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Two rounds of whole genome duplication in the ancestral vertebrate.
Dehal P, Boore JL. Dehal P, et al. Among authors: boore jl. PLoS Biol. 2005 Oct;3(10):e314. doi: 10.1371/journal.pbio.0030314. Epub 2005 Sep 6. PLoS Biol. 2005. PMID: 16128622 Free PMC article.
The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.
Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS. Dehal P, et al. Among authors: boore j. Science. 2002 Dec 13;298(5601):2157-67. doi: 10.1126/science.1080049. Science. 2002. PMID: 12481130
The phylogeny of Mediterranean tortoises and their close relatives based on complete mitochondrial genome sequences from museum specimens.
Parham JF, Macey JR, Papenfuss TJ, Feldman CR, Türkozan O, Polymeni R, Boore J. Parham JF, et al. Among authors: boore j. Mol Phylogenet Evol. 2006 Jan;38(1):50-64. doi: 10.1016/j.ympev.2005.07.015. Epub 2005 Sep 16. Mol Phylogenet Evol. 2006. PMID: 16150614
DETECTING EVOLUTIONARY TRANSFER OF GENES USING PhIGs(1).
Boore JL. Boore JL. J Phycol. 2008 Feb;44(1):19-22. doi: 10.1111/j.1529-8817.2007.00436.x. J Phycol. 2008. PMID: 27041035
Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae).
Baker RH, Morgan J, Wang X, Boore JL, Wilkinson GS. Baker RH, et al. Among authors: boore jl. BMC Genomics. 2009 Aug 5;10:361. doi: 10.1186/1471-2164-10-361. BMC Genomics. 2009. PMID: 19656405 Free PMC article.
Group II introns break new boundaries: presence in a bilaterian's genome.
Vallès Y, Halanych KM, Boore JL. Vallès Y, et al. Among authors: boore jl. PLoS One. 2008 Jan 23;3(1):e1488. doi: 10.1371/journal.pone.0001488. PLoS One. 2008. PMID: 18213396 Free PMC article.
Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction.
Boore JL, Fuerstenberg SI. Boore JL, et al. Philos Trans R Soc Lond B Biol Sci. 2008 Apr 27;363(1496):1445-51. doi: 10.1098/rstb.2007.2234. Philos Trans R Soc Lond B Biol Sci. 2008. PMID: 18192190 Free PMC article.
The use of genome-level characters for phylogenetic reconstruction.
Boore JL. Boore JL. Trends Ecol Evol. 2006 Aug;21(8):439-46. doi: 10.1016/j.tree.2006.05.009. Epub 2006 Jun 8. Trends Ecol Evol. 2006. PMID: 16762445
Naked corals: skeleton loss in Scleractinia.
Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL. Medina M, et al. Among authors: boore jl. Proc Natl Acad Sci U S A. 2006 Jun 13;103(24):9096-100. doi: 10.1073/pnas.0602444103. Epub 2006 Jun 5. Proc Natl Acad Sci U S A. 2006. PMID: 16754865 Free PMC article.
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database.
Dehal PS, Boore JL. Dehal PS, et al. Among authors: boore jl. BMC Bioinformatics. 2006 Apr 11;7:201. doi: 10.1186/1471-2105-7-201. BMC Bioinformatics. 2006. PMID: 16608522 Free PMC article.
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