Todd A. Castoe, PhD - Publications

Affiliations: 
Biology University of Texas at Arlington, Arlington, TX, United States 
Area:
Herpetology
Website:
http://www.snakegenomics.org/SnakeGenomics/Home.html

96 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Perry BW, Andrew AL, Mostafa Kamal AH, Card DC, Schield DR, Pasquesi GIM, Pellegrino MW, Mackessy SP, Chowdhury SM, Secor SM, Castoe TA. Multi-species comparisons of snakes identify coordinated signalling networks underlying post-feeding intestinal regeneration. Proceedings. Biological Sciences. 286: 20190910. PMID 31288694 DOI: 10.1098/rspb.2019.0910  1
2019 Adams RH, Castoe TA. Probabilistic species tree distances: implementing the multispecies coalescent to compare species trees within the same model-based framework used to estimate them. Systematic Biology. PMID 31086978 DOI: 10.1093/sysbio/syz031  0.88
2019 Schield DR, Card DC, Hales NR, Perry BW, Pasquesi GM, Blackmon H, Adams RH, Corbin AB, Smith CF, Ramesh B, Demuth JP, Betrán E, Tollis M, Meik JM, Mackessy SP, ... Castoe TA, et al. The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Genome Research. PMID 30898880 DOI: 10.1101/gr.240952.118  1
2019 Pinto BJ, Card DC, Castoe TA, Diaz RE, Nielsen SV, Trainor PA, Gamble T. The transcriptome of the Veiled Chameleon (Chamaeleo calyptratus): a resource for studying the evolution and development of vertebrates. Developmental Dynamics : An Official Publication of the American Association of Anatomists. PMID 30839129 DOI: 10.1002/dvdy.20  1
2019 Adams RH, Castoe TA. Statistical binning leads to profound model violation due to gene tree error incurred by trying to avoid gene tree error. Molecular Phylogenetics and Evolution. PMID 30790674 DOI: 10.1016/j.ympev.2019.02.012  0.88
2018 Strickland JL, Smith CF, Mason AJ, Schield DR, Borja M, Castañeda-Gaytán G, Spencer CL, Smith LL, Trápaga A, Bouzid NM, Campillo-García G, Flores-Villela OA, Antonio-Rangel D, Mackessy SP, Castoe TA, et al. Evidence for divergent patterns of local selection driving venom variation in Mojave Rattlesnakes (Crotalus scutulatus). Scientific Reports. 8: 17622. PMID 30514908 DOI: 10.1038/s41598-018-35810-9  1
2018 Card DC, Perry BW, Adams RH, Schield DR, Young AS, Andrew AL, Jezkova T, Pasquesi GIM, Hales NR, Walsh MR, Rochford MR, Mazzotti FJ, Hart KM, Hunter ME, Castoe TA. Novel ecological and climatic conditions drive rapid adaptation in invasive Florida Burmese pythons. Molecular Ecology. PMID 30269397 DOI: 10.1111/mec.14885  1
2018 Perry BW, Schield DR, Castoe TA. Evolution: Plasticity versus Selection, or Plasticity and Selection? Current Biology : Cb. 28: R1104-R1106. PMID 30253151 DOI: 10.1016/j.cub.2018.07.050  1
2018 Perry BW, Card DC, McGlothlin JW, Pasquesi GIM, Adams RH, Schield DR, Hales NR, Corbin AB, Demuth JP, Hoffmann FG, Vandewege MW, Schott RK, Bhattacharyya N, Chang BSW, Casewell NR, ... ... Castoe TA, et al. Molecular adaptations for sensing and securing prey and insight into amniote genome diversity from the garter snake genome. Genome Biology and Evolution. PMID 30060036 DOI: 10.1093/gbe/evy157  1
2018 Pasquesi GIM, Adams RH, Card DC, Schield DR, Corbin AB, Perry BW, Reyes-Velasco J, Ruggiero RP, Vandewege MW, Shortt JA, Castoe TA. Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Nature Communications. 9: 2774. PMID 30018307 DOI: 10.1038/s41467-018-05279-1  1
2018 Schield DR, Adams RH, Card DC, Corbin AB, Jezkova T, Hales NR, Meik JM, Perry BW, Spencer CL, Smith LL, Campillo García G, Bouzid NM, Strickland JL, Parkinson CL, Borja M, ... ... Castoe TA, et al. Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus). Molecular Phylogenetics and Evolution. PMID 29902574 DOI: 10.1016/j.ympev.2018.06.013  1
2018 Schott RK, Van Nynatten A, Card DC, Castoe TA, S W Chang B. Shifts in Selective Pressures on Snake Phototransduction Genes Associated with Photoreceptor Transmutation and Dim-Light Ancestry. Molecular Biology and Evolution. 35: 1376-1389. PMID 29800394 DOI: 10.1093/molbev/msy025  1
2018 Adams RH, Schield DR, Card DC, Castoe TA. Assessing the impacts of positive selection on coalescent-based species tree estimation and species delimitation. Systematic Biology. PMID 29757422 DOI: 10.1093/sysbio/syy034  1
2018 Card DC, Schield DR, Castoe TA. Plasticity and local adaptation explain lizard cold tolerance. Molecular Ecology. 27: 2173-2175. PMID 29737602 DOI: 10.1111/mec.14575  1
2017 Adams RH, Schield DR, Card DC, Corbin A, Castoe TA. ThetaMater: Bayesian estimation of population size parameter θ from genomic data. Bioinformatics (Oxford, England). PMID 29194472 DOI: 10.1093/bioinformatics/btx733  1
2017 Gamble T, Castoe TA, Nielsen SV, Banks JL, Card DC, Schield DR, Schuett GW, Booth W. The Discovery of XY Sex Chromosomes in a Boa and Python. Current Biology : Cb. 27: 2148-2153.e4. PMID 28690112 DOI: 10.1016/j.cub.2017.06.010  1
2017 Hales NR, Schield DR, Andrew AL, Card DC, Walsh MR, Castoe TA. Contrasting gene expression programs correspond with predator-induced phenotypic plasticity within and across-generations in Daphnia. Molecular Ecology. PMID 28628257 DOI: 10.1111/mec.14213  1
2017 Schield DR, Adams RH, Card DC, Perry BW, Pasquesi GM, Jezkova T, Portik DM, Andrew AL, Spencer CL, Sanchez EE, Fujita MK, Mackessy SP, Castoe TA. Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Ecology and Evolution. 7: 3951-3966. PMID 28616190 DOI: 10.1002/ece3.2996  1
2017 Andrew AL, Perry BW, Card DC, Schield DR, Ruggiero RP, McGaugh SE, Choudhary A, Secor SM, Castoe TA. Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python. Bmc Genomics. 18: 338. PMID 28464824 DOI: 10.1186/s12864-017-3743-1  1
2017 Adams RH, Schield DR, Card DC, Blackmon H, Castoe TA. GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data. Bioinformatics (Oxford, England). 33: 1414-1415. PMID 28453670 DOI: 10.1093/bioinformatics/btw795  1
2017 Cox RM, Cox CL, McGlothlin JW, Card DC, Andrew AL, Castoe TA. Hormonally Mediated Increases in Sex-Biased Gene Expression Accompany the Breakdown of Between-Sex Genetic Correlations in a Sexually Dimorphic Lizard. The American Naturalist. 189: 315-332. PMID 28221827 DOI: 10.1086/690105  1
2017 Schott RK, Panesar B, Card DC, Preston M, Castoe TA, Chang BS. Targeted capture of complete coding regions across divergent species. Genome Biology and Evolution. PMID 28137744 DOI: 10.1093/gbe/evx005  1
2017 Shortt JA, Card DC, Schield DR, Liu Y, Zhong B, Castoe TA, Carlton EJ, Pollock DD. Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia. Plos Neglected Tropical Diseases. 11: e0005292. PMID 28107347 DOI: 10.1371/journal.pntd.0005292  1
2016 Adams RH, Schield DR, Card DC, Blackmon H, Castoe TA. GppFst: Genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data. Bioinformatics (Oxford, England). PMID 28011784 DOI: 10.1093/bioinformatics/btw795  1
2016 Doan TM, Mason AJ, Castoe TA, Sasa M, Parkinson CL. A cryptic palm-pitviper species (Squamata: Viperidae: Bothriechis) from the Costa Rican highlands, with notes on the variation within B. nigroviridis. Zootaxa. 4138: 271-90. PMID 27470764  1
2016 McGlothlin JW, Kobiela ME, Feldman CR, Castoe TA, Geffeney SL, Hanifin CT, Toledo G, Vonk FJ, Richardson MK, Brodie ED, Pfrender ME, Brodie ED. Historical Contingency in a Multigene Family Facilitates Adaptive Evolution of Toxin Resistance. Current Biology : Cb. PMID 27291053 DOI: 10.1016/j.cub.2016.04.056  0.64
2016 Streicher JW, McEntee JP, Drzich LC, Card DC, Schield DR, Smart U, Parkinson CL, Jezkova T, Smith EN, Castoe TA. Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coralsnakes. Evolution; International Journal of Organic Evolution. PMID 27251954 DOI: 10.1111/evo.12967  1
2016 Card DC, Schield DR, Adams RH, Corbin AB, Perry BW, Andrew AL, Pasquesi GI, Smith EN, Jezkova T, Boback SM, Booth W, Castoe TA. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism. Molecular Phylogenetics and Evolution. PMID 27241629 DOI: 10.1016/j.ympev.2016.05.034  1
2016 Adams RH, Blackmon H, Reyes-Velasco J, Schield DR, Card DC, Andrew AL, Waynewood N, Castoe TA. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution. Genome / National Research Council Canada = Genome / Conseil National De Recherches Canada. 1-16. PMID 27064176 DOI: 10.1139/gen-2015-0124  1
2016 Walsh MR, Castoe T, Holmes J, Packer M, Biles K, Walsh M, Munch SB, Post DM. Local adaptation in transgenerational responses to predators. Proceedings. Biological Sciences / the Royal Society. 283. PMID 26817775 DOI: 10.1098/rspb.2015.2271  1
2015 Castoe TA, Poole AW, de Koning AP, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD. Correction: Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake. Plos One. 10: e0136465. PMID 26291821 DOI: 10.1371/journal.pone.0136465  1
2015 Saviola AJ, Pla D, Sanz L, Castoe TA, Calvete JJ, Mackessy SP. Comparative venomics of the Prairie Rattlesnake (Crotalus viridis viridis) from Colorado: Identification of a novel pattern of ontogenetic changes in venom composition and assessment of the immunoreactivity of the commercial antivenom CroFab®. Journal of Proteomics. 121: 28-43. PMID 25819372 DOI: 10.1016/j.jprot.2015.03.015  1
2015 Andrew AL, Card DC, Ruggiero RP, Schield DR, Adams RH, Pollock DD, Secor SM, Castoe TA. Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding. Physiological Genomics. 47: 147-57. PMID 25670730 DOI: 10.1152/physiolgenomics.00131.2014  1
2015 Schield DR, Card DC, Adams RH, Jezkova T, Reyes-Velasco J, Proctor FN, Spencer CL, Herrmann HW, Mackessy SP, Castoe TA. Incipient speciation with biased gene flow between two lineages of the Western Diamondback Rattlesnake (Crotalus atrox). Molecular Phylogenetics and Evolution. 83: 213-23. PMID 25534232 DOI: 10.1016/j.ympev.2014.12.006  1
2015 Jezkova T, Riddle BR, Card DC, Schield DR, Eckstut ME, Castoe TA. Genetic consequences of postglacial range expansion in two codistributed rodents (genus Dipodomys) depend on ecology and genetic locus. Molecular Ecology. 24: 83-97. PMID 25413968 DOI: 10.1111/mec.13012  1
2015 Reyes-Velasco J, Card DC, Andrew AL, Shaney KJ, Adams RH, Schield DR, Casewell NR, Mackessy SP, Castoe TA. Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom. Molecular Biology and Evolution. 32: 173-83. PMID 25338510 DOI: 10.1093/molbev/msu294  1
2015 Schield DR, Walsh MR, Card DC, Andrew AL, Adams RH, Castoe TA. EpiRADseq: Scalable analysis of genomewide patterns of methylation using next-generation sequencing Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.12435  1
2014 Li C, Zhang Y, Li J, Kong L, Hu H, Pan H, Xu L, Deng Y, Li Q, Jin L, Yu H, Chen Y, Liu B, Yang L, Liu S, ... ... Castoe TA, et al. Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience. 3: 27. PMID 25671092 DOI: 10.1186/2047-217X-3-27  1
2014 Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science (New York, N.Y.). 346: 1254449. PMID 25504731 DOI: 10.1126/science.1254449  1
2014 Card DC, Schield DR, Reyes-Velasco J, Fujita MK, Andrew AL, Oyler-McCance SJ, Fike JA, Tomback DF, Ruggiero RP, Castoe TA. Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies. Plos One. 9: e106649. PMID 25192061 DOI: 10.1371/journal.pone.0106649  1
2014 Gilbert C, Meik JM, Dashevsky D, Card DC, Castoe TA, Schaack S. Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes. Proceedings. Biological Sciences / the Royal Society. 281: 20141122. PMID 25080342 DOI: 10.1098/rspb.2014.1122  1
2014 Booth W, Schuett GW, Ridgway A, Buxton DW, Castoe TA, Bastone G, Bennett C, Mcmahan W. New insights on facultative parthenogenesis in pythons Biological Journal of the Linnean Society. 112: 461-468. DOI: 10.1111/bij.12286  1
2014 Castoe TA, De Koning APJ, 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, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes (Proceedings of the National Academy of Sciences of the United States of America (2013) 110, 51, (20645-20650) DOI: 10.1073/pnas. 1314475110) Proceedings of the National Academy of Sciences of the United States of America. 111: 3194. DOI: 10.1073/pnas.1324133111  1
2014 Fike JA, Oyler-McCance SJ, Zimmerman SJ, Castoe TA. Development of 13 microsatellites for Gunnison Sage-grouse (Centrocercus minimus) using next-generation shotgun sequencing and their utility in Greater Sage-grouse (Centrocercus urophasianus) Conservation Genetics Resources. 7: 211-214. DOI: 10.1007/s12686-014-0336-z  1
2013 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, et al. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences of the United States of America. 110: 20645-50. PMID 24297902 DOI: 10.1073/pnas.1314475110  1
2013 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, et al. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences of the United States of America. 110: 20651-6. PMID 24297900 DOI: 10.1073/pnas.1314702110  1
2013 Castoe TA, Pollock DD. Chinese alligator genome illustrates molecular adaptations. Cell Research. 23: 1254-5. PMID 24060849 DOI: 10.1038/cr.2013.134  1
2013 Reyes-Velasco J, Meik JM, Smith EN, Castoe TA. Phylogenetic relationships of the enigmatic longtailed rattlesnakes (Crotalus ericsmithi, C. lannomi, and C. stejnegeri). Molecular Phylogenetics and Evolution. 69: 524-34. PMID 23916566 DOI: 10.1016/j.ympev.2013.07.025  1
2013 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, ... ... Castoe TA, et al. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biology. 14: R28. PMID 23537068 DOI: 10.1186/gb-2013-14-3-r28  1
2013 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. Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica. Plos One. 8: e56283. PMID 23409165 DOI: 10.1371/journal.pone.0056283  1
2013 Oyler-McCance SJ, Fike JA, Castoe TA, Tomback DF, Wunder MB, Schaming TD. Development and characterization of thirteen microsatellite loci in Clark's nutcracker (Nucifraga columbiana) Conservation Genetics Resources. 5: 303-305. DOI: 10.1007/s12686-012-9789-0  1
2012 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, et al. Report from the first snake genomics and integrative biology meeting. Standards in Genomic Sciences. 7: 150-2. PMID 23451292 DOI: 10.4056/sigs.3106480  1
2012 de Koning AP, Gu W, Castoe TA, Pollock DD. Phylogenetics, likelihood, evolution and complexity. Bioinformatics (Oxford, England). 28: 2989-90. PMID 22976081 DOI: 10.1093/bioinformatics/bts555  1
2012 Lamers RP, Muthukrishnan G, Castoe TA, Tafur S, Cole AM, Parkinson CL. Phylogenetic relationships among Staphylococcus species and refinement of cluster groups based on multilocus data. Bmc Evolutionary Biology. 12: 171. PMID 22950675 DOI: 10.1186/1471-2148-12-171  1
2012 Castoe TA, Streicher JW, Meik JM, Ingrasci MJ, Poole AW, de Koning AP, Campbell JA, Parkinson CL, Smith EN, Pollock DD. Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species. Molecular Ecology Resources. 12: 1105-13. PMID 22938699 DOI: 10.1111/1755-0998.12000  1
2012 Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock DD, Höglund J. Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. Open Biology. 2: 120054. PMID 22724064 DOI: 10.1098/rsob.120054  1
2012 Castoe TA, Poole AW, de Koning AP, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD. Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. Plos One. 7: e30953. PMID 22348032 DOI: 10.1371/journal.pone.0030953  1
2012 Nakayama M, Castoe T, Sosinowski T, He X, Johnson K, Haskins K, Vignali DA, Gapin L, Pollock D, Eisenbarth GS. Germline TRAV5D-4 T-cell receptor sequence targets a primary insulin peptide of NOD mice. Diabetes. 61: 857-65. PMID 22315318 DOI: 10.2337/db11-1113  1
2012 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, et al. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biology. 13: 415. PMID 22293439 DOI: 10.1186/gb-2012-13-1-415  1
2012 Sun C, Shepard DB, Chong RA, López Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, Mueller RL. LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biology and Evolution. 4: 168-83. PMID 22200636 DOI: 10.1093/gbe/evr139  1
2012 Jadin RC, Townsend JH, Castoe TA, Campbell JA. Cryptic diversity in disjunct populations of Middle American Montane Pitvipers: A systematic reassessment of Cerrophidion godmani Zoologica Scripta. 41: 455-470. DOI: 10.1111/j.1463-6409.2012.00547.x  1
2011 de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD. Repetitive elements may comprise over two-thirds of the human genome. Plos Genetics. 7: e1002384. PMID 22144907 DOI: 10.1371/journal.pgen.1002384  1
2011 Pollock DD, de Koning AP, Kim H, Castoe TA, Churchill ME, Kechris KJ. Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions. Plos One. 6: e26105. PMID 22069446 DOI: 10.1371/journal.pone.0026105  1
2011 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, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature. 477: 587-91. PMID 21881562 DOI: 10.1038/nature10390  1
2011 Castoe TA, Fox SE, Jason de Koning A, Poole AW, Daza JM, Smith EN, Mockler TC, Secor SM, Pollock DD. A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus). Bmc Research Notes. 4: 310. PMID 21867488 DOI: 10.1186/1756-0500-4-310  1
2011 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, et al. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes. Genome Biology. 12: 406. PMID 21801464 DOI: 10.1186/gb-2011-12-7-406  1
2011 Castoe TA, Bronikowski AM, Brodie ED, Edwards SV, Pfrender ME, Shapiro MD, Pollock DD, Warren WC. A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Standards in Genomic Sciences. 4: 257-70. PMID 21677863 DOI: 10.4056/sigs.1664145  1
2011 Castoe TA, Hall KT, Guibotsy Mboulas ML, Gu W, de Koning AP, Fox SE, Poole AW, Vemulapalli V, Daza JM, Mockler T, Smith EN, Feschotte C, Pollock DD. Discovery of highly divergent repeat landscapes in snake genomes using high-throughput sequencing. Genome Biology and Evolution. 3: 641-53. PMID 21572095 DOI: 10.1093/gbe/evr043  1
2010 Castoe TA, Poole AW, Gu W, Jason de Koning AP, Daza JM, Smith EN, Pollock DD. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources. 10: 341-7. PMID 21565030 DOI: 10.1111/j.1755-0998.2009.02750.x  1
2010 Castoe TA, de Koning AP, Pollock DD. Adaptive molecular convergence: Molecular evolution versus molecular phylogenetics. Communicative & Integrative Biology. 3: 67-9. PMID 20539788  1
2010 Harris JK, Sahl JW, Castoe TA, Wagner BD, Pollock DD, Spear JR. Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing. Applied and Environmental Microbiology. 76: 3863-8. PMID 20418443 DOI: 10.1128/AEM.02585-09  1
2010 Castoe TA, de Koning APJ, Pollock DD. Adaptive molecular convergence: Molecular evolution versus molecular phylogenetics Communicative and Integrative Biology. 3: 12-17. DOI: 10.4161/cib.3.1.9793  1
2010 Daza JM, Castoe TA, Parkinson CL. Using regional comparative phylogeographic data from snake lineages to infer historical processes in Middle America Ecography. 33: 343-354. DOI: 10.1111/j.1600-0587.2010.06281.x  1
2010 Castoe TA, de Koning APJ, Pollock DD. Molecular Structure and Evolution of Genomes Evolutionary Genomics and Systems Biology. 183-202. DOI: 10.1002/9780470570418.ch10  1
2009 Castoe TA, Gu W, de Koning AP, Daza JM, Jiang ZJ, Parkinson CL, Pollock DD. Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes. Cytogenetic and Genome Research. 127: 112-27. PMID 20215734 DOI: 10.1159/000295342  1
2009 Castoe TA, de Koning AP, Kim HM, Gu W, Noonan BP, Naylor G, Jiang ZJ, Parkinson CL, Pollock DD. Evidence for an ancient adaptive episode of convergent molecular evolution. Proceedings of the National Academy of Sciences of the United States of America. 106: 8986-91. PMID 19416880 DOI: 10.1073/pnas.0900233106  1
2009 Castoe TA, Daza JM, Smith EN, Sasa MM, Kuch U, Campbell JA, Chippindale PT, Parkinson CL. Comparative phylogeography of pitvipers suggests a consensus of ancient Middle American highland biogeography Journal of Biogeography. 36: 88-103. DOI: 10.1111/j.1365-2699.2008.01991.x  1
2009 Tonsmann G, Pollock DD, Gu W, Castoe TA. Identifying DNA strands using a kernel of classified sequences 2009 Wri World Congress On Computer Science and Information Engineering, Csie 2009. 3: 703-707. DOI: 10.1109/CSIE.2009.506  1
2008 Gu W, Castoe TA, Hedges DJ, Batzer MA, Pollock DD. Identification of repeat structure in large genomes using repeat probability clouds. Analytical Biochemistry. 380: 77-83. PMID 18541131 DOI: 10.1016/j.ab.2008.05.015  1
2008 Castoe TA, Jiang ZJ, Gu W, Wang ZO, Pollock DD. Adaptive evolution and functional redesign of core metabolic proteins in snakes. Plos One. 3: e2201. PMID 18493604 DOI: 10.1371/journal.pone.0002201  1
2007 Jiang ZJ, Castoe TA, Austin CC, Burbrink FT, Herron MD, McGuire JA, Parkinson CL, Pollock DD. Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region. Bmc Evolutionary Biology. 7: 123. PMID 17655768 DOI: 10.1186/1471-2148-7-123  1
2007 Castoe TA, Stephens T, Noonan BP, Calestani C. A novel group of type I polyketide synthases (PKS) in animals and the complex phylogenomics of PKSs. Gene. 392: 47-58. PMID 17207587 DOI: 10.1016/j.gene.2006.11.005  1
2007 Castoe TA, Spencer CL, Parkinson CL. Phylogeographic structure and historical demography of the western diamondback rattlesnake (Crotalus atrox): A perspective on North American desert biogeography. Molecular Phylogenetics and Evolution. 42: 193-212. PMID 16934495 DOI: 10.1016/j.ympev.2006.07.002  1
2007 Castoe TA, Smith EN, Brown RM, Parkinson CL. Higher-level phylogeny of Asian and American coralsnakes, their placement within the Elapidae (Squamata), and the systematic affinities of the enigmatic Asian coralsnake Hemibungarus calligaster (Wiegmann, 1834) Zoological Journal of the Linnean Society. 151: 809-831. DOI: 10.1111/j.1096-3642.2007.00350.x  1
2006 Castoe TA, Parkinson CL. Bayesian mixed models and the phylogeny of pitvipers (Viperidae: Serpentes). Molecular Phylogenetics and Evolution. 39: 91-110. PMID 16504544 DOI: 10.1016/j.ympev.2005.12.014  1
2005 Castoe TA, Sasa MM, Parkinson CL. Modeling nucleotide evolution at the mesoscale: the phylogeny of the neotropical pitvipers of the Porthidium group (viperidae: crotalinae). Molecular Phylogenetics and Evolution. 37: 881-98. PMID 16024260 DOI: 10.1016/j.ympev.2005.05.013  1
2005 Doan TM, Castoe TA, Arriaga WA. Phylogenetic relationships of the genus Proctoporus sensu stricto (Squamata: Gymnophthalmidae), with a new species from Puno, southeastern Peru Herpetologica. 61: 325-336. DOI: 10.1655/04-81.1  1
2005 Doan TM, Castoe TA. Phylogenetic taxonomy of the Cercosaurini (Squamata: Gymnophthalmidae), with new genera for species of Neusticurus and Proctoporus Zoological Journal of the Linnean Society. 143: 405-416. DOI: 10.1111/j.1096-3642.2005.00145.x  1
2005 Reece JS, Castoe TA, Parkinson CL. Historical perspectives on population genetics and conservation of three marine turtle species Conservation Genetics. 6: 235-251. DOI: 10.1007/s10592-004-7821-y  1
2005 Mulvaney A, Castoe TA, Ashton KG, Krysko KL, Parkinson CL. Evidence of population genetic structure within the Florida Worm Lizard, Rhineura floridana (Amphisbaenia: Rhineuridae) Journal of Herpetology. 39: 118-124.  1
2004 Castoe TA, Doan TM, Parkinson CL. Data partitions and complex models in Bayesian analysis: the phylogeny of Gymnophthalmid lizards. Systematic Biology. 53: 448-69. PMID 15503673 DOI: 10.1080/10635150490445797  1
2004 Herron MD, Castoe TA, Parkinson CL. Sciurid phylogeny and the paraphyly of Holarctic ground squirrels (Spermophilus). Molecular Phylogenetics and Evolution. 31: 1015-30. PMID 15120398 DOI: 10.1016/j.ympev.2003.09.015  1
2003 Schargel WE, Castoe TA. The Hemipenes of Some Snakes of the Semifossorial Genus Atractus, with Comments on Variation in the Genus Journal of Herpetology. 37: 718-721.  1
2003 Doan TM, Castoe TA. Using morphological and molecular evidence to infer species boundaries within Proctoporus bolivianus Werner (Squamata: Gymnophthalmidae) Herpetologica. 59: 432-449.  1
2003 Castoe TA, Chippindale PT, Campbell JA, Ammerman LK, Parkinson CL. Molecular systematics of the middle American jumping pitvipers (Genus atropoides) and phylogeography of the Atropoides nummifer complex Herpetologica. 59: 420-431.  1
2002 Castoe TA. Microhabitat selection in Porthidium nasutum (Serpentes: Viperidae) in Costa Rica, with comments on ontogenetic variation Herpetological Review. 33: 174-175.  1
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