Publications

 

  • FY2024

    • Bernos T.A., Lajbner Z., Kotlík P., Hill J.M., Marková S., Yick J., Mandrak N.E., Jeffries K.M. (2024) Assessing the impacts of adaptation to native-range habitats and contemporary founder effects on genetic diversity in an invasive fish. Evolutionary Applications 17(10), e70006. https://doi.org/10.1111/eva.70006
    • Zoral M.A., Lajbner Z., Zifcakova L., Nakamura S., Miller J. (2024) Co-infection of Liburna oophaga sp. nov. and Ikanecator primus on cuttlefish (Sepia pharaonis) eggs and the effectiveness of peracetic acid as a treatment. Veterinary Parasitology 332, 110302. https://doi.org/10.1016/j.vetpar.2024.110302
    • Zoral M.A., Lajbner Z., Zifcakova L., Miller J. (2024) Peracetic acid treatment of squid eggs infected with parasitic copepod (Ikanecator primus gen. et sp. nov.). Scientific Reports, 14(1), 14513. https://doi.org/10.1038/s41598-024-65290-z
    • Rosa R., Santos C.P., Borges F., Amodio P., Amor M., Bower J.R., Caldwell R.L., Di Cosmo A., Court M., Fiorito G., Gestal C.,  González ÁF, Guerra Á, Hanlon RT, Hofmeister JKK, Ibáñez CM, Ikeda Y, Imperadore P, Kommritz JG, Kuba M, Hall KC, Lajbner Z, Leite T, Lopes VM, Markaida U, Moltschaniwskyj NA, Nabhitabhata J, Ortiz N, Otjacques E, Pizzulli F, Ponte G, Polese G, Raffini F, Rosas C, Roura Á, Sampaio E, Segawa S, Simakov O, Sobrino I, Storero L, Voight J, Williams BL, Zheng X, Pierce GJ, Villanueva R, Gleadall IG (2024) Past, present, and future trends in octopus research. In: Rosa R, Gleadall IG, Pierce GJ, Villanueva R (eds) Octopus Biology and Ecology, 421-454. Academic Press. https://doi.org/10.1016/B978-0-12-820639-3.00010-8

       

    FY2023

    • Baden T., Briseño J., Coffing G., Cohen-Bodénès S., Courtney A., Dickerson D., Dölen G., Fiorito G., Gestal C., Gustafson T., Heath-Heckman E., Hua Q., Imperadore P., Kimbara R., Król M., Lajbner Z., Lichilín N., Macchi F., McCoy M.J., Nishiguchi M.K., Nyholm S.V., Otjacques E., Pérez-Ferer P.A., Ponte G., Pungor J.R., Rogers T.F., Rosenthal J.J.C., Rouressol L., Rubas N., Sanchez G., Santos C.P., Schultz D.T., Seuntjens E., Songco-Casey J.O., Stewart I.E. Styfhals R., Tuanapaya S., Vijayan N., Weissenbacher A.,  Zifcakova L., Schulz G., Weertman W., Simakov O, Albertin C.B. (2023) Cephalopod-omics: emerging fields and technologies in cephalopod biology. Integrative and Comparative Biology, icad087. https://doi.org/10.1093/icb/icad087
    • Sekine S., Tarama M., Wada H., Sami M.M., Shibata T., Hayashi S. (2024) Emergence of periodic circumferential actin cables from the anisotropic fusion of actin nanoclusters during tubulogenesis. Nature Communications 15, 464. https://doi.org/10.1038/s41467-023-44684-z

       

    FY2022

    • Gutnick T., Neef A., Cherninskyi A., Ziadi-Künzli F., Di Cosmo A., Lipp H., Kuba M.J. (2023) Recording electrical activity from the brain of behaving octopus, Current Biology 33, 1171–1178. DOI: https://doi.org/10.1016/j.cub.2023.02.006
    • LeTreut G., Huber G., Kamb M., Kawagoe K., McGeever A., Miller J., Pnini R., Veytsman B., Yllanes D. (2022) A high-resolution flux-matrix model describes the spread of diseases in a spatial, Scientific Reports 12, 15946. https://doi.org/10.1038/s41598-022-19931-w
    • Zoral M.A. (2022) Medicinal plants: are they safe enough for fish health? Aquaculture International 31, 1077–1096. https://doi.org/10.1007/s10499-022-01015-1
    • Marta V., Zifčáková L., Symonová R. (2023) Hidden Compositional Heterogeneity of Fish Chromosomes in the Era of Polished Genome Assemblies. Fishes 8, no. 4: 185. https://doi.org/10.3390/fishes8040185

       

    FY2021

    • Huber G., Kamb M., Kawagoe K., Li L.M., McGeever A., Miller J., Veytsman B., Zigmond D. (2021) A minimal model for household-based testing and tracing in epidemics, Physical biology 18 (4), 045002.  https://doi.org/10.1088/1478-3975/abdacd
    • Asada K., Nakajima R., Nishibayashi T., Ziadi-Künzli F., Lajbner Z., Miller J., Gutnick T., Kuba M.J. (2021). Improving Keeping for Octopuses by Testing Different Escape-Proof Designs on Tanks for “Big Blue Octopus”(Octopus cyanea), Applied Sciences Vol. 11, Issue 18, 8547. https://doi.org/10.3390/app11188547
    • Kawagoe K., Rychnovsky M., Chang S., Huber G., Li L.M., Miller J., Pnini R., Veytsman B., Yllanes D. (2021) Epidemic dynamics in inhomogeneous populations and the role of superspreaders. Physical Review Research, Vol 3, Issue 3, page 033283-1:16. https://doi.org/10.1103/PhysRevResearch.3.033283
    • Masucci G.D., Biondi P., Reimer J.D. (2021) Impacts of coastal armouring on rubble mobile cryptofauna at shallow coral reefs in Okinawa. Plankton and Benthos Research, 16(4), 237-248. https://doi.org/10.3800/pbr.16.237
    • Masucci G.D., Biondi P., Reimer J.D. (2021) A Comparison of Size, Shape, and Fractal Diversity Between Coral Rubble Sampled From Natural and Artificial Coastlines Around Okinawa Island, Japan, Frontiers in Marine Science, 1653. https://doi.org/10.3389/fmars.2021.703698
    • Das R.R., Wada H., Masucci G.D., Singh T., Tavakoli-Kolour P., Wada N., ... & Reimer, J. D. (2021) Four-Year Field Survey of Black Band Disease and Skeletal Growth Anomalies in Encrusting Montipora spp. Corals around Sesoko Island, Okinawa. Diversity, 14(1), 32. https://doi.org/10.3390/d14010032
    • Arenas C.D., Ardaševa A., Miller J., Mikheyev A.S., Yokobayashi Y. (2022) Ribozyme Mutagenic Evolution: Mechanisms of Survival, Origins of Life and Evolution of Biospheres 51, 321–339. https://doi.org/10.1007/s11084-021-09617-0
    • Reimer J.D., Albelda R.L., Biondi P., Hardianto E., Huang S., Masucci G.D., Sayco S.L.G, Wee H.B., Zhu Y., Literature review of coral reef Restoration in and around the coral triangle from the viewpoint of Marine Biodiversity, Arquivos de Ciências do Mar, v.55, pp. 413-431. https://doi.org/10.32360/acmar.v55iEspecial.78183
    • Nakajima R., Lajbner Z., Kuba M.J., Gutnick T., Iglesias T.L., Asada K., Nishibayashi T., Miller J. (2022) Squid adjust their body color according to substrate, Scientific Reports 12, 5227. https://doi.org/10.1038/s41598-022-09209-6
    • Tláskal V., Pylro V.S., Žifčáková L., Baldrian P. (2021) Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood. Frontiers in Microbiology, 2021, 12, 668644. https://doi.org/10.3389/fmicb.2021.668644
    • Arora J., Kinjo Y., Šobotník J., Buček A., Clitheroe C., Stiblik P., Roisin Y., Žifčáková L., Park Y.C., Kim K.Y., Sillam-Dussès D., Hervé V., Lo N., Tokuda G., Brune A., Bourguignon T. (2022) The Functional Evolution of Termite Gut Microbiota. Microbiome 10, 78. https://doi.org/10.1186/s40168-022-01258-3
    • Cook K.M., Yamagiwa H., Beger M., Masucci G.D., Ross S., Lee H.Y.T., Stuart-Smith R.D., Reimer J.D. (2022) A community and functional comparison of coral and reef fish assemblages between four decades of coastal urbanisation and thermal stress. Ecology and Evolution, 12, e8736. https://doi.org/10.1002/ece3.8736
    • Drerup C. (2021) First detailed description of the burying behaviour of a bottletail squid, Sepiadarium kochii Steenstrup, 1881. Molluscan Research 41:87-91. https://doi.org/10.1080/13235818.2021.1927464
    • Al-Soudy A.S., Maselli V., Galdiero S., Kuba M.J., Polese G., Di Cosmo A. (2021) Identification and Characterization of a Rhodopsin Kinase Gene in the Suckers of Octopus vulgaris: Looking around Using Arms? Biology 10(9):936. https://doi.org/10.3390/biology10090936

       

    FY2020

    • Edsinger E., Pnini R., Ono N., Yanagisawa R., Dever K., Miller J. (2020) Social tolerance in Octopus laqueus—A maximum entropy model. Plos One Vol. 15, Issue 6, e0233834.  https://doi.org/10.1371/journal.pone.0233834 
    • Funai S.S., Sugawara H. (2020) Current algebra formulation of quantum gravity and its application to cosmology. Progress of Theoretical and Experimental Physics, Vol. 2020, Issue 9, 093B08. https://doi.org/10.1093/ptep/ptaa108, 
    • Funai S.S., Giataganas D. (2020) Thermodynamics and feature extraction by machine learning. Physics Review Research, Issue number 2, Pages 033415 https://doi.org/10.1103/PhysRevResearch.2.033415, 
    • Muhammet G., Majtánová Z., Symonová R., Pelikánová S., Unal S., Lajbner Z., Ráb P. (2020) Present and Future Salmonid Cytogenetics. Genes 11, no. 12 (2020), page 1462. https://doi.org/10.3390/genes11121462
    • Watanabe H., Bergner G., Bodendorfer N., Funai S.S., Hanada M., Rinaldi E., Schäfer A., Vranas P. (2021) Partial Deconfinement at Strong Coupling on the Lattice, Journal of High Energy Physics. https://doi.org/10.1007/JHEP02(2021)004
    • Huber G., Kamb M., Kawagoe K., Li L.M., McGeever A., Miller J., Veytsman B.A., Zigmond D. (2020) A minimal model for household-based testing and tracing in epidemics, Physical biology https://doi.org/10.1088/1478-3975/abdacd
    • Warren D.L., Dornburg A., Zapfe K., Iglesias T.L. (2021) The effects of climate change on Australia’s only endemic Pokémon: Measuring bias in species distribution models. Methods in Ecology and Evolution 12:985-95. https://doi.org/10.1111/2041-210X.13591
    • Drerup C., Sykes A.V., Cooke G.M. (2020) Behavioural aspects of the spotty bobtail squid Euprymna parva (Cephalopoda: Sepiolidae). Journal of Experimental Marine Biology and Ecology 530: 151442. https://doi.org/10.1016/j.jembe.2020.151442

       

    FY2019

    • Gao K., Miller J. (2020) Primary orthologs from local sequence context. BMC Bioinformatics https://doi.org/10.1186/s12859-020-3384-2
    • Gutnick T., Weissenbacher A, Kuba M.J. (2019) The Underestimated Giants. Operant conditioning, visual discrimination and long-term memory in giant tortoises. Animal Cognition https://doi.org/10.1007/s10071-019-01326-6
    • Funai S.S., Sugawara H. (2020) “Flavor Moonshine”, Progress of Theoretical and Experimental Physics, Volume 2020, Issue 1, January 2020, 013B03. https://doi.org/10.1093/ptep/ptz137
    • Iglesias T.L., Boal J.G., Frank M.G., Zeil J., Hanlon R.T. (2019) Cyclic nature of the REM sleep-like state in the cuttlefish Sepia officinalis. Journal of Experimental Biology 222:jeb174862 https://doi.org/10.1242/jeb.174862
    • Warren D.L., Matzke N.J., Iglesias T.L. (2020) Evaluating presence‐only species distribution models with discrimination accuracy is uninformative for many applications. Journal of Biogeography 47:167-80 https://doi.org/10.1111/jbi.13705
    • 船井正太郎. 機械学習と繰り込み群 in 『物理学者、機械学習を使う(橋本幸士)』朝倉書店. pp. 142-153. Section 10. ISBN: 978-4-254-13129-1 / Shotaro Funai. (2019) Machine Learning and Renormalization Group in “Physicists Use Machine Learning” (Koji Hashimoto)” Asakura Publishing Co., Ltd. pp. 142-153. Section 10. ISBN: 978-4-254-13129-1.

       

    FY2018

    • Dornburg A., Warren D. L., Zapfe K. L., Morris R., Iglesias T.L., Lamb A., Hogue G., Lukas L., Wong R. (2018) Testing ontogenetic patterns of sexual size dimorphism against expectations of the expensive tissue hypothesis, an intraspecific example using oyster toadfish (Opsanus tau). Ecol Evol 8, 3609-3616. https://doi.org/10.1002/ece3.3835
    • Iglesias T.L., Dornburg A., Warren D.L., Wainwright P.C., Schmitz L., Economo E.P. (2018) Eyes Wide Shut: the impact of dim-light vision on neural investment in marine teleosts. J Evol Biol 31, 1082-1092. https://doi.org/10.1111/jeb.13299
    • Lajbner Z., Pnini R., Camus M.F., Miller J., Dowling D.K. (2018) Experimental evidence that thermal selection shapes mitochondrial genome evolution. Sci Rep 8, 9500. https://doi.org/10.1038/s41598-018-27805-3
    • Funai S.S., Giataganas D. (2018) Thermodynamics and Feature Extraction by Machine Learning. https://arxiv.org/abs/1810.08179
    • Kuba M.J. (2018) 11, Vertebrate/Invertebrate – When do we start caring? in Animal Welfare in Changing World, Vol. 1 (ed Butterworth Andrew), Ch. 11, pages 108-113, CAB International. https://doi.org/10.1079/9781786392459.0108
    • Mather J.A., Kuba M.J. (2018) 14 Octopuses – Mind in the Waters, in Field and Laboratory Methods in Animal Cognition: A Comparative Guide, (eds Bueno-Guerra. Nereida. & Amici.Federica.), Ch. 14, pages 308-328, Cambridge University Press. https://doi.org/10.1017/9781108333191.016

       


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    FY2017

    • Dornburg A., Warren D.L., Zapfe K.L., Morris R., Iglesias T.L., Lamb A., Hogue G., Lukas L., Wong R. (2018) Testing ontogenetic patterns of sexual size dimorphism against expectations of the expensive tissue hypothesis, an intraspecific example using oyster toadfish (Opsanus tau). Ecology and Evolution 1–8. https://doi.org/10.1002/ece3.3835
    • Lamb AD, Watkins-Colwell GJ, Moore JA, Warren DL, Iglesias TL, Brandley MC, Dornburg A (2017) Endolymphatic sac use and reproductive activity in the Lesser Antilles endemic gecko Gonatodes antillesis (Gekkota: Sphaerodactylidae). Bulletin of the Peabody Museum of Natural History, 58(1), pp.17-29. https://doi.org/10.3374/014.058.0103

       

    FY2015

    • Garcia-Munoz M., Taillefer E., Pnini R., Vickers C., Miller J., Arbuthnott G.W. (2015) Rebuilding a realistic corticostriatal "social network" from dissociated cells. Frontiers in systems neuroscience. 9: 63. https://doi.org/10.3389/fnsys.2015.00063

       

    FY2014

    FY2013

    • Taillefer E., Miller J. (2014) "Exhaustive computation of exact duplications via super and non-nested local maximal repeats." J Bioinform Comput Biol 12(1): 1350018. https://doi.org/10.1142/S0219720013500182

       

    FY2011