PEER-REVIEWED JOURNAL ARTICLES
  1. Olson, C.J.*, M.C. Cobo, and K.M. Kocot. In press. Seven new species of Macellomeniidae Salvini-Plawen, 1978 (Mollusca, Solenogastres) from the North Atlantic. Journal of Molluscan Studies.
  2. Olesen, J., S. Gerken, K.M. Kocot, and R. Wetzer. 2025. The first report of y-larvae (Crustacea: Facetotecta) from Panama, with an overview of their occurrence in the Americas and surprising parallels to the Okinawan fauna. Journal of Crustacean Biology 45(2):ruaf026.
  3. Lawniczak, M.K.N., K.M. Kocot, J.J. Astrin, M. Blaxter, C.G. Sotero-Caio, K.B. Barker, A.K. Childers, J. Coddington, P. Davis, K. Howe, W.E. Johnson, D.D. McKenna, J. Wideman, O. Vinnere Pettersson, V. Ras, B.F. Santos and the Earth BioGenome Project Samples and Processing sub-Committee. 2025. Best Practice Guidance for Earth BioGenome Project Sample Collection and Processing: Progress and Challenges in Biodiverse Reference Genome Creation. GigaScience 14:giaf041.
  4. Sleight, V.A., M.S. Clark, M.K. Yap-Chiongco*, F. Turner, and K.M. Kocot. 2025. Genomic, transcriptomic and epigenomic signatures of ageing and cold adaptation in the Antarctic clam Laternula elliptica. Open Biology 15:250009.
  5. Atkinson, C.L. and K.M. Kocot. 2025. Introducing Freshwater Mollusk Diversity in a Biodiversity Hotspot. American Malacological Bulletin 41(1):1-3.
  6. Chen, Z., J.A. Baeza, C. Chen, M.T. Gonzalez, V.L. González, C. Greve, K.M. Kocot, P. Martinez Arbizu, J. Moles, T. Schell, E. Schwabe, J. Sun, N.L.W.S. Wong, M.K. Yap-Chiongco*, and J.D. Sigwart. 2025. A genome-based phylogeny for Mollusca is concordant with fossils and morphology. Science 387(6737): 1001-1007.
  7. Ballentine, W., N.G. Roberts*, M.K. Yap-Chiongco*, K.M. Halanych, K.M. Kocot, and K.M. Dorgan. 2025. Life among the sand grains. Frontiers for the Young Mind 13:1472123.
  8. Osborne, T.R., W.N.U. Abeyrathna, E.K. Shea, K.R. Martin, J. Li, K.M. Kocot, and E.C. Davis-Berg. 2025. Centering Inclusivity in Invertebrate Fieldwork: An Argument for Modernizing Malacological Practices. American Malacological Bulletin 41(1):1-15.
  9. Neely, W.J.*, J.M. Sarmiento*, K.L. Garner, T.S. Doggett, C.A. Cammarata, N.O. Dronen, and K.M. Kocot. 2025. New records of Levisunguis subaequalis (Maxillopoda: Pentostomida) infecting multiple turtle species across Texas. Southwestern Naturalist 69(2):1-8.
  10. Seid, C.A., A.S. Hiley, M.F. McCowin, J.I. Carvajal, H. Cha, S.T. Ahyong, O.S. Ashford, O. Breedy, D.J. Eernisse, S.K. Goffredi, M.E. Hendrickx, K.M. Kocot, C.L. Mah, A.K. Miller, N. Mongiardino Koch, R. Mooi, T.D. O’Hara, F. Pleijel, J. Stiller, E. Tilic, P. Valentich-Scott, A. Warén, M.K. Wicksten, N.G. Wilson, E.E. Cordes, L.A. Levin, J. Cortés, and G.W. Rouse. 2025. A faunal inventory of methane seeps on the Pacific margin of Costa Rica. ZooKeys 1222:1-250.
  11. Cobo, M.C.*, W.J. Farris*, C.J. Olson*, E.L. McLaughlin*, and K.M. Kocot. 2024. Autonomous Reef Monitoring Structures (ARMS) as a tool to uncover neglected marine biodiversity: two new Solenogastres (Mollusca, Aplacophora) from the Gulf of Mexico. ZooKeys 1221:401-434.
  12. Roberts, N.G.*, M.J. Gilmore*, T.H. Struck, and K.M. Kocot. 2024. Multiple Displacement Amplification Facilitates SMRT Sequencing of Microscopic Animals and the Genome of the Gastrotrich Lepidodermella squamata (Dujardin, 1841). Genome Biology and Evolution 16(12):evae254.
  13. Giorgi, A., M. Monti, D. Maggioni, P.W. Gabrielson, R.S. Steneck, K.M. Kocot, and J.B. Olson. 2024. DNA sequencing reveals higher taxonomic diversity of coralline algae (Corallinales and Hapalidiales, Rhodophyta) in the tropical western North Atlantic that complicates ecological studies. Botanica Marina. https://doi.org/10.1515/bot-2024-0021
  14. Cobo, M.C.*, W.J. Farris*, and K.M. Kocot. 2024. New data on the biodiversity of Solenogastres (Mollusca, Aplacophora) in the Mediterranean Sea: findings from the program “La Planète Revisitée Corse (2019-2022).” Zoosystema 46(21): 543-576.
  15. Bergmeier F.S.*, A. Brachmann, K.M. Kocot, F. Leasi, A.J. Poustka, M. Schrödl, J. Sevigny, W.K. Thomas, C. Todt, and K.M. Jörger. 2024. Complementing aculiferan mitogenomics: comparative characterization of mitochondrial genomes of Solenogastres (Mollusca, Aplacophora). BMC Ecology and Evolution 24:128.
  16. Liu, H., J.L. Steenwyk, X. Zhou, D.T. Schult, K.M. Kocot, X. Shen, N. King, A. Rokas, and Y. Li. 2024. A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences. PLoS Biology 22(9): e3002794.
  17. Koller, D., K.M. Kocot, B.M. Degnan, and T. Wollesen. 2024. Developmental gene expression in the eyes of the pygmy squid Xipholeptos notoides. Journal of Experimental Zoology Part B 2024:1-16.
  18. Valero-Gracia, A., N.G. Roberts*, M.K. Yap-Chiongco*, A.T. Capucho, K.M. Kocot, M. Matschiner, and T.H. Struck. 2024. First chromosome-level genome assembly of a ribbon worm from the Hoplonemertea clade, Emplectonema gracile, and its structural annotation. Genome Biology and Evolution p.evae127.
  19. Bogantes, V.E., K. Meiβner, D.S. Waits, K.M. Kocot, and K. M. Halanych. 2024. Phylogenomic reconstruction influenced by assembly and annotation parameters: Using whole genome data to unravel the relationships of Spionidae (Annelida). Zoologica Scripta 10.1111/zsc.12676.
  20. Yap-Chiongco, M.K.*, S. Pirro, R.M. Varney*, H. Saito, K.M. Halanych, and K.M. Kocot. 2024. Two draft genomes of enigmatic Solenogastres (Mollusca, Aplacophora) Epimenia babai and Neomenia megatrapezata. F1000 Research 13:318.
  21. Yap-Chiongco, M.K.*, F.S. Bergmeier*, N.G. Roberts*, K.M. Jörger, and K.M. Kocot. 2024. Phylogenomic reconstruction of Solenogastres (Mollusca, Aplacophora) informs hypotheses on body size evolution. Molecular Phylogenetics and Evolution 194:108029.
  22. Saadi, A., A.L. Oliveira, K.M. Kocot and T. Schwaha. 2023. Genomic and transcriptomic survey of bryozoan Hox and ParaHox genes with emphasis on phylactolaemate bryozoans. BMC Genomics 24:711.
  23. Song, H., Y. Wang, H. Shao, Z. Li, P. Hu, M.K. Yap-Chiongco*, P. Shi, T. Zhang, C. Li, Y. Wang, P. Ma, Jakob Vinther, H. Wang, and K.M. Kocot. 2023. Scaphopoda is the sister taxon to Bivalvia: evidence of ancient incomplete lineage sorting. Proceedings of the National Academy of Sciences 120(40): e2302361120.
  24. Cobo, M.C.*, E.L. McLaughlin*, and K.M. Kocot 2023. Four new Solenogastres (Mollusca, Aplacophora) from the South China Sea and paraphyly of Proneomeniidae Simroth, 1893. Invertebrate Systematics 37(5): 301-333.
  25. Jabr, N., P. Gonzalez, K.M. Kocot, and C.B. Cameron. 2023. The embryology, metamorphosis, and muscle development of Schizocardium karankawa sp. nov. (Enteropneusta) from the Gulf of Mexico. EvoDevo 14(1): 6.
  26. O’Brien, K.M., E.L. Crockett, B.J. Adams, C.D. Amsler, H.J. Appiah-Madson, A. Collins, H.W. Detrich III, D.L. Distel, S.M. Eppley, B.W. Frable, N.M. Franz, J.M. Grim, K.M. Kocot, A.R. Mahon, T.J. Mayfield-Meyer, J.A. Mikucki, W.E. Moser, M. Schmull, C.A. Seid, C.R. Smith, A.E. Todgham, and G.J. Watkins-Colwell. 2022. The time is right for an Antarctic biorepository network. Proceedings of the National Academy of Sciences 119(50): e2212800119.
  27. McCutcheon, M.G.*, K.M. Kocot, and M.C. Cobo Llovo*. 2022. Uncovering the biodiversity of Solenogastres (Mollusca, Aplacophora) with three new species of Proneomeniidae Simroth, 1893 and new data for Dorymenia quincarinata (Ponder, 1970). Molluscan Research 42(4): 271-286. 
  28. Batts, R.A.*, K.N. Whitman*, K. Meißner, and K.M. Kocot. 2022. Biodiversity and Phylogeny of North Atlantic Euphrosinidae (Annelida). Diversity 14(11): 996
  29. Saadi, A., J. Bibermair, J., K.M. Kocot, N.G. Roberts*, M. Hirose, A. Calcino, C. Baranyi, R. Chaichana, T. Wood, and T. Schwaha. 2022. Phylogenomics reveals deep relationships and diversification within phylactolaemate bryozoans. Proceedings of the Royal Society B 289.1986: 20221504.
  30. Kaiser, S., Błażewicz, M., Kocot, K.M., Riehl, T., Leduc, D., and Rouse, G.W. 2022. Recent and emerging innovations in deep-sea taxonomy to enhance biodiversity assessment and conservation. Frontiers in Marine Science 9: 989245
  31. Drábková, M.*, K.M. Kocot, K.M. Halanych, T.H. Oakley, L.L. Moroz, J.T. Cannon, A. Kuris, A.E. Garcia-Vedrenne, M.S. Pankey, E.A. Ellis, R.M. Varney*, J. Štefka, and J. Zrzavý. 2022. Different phylogenomic methods support monophyly of enigmatic ‘Mesozoa’ (Dicyemida+ Orthonectida, Lophotrochozoa). Proceedings of the Royal Society B 289(1978): 20220683.
  32. Varney, R.M.*, M.K. Yap-Chiongco*, N.T. Mikkelsen, and K.M. Kocot. 2022. Genome of the lepidopleurid chiton Hanleya hanleyi (Mollusca, Polyplacophora). F1000 Research 11: 555.
  33. Krug, P.J., S.A. Caplins, K. Algoso, K. Thomas, A.A. Valdes, R. Wade, N.L. Wong, D.J. Eernisse, K.M. Kocot. 2022. Phylogenomic resolution of the root of Panpulmonata, a hyperdiverse radiation of gastropods: new insight into the evolution of air breathing. Proceedings of the Royal Society B 289: 20211855.
  34. Maroni, P.J., B. J. Baker, A. Moran, A. Woods, C. Avila, G. Johnstone, J.S. Stark, K.M. Kocot, S. Lockhart, T. Saucède, G.W. Rouse, and N.G. Wilson. 2022. One Antarctic slug to confuse them all: the underestimated diversity of Doris ‘kerguelenensis.’ Invertebrate Systematics https://doi.org/10.1071/IS21073.
  35. Ahmed, A., N.G. Roberts*, F. Adediran, A.B. Smythe, K.M. Kocot, and O. Holovachov. 2022. Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences with Morphology, 18S rRNA, and Mitogenomes. Frontiers in Ecology and Evolution 9:769565.
  36. Martínez Sanjuán, J.*, Ó. García Álvarez, M. Candás, G. Díaz-Agras, and K.M. Kocot. 2022. Micro-CT 3D anatomical reconstruction of Proneomenia sluiteri Hubrecht, 1880, Dorymenia menchuescribanae García-Álvarez, Urgorri and Salvini-Plawen, 2000 and Anamenia gorgonophila (Kowalevsky, 1880) (Mollusca, Solenogastres, Cavibelonia). Frontiers in Marine Science 8: 769565.
  37. Neusser, T.P. F.S. Bergmeier, C. Egger, M.K. Yap-Chiongco*, K.M. Kocot, and Katharina M. Joger. 2021. Shallow-water interstitial malacofauna of the Azores. Acoreana Suplemento 11: 103-123.
  38. Taylor, J., Devey, C., Le Saout, M., Petersen, S., M., Frutos, I., I., Linse, K., Loerz, A.-N., Pałgan, D., Tandberg, A.H., Svavarsson, J., Thorhallsson, D., Tomkowicz, A., Egilsdottir, H., Ragnarsson, S.A., Renz, J., Markasheva, L., Gollner, S., Paulus, E., Diaz, G., Tato, R., Kongsrud, J., Beermann, J., Kocot, K.M., Meißner, K., Bartholomä, A., Hoffman, L., Vannier, P., Marteinsson, V., Rapp H.T. and Brix, S. 2021. The geological and faunal composition of Steinahóll Vent Sites, Reykjanes Ridge, Iceland. Frontiers in Marine Science 8:520713.
  39. Sun, J., R. Li, C. Chen, J.D. Sigwart, and K.M. Kocot, 2021. Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes. Philosophical Transactions of the Royal Society B 376: 1825.
  40. Davis-Berg, E.C. and K.M. Kocot. 2021. Innovation in teaching and learning invertebrate zoology in remote and online classrooms. Invertebrate Biology e12329.
  41. Cobo, M.C.* and K.M. Kocot. 2021. On the diversity of abyssal Dondersiidae (Mollusca, Aplacophora) with the description of a new genus, seven new species, and a review of the family. Zootaxa 4933(1): 63-97.
  42. Varney, R.M.*, D.I. Speiser, C. McDougall, B.M. Degnan, and K.M. Kocot. 2021. The iron responsive genome of the chiton Acanthopleura granulata (Mollusca, Aculifera). Genome Biology and Evolution 13(1): evaa263.
  43. Varney, R.M.*, B. Brenzinger, M.A.E. Malaquias, C.P. Meyer, M. Schrödl, and K.M. Kocot. 2021. Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics. BMC Evolutionary Biology 21:6.
  44. Ramírez-Guerrero, G.M., K.M. Kocot, and C.B. Cameron. 2020. Zooid morphology and molecular phylogeny of the graptolite Rhabdopleura annulata (Hemichordata, Pterobranchia) from Heron Island, Australia. Canadian Journal of Zoology 98(12):844-849.
  45. Kong, L., Y. Li, K.M. Kocot, Y. Yang, L. Qi, Q. Li, and K.M. Halanych. 2020. Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions and contractions in mitochondrial genome size. Molecular Phylogenetics and Evolution 150:106857.
  46. Cobo, M.C.* and K.M. Kocot. 2020. Micromenia amphiatlantica sp. nov.: First solenogaster (Mollusca, Aplacophora) with an amphi-Atlantic distribution and insight into abyssal solenogaster diversity. Deep Sea Research Part I 157:103189.
  47. Kocot, K.M., A.J. Poustka, I. Stöger, K.M. Halanych, and M. Schrödl. 2020. New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships. Scientific Reports 10:101.
  48. Laumer, C.E., R. Fernández, S. Lemer, D. Combosch, K.M. Kocot, A. Riesgo, S.C.S. Andrade, W. Sterrer, M.V. Sørensen, and G. Giribet. 2019. Revisiting metazoan phylogeny with genomic sampling of all phyla. Proceedings of the Royal Society B: Biological Sciences 286: 20190831.
  49. Varney, R.M.*, P. Funch, K.M. Kocot, and M.V. Sørensen. 2019. A new species of Echinoderes (Cyclorhagida: Echinoderidae) from the San Juan Islands, Washington State, USA, and insights into the kinorhynch transcriptome. Zoologischer Anzeiger 282: 52-63.
  50. Smythe, A.B., O. Holovachov, and K.M. Kocot. 2019. Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny. BMC Evolutionary Biology 19:121.
  51. Sogabe, S., W. L. Hatleberg, K.M. Kocot, T. E. Say, D. Stoupin, K. Roper, S. Fernandez-Valverde, S. M. Degnan, and B. M. Degnan. 2019. Pluripotency and the origin of animal multicellularity. Nature. 570: 519-522.
  52. Kocot, K.M., C. Todt, N.T. Mikkelsen, and K.M. Halanych. 2019. Phylogenomics of Aplacophora (Mollusca, Aculifera) and a solenogaster without a foot. Proceedings of the Royal Society B: Biological Sciences 286(1902):20190115.
  53. Mikkelsen, N.T., C. Todt, K.M. Kocot, K.M. Halanych, and E. Willassen. 2018. Molecular phylogeny of Caudofoveata (Mollusca) challenges traditional views. Molecular Phylogenetics and Evolution 132: 138-150.
  54. Galaska, M.P., Y. Li, K.M. Kocot, A.R. Mahon, and K.M. Halanych. 2019. Conservation of mitochondrial genome arrangements in brittle stars (Echinodermata, Ophiuroidea). Molecular Phylogenetics and Evolution 130:115-120.
  55. Li, Y., K.M. Kocot, M.G. Tassia, J.T. Cannon, M. Bernt, and K.M. Halanych. 2018. Mitogenomics reveals a novel genetic code in Hemichordata. Genome Biology and Evolution evy254.
  56. Pabst, E.A.* and K.M. Kocot. 2018. Phylogenomics confirms monophyly of Nudipleura (Gastropoda: Heterobranchia). Journal of Molluscan Studies 84(3): 259–265.
  57. Mikkelsen, N.T., K. M. Kocot, and K.M. Halanych. 2018. Mitogenomics reveals phylogenetic relationships of caudofoveate aplacophoran molluscs. Molecular Phylogenetics and Evolution. 127: 429-436.
  58. Rodriguez, J., T.P. Jones, P. Sierwald, P.E. Marek, W.A. Shear, M.S. Brewer, K.M. Kocot, and J.E. Bond. 2018. Step-wise evolution of complex chemical defenses in millipedes: a phylogenomic approach. Scientific Reports 8: 3209.
  59. Kocot, K.M., Tassia, M.G., Halanych, K.M. and Swalla, B.J., 2018. Phylogenomics offers resolution of major tunicate relationships. Molecular Phylogenetics and Evolution 121: 166-173.
  60. Kersken, D., K.M. Kocot, D. Janussen, T. Schell, M. Pfenninger, and P.M. Arbizu. 2018. First insights into the phylogeny of deep-sea glass sponges (Hexactinellida) from polymetallic nodule fields in the Clarion-Clipperton Fracture Zone (CCFZ), northeastern Pacific. Hydrobiologia 108: 101-112.
  61. Whelan, N.V., K. M. Kocot, T. P. Moroz, K. Mukherjee, P. Williams, G. Paulay, L. L. Moroz and K. M. Halanych. 2017. Ctenophore relationships and their placement as the sister group to all other animals. Nature Ecology & Evolution 1(11): 1737.
  62. Marlow, J., Borrelli, C., Jungbluth, S.P., Hoffman, C., Marlow, J., Girguis, P.R., and the AT36 Team. 2017. Opinion: Telepresence is a potentially transformative tool for field science. Proceedings of the National Academy of Sciences 114: 4841-4844.
  63. Hall, M.R., K.M. Kocot, K.W. Baughman, S.L. Fernandez-Valverde, M.E.A. Gauthier, W.L. Hatleberg, A. Krishnan, C. McDougall, C.A. Motti, E. Shoguchi, T. Wang, X. Xiang, M. Zhao, U. Bose, C. Shinzato, K. Hisata, M. Fujie, M. Kanda, S.F. Cummins, N. Satoh, S.M. Degnan, and B.M. Degnan. 2017. The crown-of-thorns starfish genome as a guide for biocontrol of this coral reef pest. Nature 544: 231-234.
  64. Halanych, K.M. and K.M. Kocot. 2017. Genome evolution: Shellfish genes. Nature Ecology and Evolution 1:0142.
  65. Voolstra, C.R., GIGA Community of Scientists, G. Wörheide, and J.V. Lopez. 2017. Advancing genomics through the Global Invertebrate Genomics Alliance (GIGA). Invertebrate Systematics, 31(1): 1-7.
  66. Tanner, A.R., D. Fuchs, I.E. Winkelmann, M.T.P. Gilbert, M.S. Pankey, A.M. Ribeiro, K.M. Kocot, K.M. Halanych, T.H. Oakley, R.R. da Fonesca, D. Pisani, J. Vinther. 2017. Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution. Proceedings of the Royal Society B: Biological Sciences 284: 20162818.
  67. Stöger, I., Kocot, K.M., Poustka, A.J., Wilson, N.G., Ivanov, D., Halanych, K.M., and Schrödl, M. 2017. Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal. BMC Evolutionary Biology 16:274.
  68. Kocot K.M., T.H. Struck, J. Merkel, D.S. Waits, C. Todt, P.M. Brannock, D.A. Weese, J.T. Cannon, L.L. Moroz, B. Lieb, and K.M. Halanych. 2017. Phylogenomics of Lophotrochozoa with consideration of systematic error. Systematic Biology 66(2): 256-282.
  69. Li, Y., K.M. Kocot, N.V. Whelan, S.R. Santos, D.S. Waits, D.J. Thornhill, and K.M. Halanych. 2016. Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods. Zoologica Scripta 46(2): 200–213.
  70. Kocot, K.M., F. Aguilera, C. McDougall, D.J. Jackson, and B.M. Degnan. 2016. Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization. Frontiers in Zoology 13(1): 1.
  71. Garrison, N.L., J. Rodriguez, I. Agnarsson, J.A. Coddington, C.E. Griswold, C.A Hamilton, M. Hedin, K.M. Kocot, J.M. Ledford, and J.E. Bond. 2016. Spider phylogenomics: untangling the Spider Tree of Life. PeerJ 4:e1719.
  72. Halanych, K. M., N.V. Whelan, K.M. Kocot, A.B. Kohn, and L. L. Moroz. 2016. Miscues misplace sponges. Proceedings of the National Academy of Sciences, 201525332.
  73. Kocot, K.M. 2016. On 20 years of Lophotrochozoa. Organisms Diversity and Evolution, 16: 329-343.
  74. Whelan, N.V., K.M. Kocot, L.L. Moroz, and K.M. Halanych. 2015. Employing phylogenomics to resolve basal animal phylogeny. Integrative and Comparative Biology 55(6): 1084-1095.
  75. Whelan, N.V., K.M. Kocot, L.L. Moroz, and K.M. Halanych. 2015. Error, signal, and the placement of Ctenophora sister to all other animals. Proceedings of the National Academy of Sciences 112(18): 5773-5778.
  76. Havird, J.C., K.M. Kocot, P.M. Brannock, J.T. Cannon, D.S. Waits, D.A. Weese, S.R. Santos, and K.M. Halanych. 2015. Reconstruction of cyclooxygenase evolution in animals suggests variable, lineage-specific duplications, and homologs with low sequence identity. Journal of Molecular Evolution 80(3-4): 1-16.
  77. Li, Y., K.M. Kocot, S.R. Santos, D.J. Thornhill, and K.M. Halanych. 2015. Mitogenomics reveals phylogeny and dramatic size variations of control regions in the deep-sea family Siboglinidae (Annelida). Molecular Phylogenetics and Evolution 85: 221-229.
  78. Kocot, K.M. and C. Todt. 2014. Three new species of meiofaunal solenogasters (Mollusca, Aplacophora) from Friday Harbor, WA, USA. Journal of Natural History 48: 3007-3031.
  79. Whelan, N.V. K.M. Kocot, S.R. Santos, and K.M. Halanych. 2014. Nemertean toxin genes revealed through transcriptome sequencing. Genome Biology and Evolution 6(12):3314-3325.
  80. Cannon, J.T., K.M. Kocot, D.S. Waits, D.A. Weese, B.J. Swalla, S.R. Santos, and K.M. Halanych. 2014. Phylogenomic Resolution of the hemichordate and echinoderm clade. Current Biology 24(23): 2827-2832.
  81. Halanych, K.M. and K.M. Kocot. 2014. Repurposed transcriptomes facilitate discovery of innate immunity Toll-Like Receptor (TRLs) genes across Lophotrochozoa. Biological Bulletin 227.2: 201-209.
  82. Todt, C. and K.M. Kocot. 2014. New records for Proneomenia sluiteri (Mollusca: Solenogastres) from Iceland and description of a new species, the brooding Proneomenia custodiens n. sp. Polish Journal of Polar Research 35(2): 291-310.
  83. Brix, S., K. Meißner, B. Stransky, K.M. Halanych, R. Jennings, K. Kocot, and J. Svavarsson. 2014. The idea of the IceAGE project – a follow up of BIOICE. Polish Journal of Polar Research 35(2): 141-150.
  84. Moroz, L.L., K.M. Kocot, M.R. Citarella, S. Dosung, T.P. Norekian, I.S. Povolotskaya, A.P. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, D. Reshetov, A. Ptitsyn, K. Mukherjee, T.P. Moroz, E. Dabe, F. Yu, V.V. Kapitonov, J. Jurka, Y. Bobkov, J.J. Swore, D.O. Girardo, R. Bruders, C.E. Mills, V.V. Solovyev, J. Rast, B. J. Swalla, F.A. Kondrashov, J.V. Sweedler, E.I. Rogaev, K.M. Halanych, and A.B. Kohn. 2014. The genome of the ctenophore and the emergence of nervous systems. Nature 510: 109-114.
  85. Doty, K.E., A.M. Betzelberger, K.M. Kocot, and M.E. Cook. 2014. Immunofluorescence localization of the tubulin cytoskeleton during cell division and cell growth in members of the coleochaetales. Journal of Phycology 50(4): 624-639.
  86. Kocot, K.M., M.R. Citarella, L.L. Moroz, and K.M. Halanych. 2013. PhyloTreePruner: a phylogenetic tree-based approach for selection of orthologous sequences for phylogenomics. Evolutionary Bioinformatics 2013(9): 429-435.
  87. Kocot, K.M., K.M. Halanych, and P.J. Krug. 2013. Phylogenomics supports the Panpulmonata hypothesis: Resolving key steps in the evolutionary radiation of gastropod molluscs. Molecular Phylogenetics and Evolution 69(3): 764-771.
  88. Kocot, K.M. 2013. Recent advances and unanswered questions in deep molluscan phylogenetics. American Malacological Bulletin 31(1): 1-14.
  89. Scheltema, A.M., C. Schander, and K.M. Kocot. 2012. Hard and soft anatomy in two genera of Dondersiidae (Mollusca, Aplacophora, Solenogastres). Biological Bulletin 222: 233-269.
  90. Kohn, A.B., M.R. Citarella, K.M. Kocot, Y.V. Bobkova, K.M. Halanych, and Leonid L Moroz. 2012. Rapid evolution of the compact and unusual mitochondrial genome in the ctenophore, Pleurobrachia bachei. Molecular Phylogenetics and Evolution 63: 203-207.
  91. Pierce, S.K., X. Fang, J.A. Schwartz, X. Jiang W. Zhao, N.E. Curtis, K.M. Kocot, B. Yang, and J. Wang. 2011. Transcriptomic evidence for the expression of horizontally transferred algal nuclear genes in the photosynthetic sea slug, Elysia chlorotica. Molecular Biology and Evolution 29(6): 1545-1556.
  92. Kocot, K.M., J.T. Cannon, C. Todt, A.B. Kohn, M.R. Citarella, A. Meyer, C. Schander, S.R. Santos, L.L. Moroz, B. Lieb, and K.M. Halanych. 2011. Phylogenomics reveals deep molluscan relationships. Nature 477: 452-456.
  93. Kocot, K.M. and S.R. Santos. 2009. Secondary structural modeling of the second internal transcribed spacer (ITS2) from Pfiesteria-like dinoflagellates (Dinophyceae). Harmful Algae 8(3):441-446.
  94. Jannot, J.E., J. Brinton, K.M. Kocot, O. Akman, and S.A. Juliano. 2009. Ontogenetic mechanisms underlying a geographic size cline in a grasshopper, Romalea microptera. Annals of the Entomological Society of America 102(3) 467-475.
*Kocot lab student or postdoc
 
PEER-REVIEWED BOOK CHAPTERS
  1. Kocot, K.M., C. McDougall, and B.M. Degnan. 2016. Developing Perspectives on Molluscan Shells, Part 1: Introduction and Molecular Biology. Physiology of Molluscs. S. Saleuddin, Ed. Apple Academic Press, Waretown, NJ, USA.
  2. Cannon, J.T. and K.M. Kocot 2016. Phylogenomics using transcriptome data. Methods in Molecular Biology. 1452(Marine Genomics: Methods and Protocols): 65-80.
  3. Kocot, K.M., J.T. Cannon, and K.M. Halanych. 2010. Elucidating animal phylogeny: advances in knowledge and forthcoming challenges. In: Key Transitions in Metazoan Evolution. B. Schierwater and R. DeSalle Eds. Science Publishers, Ensfield, NH, USA.
 
PEER-REVIEWED NOTES & SHORT COMMUNICATIONS
  1. Kocot, K.M., T. Wollesen, R.M. Varney*, M.L. Schwartz, G. Steiner, and A. Wanninger. 2019. Complete mitochondrial genomes of two scaphopod molluscs. Mitochondrial DNA Part B 4(2): 3161-3162.
  2. Kocot, K.M., 2017. Introduction to the AMS Symposium “Phylogenomics of Mollusks,” 82nd Annual Meeting of the American Malacological Society. American Malacological Bulletin, 35(1): 70-72.
  3. Kocot, K.M., N.W. Jeffery, K. Mulligan, K.M. Halanych, and T.R. Gregory. 2015. Genome size estimates for Aplacophora, Polyplacophora and Scaphopoda: small solenogasters and sizeable scaphopods. Journal of Molluscan Studies 82(1): 216-219
  4. Kocot, K.M. and K.M. Halanych. 2009. Investigation of molluscan phylogeny using nuclear protein-coding genes. The Malacologist 53: 18-20.
  5. Kocot, K.M., J.L. Baldwin, R.L. Preston, and G.W. Kidder. 2005. The efficacy of wire minnow traps in assessing populations of Fundulus heteroclitus. Bulletin of the Mount Desert Island Biological Laboratory 44:65-66.
*Kocot lab student or postdoc