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2023

  • Perry, B.W., A.L. McDonald, S. Trojahn, M.W. Saxton, E.P. Vincent, C. Lowry, B.D. Evans Hutzenbiler, O.E. Cornejo, C.T. Robbins, H.T. Jansen, and J.L. Kelley. 2023. Feeding during hibernation shifts gene expression toward active season levels in brown bears (Ursus arctos). Physiological Genomics. 55:9, 368-380. doi.org/10.1152/physiolgenomics.00030.2023. PDF.

  • Perry, B.W., M.W. Saxton, H.T. Jansen, C.R. Quackenbush, B.D. Evans Hutzenbiler, C.T. Robbins, J.L. Kelley, and O.E. Cornejo. 2023. A multi‐tissue gene expression dataset for hibernating brown bears. BMC Genomic Data. 24, 33. doi.org/10.1186/s12863-023-01136-3

  • Smith, C.F., Z.L. Nikolakis, B.W. Perry, D.R. Schield, J.M. Meik, A.J. Saviola, T.A. Castoe, J. Parker, & S.P. Mackessy. 2023. The best of both worlds? Rattlesnake hybrid zones generate complex combinations of divergent venom phenotypes that retain high toxicity. Biochimie. 213, 176-189. doi.org/10.1016/j.biochi.2023.07.008

  • Westfall, A.K., S.S. Gopalan, B.W. Perry, R.H. Adams, A.J. Saviola, S.P. Mackessy, & T.A. Castoe. 2023. Single‐cell heterogeneity in snake venom expression is hardwired by co‐option of regulators from progressively activated pathways. Genome Biology and Evolution. 15:6.  doi.org/10.1093/gbe/evad109

  • Smith, C.F., Z.L. Nikolakis, B.W. Perry, D.R. Schield, N.R. Balchan, J. Parker, K. Ivey, K.C. Hansen, A.J. Saviola, T.A. Castoe, & S.P. Mackessy. 2023. Snakes on a plain: Biotic and abiotic factors determine venom compositional variation in a wide‐ranging generalist rattlesnake. BMC Biology. 21:136. doi.org/10.1186/s12915‐023‐01626‐x

2022

  • Saxton, M.W.*, B.W. Perry*, B.D. Evans Hutzenbiler, S. Trojahn, A. Gee, A.P. Brown, G.E. Merrihew, J. Park, O.E. Cornejo, M.J. MacCoss, C.T. Robbins, H.T. Jansen, and J.L. Kelley. 2022. Serum plays an important role in reprogramming the seasonal transcriptional profile of brown bear adipocytes. iScience. doi.org/10.1016/j.isci.2022.105084 [Press Release]
    *Co-first authors

  • Perry, B.W., E.E. Armstrong, C.T. Robbins, H.T. Jansen, and J.L. Kelley. 2022. Temporal analysis of gene expression and isoform switching in brown bears (Ursus arctos). Integrative and Comparative Biology. doi.org/10.1093/icb/icac093

  • Perry, B.W., S.S. Gopalan, G.I.M. Pasquesi, D.R. Schield, A.K. Westfall, C. Smith, I. Koludarov, P.T. Chippindale, M.W. Pellegrino, E.B. Choung, S.P. Mackessy, and T.A. Castoe. 2022. Snake venom expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways. Genome Research. doi/10.1101/gr.276251.121 [Press Release]

  • Nikolakis, Z.L., D.R. Schield, A.K. Westfall, B.W. Perry, K.N. Ivey, R.W. Orton, N.R. Hales, R.H. Adams, J.M. Meik, J. Parker, C.F. Smith, Z. Gompert, S.P. Mackessy, and T.A. Castoe. 2022. Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone. Evolution. doi.org/10.1111/evo.14612
  • Armstrong, E.E., B.W. Perry, Y. Huang, K.V. Garimella, H.T. Jansen, C.T. Robbins, N.R. Tucker, and J.L. Kelley. 2022. A beary good genome: Haplotype-resolved, chromosome-level assembly of the brown bear (Ursus arctos). Genome Biology and Evolution. doi.org/10.1093/gbe/evac125
  • Schield, D.R., B.W. Perry, D.C. Card, G.I.M. Pasquesi, A.K. Westfall, S.P. Mackessy, and T.A. Castoe. 2022. The rattlesnake W chromosome: A GC-rich retroelement refugium with retained gene function across ancient evolutionary strata. Genome Biology and Evolution. doi:10.1093/gbe/evac116
  • Schield, D.R., B.W. Perry, R.H. Adams, M.L. Holding, Z.L. Nikolakis, S.S. Gopalan, C.F. Smith, J.M. Parker, J.M. Meik, S.P. Mackessy, and T.A. Castoe. 2022. The roles of balancing selection and recombination in the evolution of rattlesnake venom. Nature Ecology and Evolution. doi.org/10.1038/s41559-022-01829-5

  • Gopalan, S.S., B.W. Perry, D.R. Schield, C. Smith, S.P. Mackessy, and T.A. Castoe. 2022. Origins, genomic structure, and copy number variation of snake venom myotoxins. Toxicon. doi.org/10.1016/j.toxicon.2022.06.014

  • Lund, A.J., K.J. Wade, Z.L. Nikolakis, K. Ivey, B.W. Perry, H. Pike, S.H. Paul, T.A. Castoe, D.D. Pollock, E.J. Carlton. 2022. Integrating genomic and epidemiologic data to accelerate progress towards schistosomiasis elimination. eLife. doi.org/10.7554/eLife.79320

  • Westfall, A.K., B.W. Perry, A.H.M. Kamal, N.R. Hales, J.C. Kay, M. Sapkota, D.R. Schield, M.W. Pellegrino, S.M. Secor, S.M. Chowdhury, & T.A. Castoe. 2022. Identification of an integrated stress and growth response signaling switch that directs vertebrate intestinal regeneration. BMC Genomics. doi.org/10.1186/s12864-021-08226-5

2021

  • Schort, J.A., L.E. Timm, N.R. Hales, Z.L. Nikolakis, D.R. Schield, B.W. Perry, Y. Liu, B. Zhong, T.A. Castoe, E.J. Carlton, & D.D. Pollock. 2021. Population genomic analyses of schistosome parasites highlights critical challenges facing end-game elimination efforts. Scientific Reports. doi.org/10.1038/s41598-021-86287-y

  • Schield, D.R., B.W. Perry, Z.L. Nikolakis, S.P. Mackessy, and T.A. Castoe. 2021. Population genomic analyses confirm male-biased mutation rates in snakes. Journal of Heredity. doi:10.1093/jhered/esab005

  • Nikolakis, Z.L., N.R. Hales, B.W. Perry, D.R. Schield, L.E. Timm, Y. Liu, B. Zhong, K.J. Kechris, E.J. Carlton, D.D. Pollock, and T.A. Castoe. 2021. Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum). PLOS Neglected Tropical Diseases. doi.org/10.1371/journal.pntd.0009020

2020

  • Perry, B.W., D.R. Schield, A.K. Westfall, S.P. Mackessy, & T.A. Castoe. 2020. Physiological demands and signaling associated with snake venom production and storage illustrated by transcriptional analyses of venom glands. Scientific Reports. doi.org/10.1038/s41598-020-75048-y.

  • Perry, B.W., D.R. Schield, R.H. Adams, & T.A. Castoe. 2020. Microchromosomes exhibit distinct features of vertebrate chromosome structure and function with underappreciated ramifications for genome evolution. Molecular Biology and Evolution. doi.org/10.1093/molbev/msaa253

  • Boni, M.F, P. Lemey, X. Jiang, T.T. Lam, B.W. Perry, T.A. Castoe, A. Rambaut, & D.L. Robertson. 2020. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. Nature Microbiology. doi.org/10.1038/s41564-020-0771-4.

  • Pollock, D.D., T.A. Castoe, B.W. Perry, S. Lytras, K. Wade, D.L. Robertson, E.C. Holmes, M.F. Boni, S.L. Kosakovsky Pond, R. Parry, E.J. Carlton, J. Wood, P.S. Pennings, & R.A. Goldstein. 2020. Viral CpG deficiency provides no evidence that dogs were intermediate hosts for SARS-CoV-2. Molecular Biology and Evolution. doi:10.1093/molbev/msaa178.

  • Kazi, M.I., B.W. Perry, D.C. Card, R.D. Schargel, H.B. Ali, V.C. Obuekwe, M. Sapkota, K.N. Kang, M.W. Pellegrino, D.E. Greenberg, T.A. Castoe, & J.M. Boll. 2020. Discovery and characterization of New Delhi metallo-β-lactamase-1 inhibitor peptides that potentiate meropenem-dependent killing of carbapenemase-producing Enterobacteriaceae. Journal of Antimicrobial Chemotherapy. doi.org/10.1093/jac/dkaa242.

  • Pasquesi, G.I.M., B.W. Perry, R.P. Ruggiero, M.W. Vandewege, D.R. Schield, and T.A. Castoe. 2020. Vertebrate lineages exhibit diverse patterns of transposable element regulation and expression across tissues. Genome Biology and Evolution. 12:506-521.

  • Schield, D.R., G.I.M. Pasquesi, B.W. Perry, R.H. Adams, Z.L. Nikolakis, A.K. Westfall, R.W. Orton, J.M. Meik, S.P. Mackessy, and T.A. Castoe. 2020. Snake recombination landscapes are concentrated in functional regions despite PRDM9. Molecular Biology and Evolution. doi: 10.1093/molbev/msaa003.

  • Schield, D.R., B.W. Perry, G.I.M. Pasquesi, R.W. Orton, Z.L. Nikolakis, A.K. Westfall, and T.A. Castoe. Applications of genomics and related technologies for studying reptile venoms. In press. Handbook of Venoms and Toxins of Reptiles, Second Edition.

 

2019

  • Card, D.C., R.H. Adams, D.R. Schield, B.W. Perry, A.B. Corbin, G.I.M. Pasquesi, K. Row, J. Daza, W. Booth, C. Montgomery, S. Boback, T.A. Castoe. 2019. Genomic basis of convergent island phenotypes in boa constrictors. Genome Biology and Evolution. 11:3123-3143.

  • Perry, B.W., A.L. Andrew, A.H.M. Kamal, D.C. Card, D.R. Schield, G.I.M. Pasquesi, M.W Pellegrino, S.P. Mackessy, S.M. Chowdhury, S.M. Secor, and T.A. Castoe. 2019. Multi-species transcriptomic and proteomic analyses identify mechanisms underlying regenerative intestinal growth following feeding in snakes. Proceedings of the Royal Society of London B. 286:20190910.

  • Schield, D.R.*, B. W. Perry*, R. H. Adams, D. C. Card, T. Jezkova, G. I.M. Pasquesi, Z. L. Nikolakis, K. Row, J. M. Meik, C. F. Smith, S. P. Mackessy, and T. A. Castoe. 2019. Allopatric divergence and secondary contact with gene flow – a recurring theme in rattlesnake speciation. Biological Journal of the Linnean Society. 128:149-169.
    (*Co-first authors)

  • Schield, D.R., D.C. Card, N.M. Hales, B.W. Perry, G.I.M. Pasquesi, H. Blackmon, R.H. Adams, A.B. Corbin, C.F. Smith, B. Ramesh, J.P. Demuth, E. Betran, M. Tollis, J.M. Meik, S.P. Mackessy and T.A. Castoe. 2019. The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Genome Research. 29:590-601.

 

2018

  • Card, D.C, B.W. Perry, R.H. Adams, D.R. Schield, A. Young, A.L. Andrew, T. Jezkova, G.I.M. Pasquesi, N.R. Hales, M. Walsh, M. Rochford, F. Mazzotti, K. Hart, M. Hunter, T.A. Castoe. 2018. Genomic adaptation of invasive Florida Burmese pythons to increased prey availability and thermal stress. Molecular Ecology. 27:4744-4757.

  • Perry, B.W., D.R. Schield, T.A. Castoe. 2018. Evolution: Plasticity versus selection, or plasticity and selection? Invited Dispatch article at Current Biology. 28:R1104-R1106.

  • Perry, B.W., D.C. Card, J.W. McGlothlin, G.I.M. Pasquesi, R.H. Adams, D.R. Schield, N.R. Hales, A.B. Corbin, J.P. Demuth, F.G. Hoffmann, M.W. Vandewege, R. Schott, N. Bhattacharyya, B.S.W. Chang, N.R. Casewell, G. Whiteley, J. Reyes-Velasco, S.P. Mackessy, K.B. Storey, K.K. Biggar, C.N. Passow, C. Kuo, S.E. McGaugh, A.M. Bronikowski, J. de Koning, S.V. Edwards, M.E. Pfrender, P. Minx, E.D. Brodie III, E.D. Brodie, Jr., W.C. Warren, T.A. Castoe. 2018. Molecular adaptations for sensing and securing prey and insight into amniote genome diversity from the garter snake genome. Genome Biology and Evolution. 10:2110-2129.

  • Schield, D.R., D.C. Card, R.H. Adams, A.B. Corbin, T. Jezkova, N.R. Hales, J.M. Meik, B.W. Perry, C.L. Spencer, L.L. Smith, G.C. Garcia, N.M. Bouzid, J.L. Strickland, C.L. Parkinson, M. Borja-Jimenez, C. Castaneda-Gaytan, R.W. Bryson, O.A. Flores-Villela, S.P. Mackessy, T.A. Castoe. 2018. Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus). Molecular Phylogenetics and Evolution. 127:669-681.

  • Pasquesi, G.I.M., R.H. Adams, D.C. Card, D.R. Schield, B.W. Perry, A.B. Corbin, J. Reyes-Velasco, R.P. Ruggiero, M.W. Vandewege, T.A. Castoe. 2018. Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Nature Communications. 9:2774.

 

2017

  • Schield, D.R., R.H. Adams, D.C. Card, B.W. Perry, G.M. Pasquesi, T. Jezkova, D.M. Portik, A.L. Andrew, C.L. Spencer, E.E. Sanchez, M.K. Fujita, S.P. Mackessy, T.A. Castoe. 2017. 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.

  • Andrew, A.L.*, B.W. Perry*, D.C. Card, D.R. Schield, R.P. Ruggiero, S.E. McGaugh, A. Choudhary, S.M. Secor, T.A. Castoe. 2017. Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python. BMC Genomics. 18:338.
    (*Co-first authors)

2016

  • Card, D.C., D.R. Schield, R.H. Adams, A.B. Corbin, B.W. Perry, A.L. Andrew, G. Pasquesi, E.N. Smith, T. Jezkova, S.M. Boback, W. Booth, T.A. Castoe. 2016. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism. Molecular Phylogenetics and Evolution. 102:104-116.

  • Pomento, A.M*, Perry, B.W.*, R.D. Denton, H.L. Gibbs, M.L. Holding. 2016. No safety in the trees: Evidence of local and lineage-level adaptation of the Eastern gray squirrel (Sciurus carolinensis) to resisting venom of sympatric rattlesnakes. Toxicon. 18:149-155.
    (*Co-first authors)