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Results: 1 to 20 of 28

1.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

Card DC, Schield DR, Reyes-Velasco J, Fujita MK, Andrew AL, Oyler-McCance SJ, Fike JA, Tomback DF, Ruggiero RP, Castoe TA.

PLoS One. 2014 Sep 5;9(9):e106649. doi: 10.1371/journal.pone.0106649. eCollection 2014.

PMID:
25192061
[PubMed - in process]
Free PMC Article
2.

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

Castoe TA, de Koning AP, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, Polanco D, Dobry J, Vandewege MW, Li Q, Schott RK, Kapusta A, Minx P, Feschotte C, Uetz P, Ray DA, Hoffmann FG, Bogden R, Smith EN, Chang BS, Vonk FJ, Casewell NR, Henkel CV, Richardson MK, Mackessy SP, Bronikowski AM, Yandell M, Warren WC, Secor SM, Pollock DD.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20645-50. doi: 10.1073/pnas.1314475110. Epub 2013 Dec 2. Erratum in: Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3194. Proc Natl Acad Sci U S A. 2013 Dec 17;110(51). doi:10.1073/pnas.1324133111. Bronikowsi, Anne M [corrected to Bronikowski, Anne M].

PMID:
24297902
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.

Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wüster W, Woods AE, Logan JM, Harrison RA, Castoe TA, de Koning AP, Pollock DD, Yandell M, Calderon D, Renjifo C, Currier RB, Salgado D, Pla D, Sanz L, Hyder AS, Ribeiro JM, Arntzen JW, van den Thillart GE, Boetzer M, Pirovano W, Dirks RP, Spaink HP, Duboule D, McGlinn E, Kini RM, Richardson MK.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20651-6. doi: 10.1073/pnas.1314702110. Epub 2013 Dec 2.

PMID:
24297900
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Chinese alligator genome illustrates molecular adaptations.

Castoe TA, Pollock DD.

Cell Res. 2013 Nov;23(11):1254-5. doi: 10.1038/cr.2013.134. Epub 2013 Sep 24.

PMID:
24060849
[PubMed - in process]
Free PMC Article
5.

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

Shaffer HB, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning AP, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK.

Genome Biol. 2013 Mar 28;14(3):R28. doi: 10.1186/gb-2013-14-3-r28.

PMID:
23537068
[PubMed - in process]
Free PMC Article
6.

Report from the first snake genomics and integrative biology meeting.

Castoe TA, Braun EL, Bronikowski AM, Cox CL, Rabosky AR, Jason de Koning AP, Dobry J, Fujita MK, Giorgianni MW, Hargreaves A, Henkel CV, Mackessy SP, O'Meally D, Rokyta DR, Secor SM, Streicher JW, Wray KP, Yokoyama KD, Pollock DD.

Stand Genomic Sci. 2012 Oct 10;7(1):150-2. doi: 10.4056/sigs.3106480. Epub 2012 Sep 24.

PMID:
23451292
[PubMed]
Free PMC Article
7.

Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica.

Ornelas JF, Sosa V, Soltis DE, Daza JM, González C, Soltis PS, Gutiérrez-Rodríguez C, de los Monteros AE, Castoe TA, Bell C, Ruiz-Sanchez E.

PLoS One. 2013;8(2):e56283. doi: 10.1371/journal.pone.0056283. Epub 2013 Feb 7.

PMID:
23409165
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Phylogenetics, likelihood, evolution and complexity.

de Koning AP, Gu W, Castoe TA, Pollock DD.

Bioinformatics. 2012 Nov 15;28(22):2989-90. doi: 10.1093/bioinformatics/bts555. Epub 2012 Sep 12.

PMID:
22976081
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data.

Lamers RP, Muthukrishnan G, Castoe TA, Tafur S, Cole AM, Parkinson CL.

BMC Evol Biol. 2012 Sep 6;12:171. doi: 10.1186/1471-2148-12-171.

PMID:
22950675
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species.

Castoe TA, Streicher JW, Meik JM, Ingrasci MJ, Poole AW, de Koning AP, Campbell JA, Parkinson CL, Smith EN, Pollock DD.

Mol Ecol Resour. 2012 Nov;12(6):1105-13. doi: 10.1111/1755-0998.12000. Epub 2012 Sep 1.

PMID:
22938699
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development.

Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock DD, Höglund J.

Open Biol. 2012 Apr;2(4):120054. doi: 10.1098/rsob.120054.

PMID:
22724064
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.

Castoe TA, Poole AW, de Koning AP, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD.

PLoS One. 2012;7(2):e30953. doi: 10.1371/journal.pone.0030953. Epub 2012 Feb 14.

PMID:
22348032
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ Jr, Glenn TC, Green RE, Ray DA.

Genome Biol. 2012 Jan 31;13(1):415. doi: 10.1186/gb-2012-13-1-415.

PMID:
22293439
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders.

Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL.

Genome Biol Evol. 2012;4(2):168-83. doi: 10.1093/gbe/evr139. Epub 2011 Dec 26.

PMID:
22200636
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Repetitive elements may comprise over two-thirds of the human genome.

de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD.

PLoS Genet. 2011 Dec;7(12):e1002384. doi: 10.1371/journal.pgen.1002384. Epub 2011 Dec 1.

PMID:
22144907
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions.

Pollock DD, de Koning AP, Kim H, Castoe TA, Churchill ME, Kechris KJ.

PLoS One. 2011;6(11):e26105. doi: 10.1371/journal.pone.0026105. Epub 2011 Nov 1.

PMID:
22069446
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The genome of the green anole lizard and a comparative analysis with birds and mammals.

Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K.

Nature. 2011 Aug 31;477(7366):587-91. doi: 10.1038/nature10390.

PMID:
21881562
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus).

Castoe TA, Fox SE, Jason de Koning A, Poole AW, Daza JM, Smith EN, Mockler TC, Secor SM, Pollock DD.

BMC Res Notes. 2011 Aug 25;4:310. doi: 10.1186/1756-0500-4-310.

PMID:
21867488
[PubMed]
Free PMC Article
19.

Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes.

Castoe TA, de Koning JA, Hall KT, Yokoyama KD, Gu W, Smith EN, Feschotte C, Uetz P, Ray DA, Dobry J, Bogden R, Mackessy SP, Bronikowski AM, Warren WC, Secor SM, Pollock DD.

Genome Biol. 2011 Jul 28;12(7):406. doi: 10.1186/gb-2011-12-7-406.

PMID:
21801464
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A proposal to sequence the genome of a garter snake (Thamnophis sirtalis).

Castoe TA, Bronikowski AM, Brodie ED 3rd, Edwards SV, Pfrender ME, Shapiro MD, Pollock DD, Warren WC.

Stand Genomic Sci. 2011 Apr 29;4(2):257-70. doi: 10.4056/sigs.1664145.

PMID:
21677863
[PubMed]
Free PMC Article

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