Publications

Mincarone MM, Plachetzki DC, McCord CL, Winegard TM, Fernholm B, Gonzalez CJ, Fudge DS. Review of the hagfishes (Myxinidae) from the Galapagos Islands, with descriptions of four new species and their phylogenetic relationships. Zoological Journal of the Linnean Society. 2021 Feb 1.

Plachetzki DC, Pankey MS, MacManes MD, Lesser MP, Walker CW. The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis. Genome Biol Evol. 2020;12(10):1681-1693. doi:10.1093/gbe/evaa143

Spillane JL, LaPolice TM, MacManes MD, Plachetzki DC. Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference. bioRxiv. 2020 Jan 1. doi: https://doi.org/10.1101/2020.07.23.216606

Wang X, Plachetzki DC, Cote RH. The N termini of the inhibitory γ-subunits of phosphodiesterase-6 (PDE6) from rod and cone photoreceptors differentially regulate transducin-mediated PDE6 activation. Journal of Biological Chemistry. 2019 May 24;294(21):8351-60.

Bernards, MA, Schorno, S, McKenzie, E, Winegard, TE, Oke, I, Plachetzki, DC, and DS Fudge. Unraveling skein deployment in hagfish slime: Insights from transcriptomics and in vitro assays Journal of Experimental Biology (in press)

Mahato, S, Nie, J, Plachetzki, DC, and AC Zelhof. A mosaic of independent innovations involving eyes shut are critical for the evolutionary transition from fused to open rhabdoms . Developmental Biology 443:2, 188-202

Kayal, E, Bentlage, B, Pankey, MS, Ohdera, A, Medina, M, Plachetzki DC, Collins AG, and JF Ryan. Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. BMC Evolutionary Biology 18:68

Hausken, KN, Tizon, B, Shpilman, M, Barton, S, Decatur, W, Plachetzki DC, Kavanaugh, S, Ul-Hasan, S, Levavi-Sivan, B, and SA Sower. Cloning and characterization of a second lamprey pituitary glycoprotein hormone, thyrostimulin (GpA2/GpB5). General and Comparative Endocrinology 1:264,16-27

Zelhof, A, Mahato, S, Nie, J, Plachetzki, DC. A mosaic of independent innovations involving eyes shut are critical for the evolutionary transition from closed to open rhabdoms . bioRxiv

Schuelke, TA, Wu, G, Westbrook, A, Woeste K, DC Plachetzki, Broders, K, and MD MacManes. Comparative genomics of pathogenic and non-pathogenic beetle-vectored fungi in the genus Geosmithia. Genome Biology and Evolution. Volume 9, Issue 12, 1

Kayal E, Bastian B, Pankey MS, Ohdera A, Medina M, Plachetzki DC, Collins A, and JF Ryan JF. Comprehensive phylogenomic analyses resolve cnidarian relationships and the origins of key organismal traits. PeerJ Preprints

Kelly, M, Pankey, MS, DeBiasse, M, and Plachetzki DC. Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod. Functional Ecology Volume 31, 2

Plachetzki, DC, Tsai, PS, Kavanaugh, SI, and SA Sower. Ancient origins of metazoan gonadotropin-releasing hormone and their receptors revealed by phylogenomic analyses. General and Comparative Endocrinology Volume 234, 1 August

Kim, JW, Yang, HJ, Oel, AP, Brooks, MJ, Jia, L, Plachetzki DC, Li, W, Allison, WT, and A Swaroop. Recruitment of rod photoreceptors from short wavelength sensitive cones during the evolution of nocturnal vision in mammals. Developmental Cell Volume 37, Issue 6, p520–532, 20 June 2016

Schuelke, TA, Westbrook, A, Woeste, K, Plachetzki, DC, Broders, K, and M MacManes. Comparative genomics of beetle-vectored fungal pathogens reveals a reduction in genome size and independent evolution of pathogenicity of two tree pathogens bioRxiv

Borowiec, ML, Kee, EK, Chiu, JC, and Plachetzki DC. Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC Genomics DOI: 10.1186/s12864-015-2146-4

Borowiec, ML, Lee, EK, Chiu, JC, and DC Plachetzki. Dissecting phylogenetic signal and accounting for bias in whole-genome data sets: a case study of the Metazoa bioRxiv

Thomson, RC, Plachetzki, DC, Mahler, DL, and BR Moore. A critical appraisal of the use of microRNA data in phylogenetics. Proceedings of the National Academey of Sciences U S A. doi: 10.1073/pnas.1407207111

Chen, ZX, Sturgill, D, Qu, J, Jiang, H, Park, S, Boley, N, Suzuki, AM, Fletcher, AR, Plachetzki, DC, FitzGerald, PC, Artieri, CG, Atallah, J, Barmina, O, Brown, JB, Blankenburg, KP, Clough, E, Dasgupta, A, Gubbala, S, Han, Y, Jayaseelan, JC, Kalra, D, Kim, YA, Kovar, CL, Lee, SL, Li, M, Malley, JD, Malone, JH, Mathew, T, Mattiuzzo, NR, Munidasa, M, Muzny, DM, Ongeri, F, Perales, L, Przytycka, TM, Pu, LL, Robinson, G, Thornton, RL, Saada, N, Scherer, SE, Smith, HE, Vinson, C, Warner, CB, Worley, KC, Wu, YQ, Zou, X, Cherbas, P, Kellis, M, Eisen, MB, Piano, F, Kionte, K, Fitch, DH, Sternberg, PW, Cutter, AD, Duff, MO, Hoskins, RA, Graveley, BR, Gibbs, RA, Bickel, PJ, Kopp, A, Carninci, P, Celniker, SE, Oliver, B, and S Richards. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research 24: 1209-1223. doi: 10.1101/gr.159384.113

Plachetzki, DC, Pankey, MS, Johnson, BR, Ronne, EJ, Kopp A, and RK Grosberg. Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan, Hydractinia symbiolongicarpus. Integrative and Comparative Biology DOI: 10.1093/icb/icu080.

Wexler, JR, Plachetzki, DC, and A Kopp. Pan-metazoan phylogeny of the DMRT gene family: a framework for functional studies. Development Genes and Evolution 224 (3): 175-81. DOI 10.1007/s00427-014-0473-0

Plachetzki, DC, Pankey, MS, Johnson, BR, Ronne, EJ, Kopp, A, and RK Grosberg. Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan, Hydractinia symbiolongicarpus. bioRxiv

Thomson, R, Plachetzki, DC, Mahler, L, and B Moore. Estimating Phylogeny from microRNA Data: A Critical Appraisal. bioRxiv

Atallah, J, Plachetzki, DC, Jasper, WC, and BR Johnson. The Utility of Shallow RNA-Seq for Documenting Differential Gene Expression in Genes with High and Low Levels of Expression. PloS one, 10.1371/journal.pone.0084160

Johnson, BR, Atallah, J, and DC Plachetzki. The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions. BMC genomics 14 (1), 586

Heyland, A, Plachetzki, DC, O’Donnely, E, Bobkova, Y, and LL Moroz. Distinct expression patterns of glycoprotein hormone subunits in the lophotrochozoan Aplysia: implications for the evolution of neuroendocrine systems in animals. Endocrinology, Sep 13.

Plachetzki, DC, Fong, CR and TH Oakley. Cnidocyte discharge is attenuatedby light and opsin-mediated phototransduction. BMC Biology, 10(1):17.(with great commentary by Thomas Holstein; highly accessed)

Rivera, AS, Ozturk, N, Fahey, B, Plachetzki, DC, Degnan, BM, Sancar, A, and TH Oakley. Blue light-receptive Cryptochrome is expressed in a sponge eye lacking neurons and opsin. Journal of Experimental Biology 215:1278-1286 (with cover and commentary)

Srivastava, M, Simakov, O, Chapman, J, Fahey, B, Gauthier, ME, Mitros, T, Richards, GS, Conaco, C, Dacre, M, Hellsten, U, Larroux, C, Putnam, NH, Stanke, M, Adamska, M, Darling, A, Degnan, SM, Oakley, TH, Plachetzki, DC, Zhai, Y, Adamski, M, Calcino, A, Cummins, SF, Goodstein, DM, Harris, C, Jackson, DJ, Leys, SP, Shu, S, Woodcroft, BJ, Vervoort, M, Kosik, KS, Manning, G, Degnan, BM, and DS Rokhsar. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466, 720-6

Plachetzki, DC, Fong, CR, and TH Oakley. The evolution of phototransduction from an ancestral cyclic nucleotide gated pathway. Proceedings of the Royal Society B.

Rivera, AS, Pankey, MS, Plachetzki, DC, Villacorta, C, Syme, AE, Serb, JM, Omilian, AR, and TH and Oakley. Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. BMC Evolutionary Biology 10, 123 (highly accesed)

Grosberg, R, and Plachetzki, DC. Marine Invertebrates: Genetics of Colony Recognition. In Encyclopedia of Animal Behavior, vol. 2 (ed. M. D. Breed and J Moore), pp. 381-388. Oxford: Academic Press

Oakley, TH, and DC Plachetzki. Key transitions during animal phototransduction evolution: co-duplication as a null hypothesis for the evolutionary origins of novel traits. In Key Transitions in Animal Evolution (ed. R. Desalle and B. Shierwater), pp. 340. New York: CRC Press

Oakley, TH, and DC Plachetzki. The evolution of opsins. In: Encyclopedia of the Eye. In, Barbara Batelle Ed. Elsevier.

Blackburn, DC, Conley, KW, Plachetzki, DC, Kempler, K, Battelle, BA, and NL Brown. Isolation and expression of Pax6 and atonal homologues in the American horseshoe crab, Limulus polyphemus. Developmental Dynamics 237, 2209-19. (with cover)

Oakley, TH, Plachetzki, DC and AS Rivera. Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors. Arthropod Structure and Development 36, 386-400.

Plachetzki, DC and TH Oakley. Key transitions during animal phototransduction evolution: Novelty, tree thinking, co-option and co-duplication. Integrative and Comparative Biology, doi:10.1093/icb/icm050

Plachetzki, DC, Degnan, BM, and TH Oakley. The origins of novel protein interactions during animal opsin evolution. PLoS One 2, e1054. (highly accessed)

Harzsch, S, Diploma, K, Plachetzki, DC, Brown, N, Melzer, R, Kempler, and B Battelle. Evolution of arthropod visual systems: development of the eyes and central visual pathways in the horseshoe crab Limulus polyphemus Linnaeus, 1758 (Chelicerata, Xiphosura). Developmental Dynamics 20;235(10):2641-2655.

Plachetzki, DC, Serb, JM, and TH Oakley. New insights into the evolutionary history of photoreceptor cells. Trends in Ecology and Evolution 20, 465-7.

Szuchet, S, Plachetzki, DC, Seeger, MA, Domowicz, MS, and FGSzele. NOVOcan: a molecular link among selected glial cells. Biophysical Chemistry 108, 245-58.

Szuchet, S, Plachetzki, DC and R. Karialukas. Oligodendrocytes express an alpha/beta-interferon-susceptible Mx gene: molecular characterization of the encoded protein. Glia 37, 183-9.

Szuchet, S, Plachetzki, DC and KS Eaton. Oligodendrocyte transmembrane protein: a novel member of the glutamate-binding protein subfamily. Biochemical and Biophysical Research Commununications 283, 900-7.