Spillane JL, LaPolice TM, MacManes MD, Plachetzki DC. Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference. BMC ecology and evolution. 2021 Dec;21(1):1-7.

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 Jun;192(2):453-74.

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.

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,, Fudge DS. Unraveling inter-species differences in hagfish slime skein deployment Journal of Experimental Biology. 2018 Dec 15;221(24).

Mahato S, Nie J, Plachetzki DC, Zelhof AC. A mosaic of independent innovations involving eyes shut are critical for the evolutionary transition from fused to open rhabdoms . Developmental Biology. 2018 Nov 15;443(2):188-202.

Kayal E, Bentlage B, Pankey MS, Ohdera A, Medina M, Plachetzki DC, Collins AG, and Ryan JF. Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits. BMC Evolutionary Biology. 2018 Dec;18(1):1-8.

Hausken KN, Tizon B, Shpilman M, Barton S, Decatur W, Plachetzki DC, Kavanaugh S, Ul-Hasan S, Levavi-Sivan B, Sower SA. Cloning and characterization of a second lamprey pituitary glycoprotein hormone, thyrostimulin (GpA2/GpB5). General and Comparative Endocrinology. 2018 Aug 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, Plachetzki DC, Broders K, MacManes MD. Comparative genomics of pathogenic and non-pathogenic beetle-vectored fungi in the genus Geosmithia. Genome Biology and Evolution. 2017 Dec;9(12):3312-27.

Kayal E, Bastian B, Pankey MS, Ohdera A, Medina M, Plachetzki DC, Collins A, Ryan JF. Comprehensive phylogenomic analyses resolve cnidarian relationships and the origins of key organismal traits. PeerJ Preprints. 2017 Aug 21.

Kelly M, Pankey MS, DeBiasse M, Plachetzki DC. Adaptation to heat stress reduces phenotypic and transcriptional plasticity in a marine copepod. Functional Ecology. 2017 Feb;31(2):398-406.

Plachetzki DC, Tsai PS, Kavanaugh SI, Sower SA. 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, Swaroop A. Recruitment of rod photoreceptors from short wavelength sensitive cones during the evolution of nocturnal vision in mammals. Developmental Cell. 2016 Jun 20;37(6):520-32.

Schuelke TA, Westbrook A, Woeste K, Plachetzki DC, Broders K, MacManes M. Comparative genomics of beetle-vectored fungal pathogens reveals a reduction in genome size and independent evolution of pathogenicity of two tree pathogens bioRxiv. 2016 Jan 1:093856.

Borowiec ML, Kee EK, Chiu JC, Plachetzki DC. Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC Genomics. 2015 Dec;16(1):1-5.

Borowiec ML, Lee EK, Chiu JC, Plachetzki DC. 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, Moore BR. A critical appraisal of the use of microRNA data in phylogenetics. Proceedings of the National Academey of Sciences. 2014 Sep 2;111(35):E3659-68.

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, Richards S. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research. 2014 Jul 1;24(7):1209-23.

Plachetzki DC, Pankey MS, Johnson BR, Ronne EJ, Kopp A, Grosberg RK. Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan, Hydractinia symbiolongicarpus. Integrative and Comparative Biology 2014 Jun 15;54(2):276-83.

Wexler JR, Plachetzki DC, Kopp A. Pan-metazoan phylogeny of the DMRT gene family: a framework for functional studies. Development Genes and Evolution. 2014 May 1;224(3):175-81.

Atallah J, Plachetzki DC, Jasper WC, Johnson BR. The Utility of Shallow RNA-Seq for Documenting Differential Gene Expression in Genes with High and Low Levels of Expression. PloS one. 2013 Dec 16;8(12):e84160

Johnson BR, Atallah J, Plachetzki DC. The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions. BMC genomics. 2013 Dec;14(1):1-8.

Heyland A, Plachetzki DC, O’Donnely E, Bobkova Y, Moroz LL. Distinct expression patterns of glycoprotein hormone subunits in the lophotrochozoan Aplysia: implications for the evolution of neuroendocrine systems in animals. Endocrinology. 2012 Nov 1;153(11):5440-51.

Plachetzki DC, Fong CR, Oakley TH. Cnidocyte discharge is attenuatedby light and opsin-mediated phototransduction. BMC Biology. 2012 Dec;10(1):1-0.(with great commentary by Thomas Holstein; highly accessed)

Rivera AS, Ozturk N, Fahey B, Plachetzki DC, Degnan BM, Sancar A, Oakley TH. Blue light-receptive Cryptochrome is expressed in a sponge eye lacking neurons and opsin. Journal of Experimental Biology. 2012 Apr 15;215(8):1278-86. (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, Rokhsar DS. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature. 2010 Aug;466(7307):720-6.

Plachetzki DC, Fong CR, Oakley TH. The evolution of phototransduction from an ancestral cyclic nucleotide gated pathway. Proceedings of the Royal Society B. 2010 Jul 7;277(1690):1963-9.

Rivera AS, Pankey MS, Plachetzki DC, Villacorta C, Syme AE, Serb JM, Omilian AR, Oakley TH. Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. BMC Evolutionary Biology. 2010 Dec;10(1):123. (highly accesed)

Grosberg R, Plachetzki DC. Marine Invertebrates: Genetics of Colony Recognition. Encyclopedia of Animal Behavior.2010 Jan 1:381-8.

Oakley TH, Plachetzki DC. 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), CRC Press; 2011.

Oakley TH, and Plachetzki DC. The evolution of opsins. Encyclopedia of the Eye. In, Barbara Batelle Ed. Elsevier.2010 May 27.

Blackburn DC, Conley KW, Plachetzki DC, Kempler K, Battelle BA, Brown NL. Isolation and expression of Pax6 and atonal homologues in the American horseshoe crab, Limulus polyphemus. Developmental Dynamics. 2008 Aug;237(8):2209-19. (with cover)

Oakley, TH, Plachetzki DC and Rivera AS. Furcation, field-splitting, and the evolutionary origins of novelty in arthropod photoreceptors. Arthropod Structure and Development. 2007 Dec 1;36(4):386-400.

Plachetzki DC, Oakley TH. Key transitions during animal phototransduction evolution: Novelty, tree thinking, co-option and co-duplication. Integrative and Comparative Biology. 2007 Nov 1;47(5):759-69.

Plachetzki DC , Degnan BM, Oakley TH. The origins of novel protein interactions during animal opsin evolution. PLoS One. 2007 Oct 17;2(10):e1054.(highly accessed)

Harzsch S, Diploma K, Plachetzki DC, Brown N, Melzer R, Kempler KE, Battelle B. 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. 2006 Oct;235(10):2641-55.

Plachetzki DC, Serb JM, Oakley TH. New insights into the evolutionary history of photoreceptor cells. Trends in Ecology and Evolution. 2005 Sep 1;20(9):465-7.

Szuchet S, Plachetzki DC, Seeger MA, Domowicz MS, Szele FG. NOVOcan: a molecular link among selected glial cells. Biophysical Chemistry. 2004 Mar 1;108(1-3):245-58.

Szuchet S, Plachetzki DC, Karialukas R. Oligodendrocytes express an alpha/beta-interferon-susceptible Mx gene: molecular characterization of the encoded protein. Glia 2002 Feb;37(2):183-9.

Szuchet S, Plachetzki DC, Eaton KS. Oligodendrocyte transmembrane protein: a novel member of the glutamate-binding protein subfamily. Biochemical and Biophysical Research Commununications. 2001 May 18;283(4):900-7.