casola C, Feschotte C and Betr\u00e1n E (2007) “Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila<\/strong>“. Genome Biol 8:R11. (paper<\/a>)<\/p>\n

 <\/p>\n

Letters to editor<\/strong><\/p>\n

Casola C. “TP53 retropseudogenes and cancer resistance in elephants”. JAMA<\/a> 2016 Apr 26;315(16):1788-9..<\/p>\n","protected":false},"excerpt":{"rendered":"

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