KOLÍSKO, M., FLEGONTOVA, O., KARNKOWSKA, A., LAX, G., MARITZ, J. M., PÁNEK, T., TÁBORSKÝ, P., CARLTON, J.M., ČEPIČKA, I., HORÁK, A., LUKEŠ, J., SIMPSON, A. G. B., TAI, V., 2020. EukRef-excavates: seven curated SSU ribosomal RNA gene databases, Database, Volume 2020, 2020, baaa080​. https://doi.org/10.1093/database/baaa080.

BOURLAND, W., ROTTEROVÁ, J., ČEPIČKA, I., 2020. Description of Three New Genera of Metopidae (Metopida, Ciliophora): Pileometopus Gen. Nov., Castula Gen. Nov., and Longitaenia Gen. Nov., with Notes on the Phylogeny and Cryptic Diversity of Metopid Ciliates. Protist, 125740.​

ROTTEROVÁ, J., SALOMAKI, E., PÁNEK T., BOURLAND, W., ŽIHALA, D., TÁBORSKÝ, P., EDGCOMB, V. P., BEINART, R. A., KOLÍSKO, M., ČEPIČKA, I., 2020. Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis. Current Biology 8:1–14. https://doi.org/10.1016/j.cub.2020.03.064.

KOLÁTKOVÁ, V., ČEPIČKA, I., GARGIULO, G.M., VOHNÍK, M., 2020. Enigmatic Phytomyxid Parasite of the Alien Seagrass Halophila stipulacea: New Insights into Its Ecology, Phylogeny, and Distribution in the Mediterranean Sea. Microbial Ecology, 79: 631–643 (2020).

 

PETRŽELKOVÁ, K., SMEJKALOVÁ, P., CÉZA, V., PAFČO, B., SHUTT-PHILLIPS, K., TODD, A., JIRKŮ-POMAJBÍKOVÁ, K., BENAVIDES, J., MODRÝ, D., ČEPIČKA, I., 2020. Sympatric western lowland gorillas, central chimpanzees and humans are infected with different trichomonads. Parasitology, 147(2), 225-230.

SIMPSON A.G.B., ČEPIČKA I., 2019. Amitochondriate Protists (Diplomonads, Parabasalids and Oxymonads). Editor: Thomas M. Schmidt, Encyclopedia of Microbiology (Fourth Edition), Academic Press, 2019, Pages 86-98.​

HAMPL V, ČEPIČKA I, ELIÁŠ M., 2019. Was the mitochondrion necessary to start eukaryogenesis? Trends in Microbiology, 27(2): 96-104 (2019).

HANOUSKOVÁ, P, TÁBORSKÝ, P., ČEPIČKA, I., 2019. Dactylomonas gen. nov., a novel lineage of heterolobosean flagellates with unique ultrastructure, closely related to the amoeba Selenaion koniopes Park, De Jonckheere & Simpson, 2012. Journal of Eukaryotic Microbiology, 66(1): 120-139 (2019).

ADL S, BASS D, LANE CE, LUKEŠ J, SCHOCH CL, SMIRNOV A, AGATHA S, BERNEY C, BROWN M, BURKI F, CÁRDENAS P, ČEPIČKA I, CHISTYAKOVA L, DEL CAMPO J, DUNTHORN M, EDVARDSEN B, EGLIT Y, GUILLOU L, HAMPL V, HEISS AA, HOPPENRATH M, JAMES TY, KARPOV S, KIM E, KOLISKO M, KUDRYAVTSEV A, LAHR DJG, LARA E, LE GALL L, LYNN D, MANN DG, MASSANA I, MOLERA R, MITCHELL EAD, MORROW C, PARK JS, PAWLOWSKI JW, POWELL MJ, RICHTER DJ, RUECKERT S, SHADWICK L, SHIMANO S, SPIEGEL FW, TORRUELLA I, CORTES G, YOUSSEF N, ZLATOGURSKY V, ZHANG Q. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology, 66(1): 4-119 (2019).

ROTTEROVÁ J, BOURLAND W, ČEPIČKA I., 2018. Corrigendum to "Tropidoatractidae fam. nov., a deep branching lineage of Metopida (Armophorea, Ciliophora) found in diverse habitats and possessing prokaryotic symbionts" [Protist 169 (July (3)) (2018) 362-405].​ Protist, 169(5):788-789.

VACEK V, NOVÁK LVF, TRETLI SC, TÁBORSKÝ P, ČEPIČKA I, KOLÍSKO M, KEELING PJ, HAMPL V. 2018. Fe-S cluster assembly in oxymonads and related protists. Molecular Biology and Evolution, 35(11): 2712-2718.

TREITLI SC, KOTYK M, YUBUKI N, JIROUNKOVÁ E, VLASÁKOVÁ J, SMEJKALOVÁ P, ŠÍPEK P, ČEPIČKA I, HAMPL V. 2018. Molecular and morphological diversity of the oxymonad genera Monocercomonoides and Blattamonas gen. nov. Protist, 169(5):744-783.

BOURLAND W, ROTTEROVÁ JČEPIČKA I. 2018. Morphologic and molecular characterization of Brachonella pulchra (Kahl, 1927) comb. nov. (Armophorea, Ciliophora) with comments on cyst structure and formation. International Journal of Systematic and Evolutionary Microbiology, 68(9):3052-3065.​

 

BEINART RA, ROTTEROVÁ JČEPIČKA I, GAST RJ, Edgcomb VP. 2018. The genome of an endosymbiont methanogen is very similar to those of its free-living relatives. Environmental Microbiology, 20(7):2538-2551.

ROTTEROVÁ J, BOURLAND W, ČEPIČKA I. , 2018. Tropidoatractidae fam. nov., a deep branching lineage of Metopida (Armophorea, Ciliophora) found in diverse habitats and possessing prokaryotic symbionts. Protist, 169: 362-405.

 

BOURLAND W, ROTTEROVÁ J, LUO X., ČEPIČKA I., 2018. The little-known freshwater metopid ciliate, Idiometopus turbo (Dragesco and Dragesco-Kernéis, 1986) nov. gen., nov. comb., originally discovered in Africa, found on the Micronesian island of Guam. Protist, 169: 494-506.

BOURLAND W, ROTTEROVÁ JČEPIČKA I., 2017. Morphologic and molecular characterization of seven species of the remarkably diverse and widely distributed metopid genus Urostomides Jankowski, 1964 (Armophorea, Ciliophora). European Journal of Protistology, 61: 194-232.

Warren, A., Patterson, D.J., Dunthorn, M., Clamp, J.C., Achilles-Day, U.E.M., Aescht, E., Al-Farraj, S.A., Al-Quraishy, S., Al-Rasheid, K., Carr, M., Day, J.G., Dellinger, M., El-Serehy, H.A., Fan, Y., Gao, F., Gao, S., Gong, J., Gupta, R., Hu, X., Kamra, K., Langlois, G., Lin, X., Lipscomb, D., Lobban, C.S., Luporini, P., Lynn, D.H., Ma, H., Macek, M., Mackenzie-Dodds, J., Makhija, S., Mansergh, R.I., Martín-Cereceda, M., McMiller, N., Montagnes, D.J.S., Nikolaeva, S., Ong’ondo, G.O., Pérez-Uz, B., Purushothaman, J., Quintela-Alonso, P., ROTTEROVÁ, J., Santoferrara, L., Shao, C., Shen, Z., Shi, X., Song, W., Stoeck, T., La Terza, A., Vallesi, A., Wang, M., Weisse, T., Wiackowski, K., Wu, L., Xu, K., Yi, Z., Zufall, R., Agatha, S., 2017. Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata, Ciliophora). Journal of Eukaryotic Microbiology, 64: 539 – 554.

TÁBORSKÝ P, PÁNEK T, ČEPIČKA I., 2017. Anaeramoebidae fam. nov., a novel lineage of anaerobic amoebae and amoeboflagellates of uncertain phylogenetic position. Protist, 168: 495-526.

KANG S, TICE AK, SPIEGEL FW, SILBERMAN JD, PÁNEK T, ČEPIČKA I, KOSTKA M, KOSAKYAN A, ALCANTÂRA DM, ROGER AJ, SHADWICK LL, SMIRNOV A, KUDRYAVTSEV A, LAHR DJG, BROWN MW, 2017. Between a pod and a hard test: the deep evolution of amoebae. Molecular Biology and Evolution, 34: 2258-2270.

YUBUKI N, ZADROBÍLKOVÁ E, ČEPIČKA I. 2017. Ultrastructure and molecular phylogeny of Iotanema spirale gen. et sp. nov., a new lineage of endobiotic Fornicata with strikingly simplified ultrastructure. Journal of Eukaryotic Microbiology, 64: 422-433.

BOURLAND W, ROTTEROVÁ JČEPIČKA I. 2017. Redescription and molecular phylogeny of the type species for two main metopid genera, Metopus es (Müller, 1776) Lauterborn, 1916 and Brachonella contorta (Levander, 1894) Jankowski, 1964 (Metopida, Ciliophora), based on broad geographic sampling. European Journal of Protistology, 59: 134-154.

SVOBODOVÁ M, DOLNIK OV, ČEPIČKA I, RÁDROVÁ J. 2017. Biting midges (Ceratopogonidae) as vectors of avian trypanosomes. Parasites & Vectors, 10: 224.

LEGER MM, KOLISKO M, KAMIKAWA R, STAIRS CW, KUME K, ČEPIČKA I, SILBERMAN JD, ANDERSSON JO, Xu F, YABUKI A, EME L, ZHANG Q, TAKISHITA K, INAGAKI Y, SIMPSON AGB, HASHIMOTO T, ROGER AJ. 2017. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nature Ecology & Evolution, 1: 0092.

PÁNEK T, ŽIHALA D, SOKOL M, DERELLE R, KLIMEŠ V, HRADILOVÁ M, ZADROBÍLKOVÁ E, SUSKO E, ROGER AJ, ČEPIČKA I, ELIÁŠ M. 2017. Nuclear genetic codes with a different meaning of the UAG and the UAA codon. BMC Biology, 15: 8.

YUBUKI N, ČEPIČKA I, LEANDER BS. 2016. Evolution of the microtubular cytoskeleton (flagellar apparatus) in parasitic protists. Molecular and Biochemical Parasitology, 209: 26-34.

NOVÁK L, ZUBÁČOVÁ Z, KARNKOWSKA A, KOLISKO M, HROUDOVÁ M, STAIRS CW, SIMPSON AGB, KEELING PJ, ROGER AJ, ČEPIČKA I, HAMPL V. 2016. Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. BMC Evolutionary Biology, 16: 197.

FALTEISEK L, DUCHOSLAV V, ČEPIČKA I. 2016. Substantial variability of multiple microbial communities collected as similar acidic mine water outlets. Microbial Ecology, 72: 163-174.

JIRKŮ-POMAJBÍKOVÁ K, ČEPIČKA I, KALOUSOVÁ B, JIRKŮ M, STEWART F, LEVECKE B, MODRÝ D, PIEL AK, PETRŽELKOVÁ KJ. 2016. Molecular identification of Entamoebaspecies in savanna woodland chimpanzees (Pan troglodytes schweinfurthii). Parasitology, 143: 741-748.

PÁNEK T, ZADROBÍLKOVÁ E, WALKER G, BROWN MW, GENTEKAKI E, HROUDOVÁ M, KANG S, ROGER AJ, TICE AK, VLČEK Č, ČEPIČKA I. 2016. First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deap lineage of the group. Molecular Phylogenetics and Evolution, 98: 41-51.

ZADROBÍLKOVÁ E, WALKER G, ČEPIČKA I. 2016: Morphological and molecular diversity of the neglected genus Rhizomastix Alexeieff, 1911 (Amoebozoa: Archamoebae) with description of five new species. Journal of Eukaryotic Microbiology, 63: 181-197.

PÁNEK T, TÁBORSKÝ P, PACHIADAKI MG, HROUDOVÁ M, VLČEK Č, EDGCOMB VP, ČEPIČKA I. 2015. Combined culture-based and culture-independent approaches provide insights into diversity of jakobids, an extremely plesiomorphic eukaryotic lineage. Frontiers in Microbiology, 6: 1288.

DVOŘÁKOVÁ N, ČEPIČKA I, QABLAN MA, GIBSON W, BLAŽEK R, ŠIROKÝ P. 2015. Phylogeny and morphological variability of trypanosomes from African pelomedusid turtles with redescription of Trypanosoma mocambicum Pienaar, 1962. Protist, 166: 599-608.

ZHANG Q, TÁBORSKÝ P, SILBERMAN JD, PÁNEK T, ČEPIČKA I, SIMPSON AGB. 2015: Marine isolates of Trimastix marina form a plesiomorphic deep-branching lineage within Preaxostyla, separate from other known trimastigids (Paratrimastix n. gen.)  Protist, 166: 468-491.

KUNCA T, SMEJKALOVÁ P, ČEPIČKA I. 2015: Trichomoniasis in European sparrowhawks in the Czech Republic. Folia Parasitologica, 62: 035.

YUBUKI N, PÁNEK T, YABUKI A, ČEPIČKA I, TAKISHITA K, INAGAKI Y, LEANDER BS. 2015: Morphological identities of two different marine stramenopile environmental sequence clades: Bicosoeca kenaiensis (Hilliard, 1971) and Cantina marsupialis (Larsen and Patterson, 1990) gen. nov., comb. nov. Journal of Eukaryotic Microbiology, 62: 532-542.

CÉZA V, PÁNEK T, SMEJKALOVÁ P, ČEPIČKA I. 2015: Molecular and morphological diversity of the genus Hypotrichomonas (Parabasalia: Hypotrichomonadida), with descriptions of six new species. European Journal of Protistology, 51: 158-172.

ZADROBÍLKOVÁ E, WALKER G, ČEPIČKA I. 2015: Morphological and molecular evidence support a close relationship between the free-living archamoebae Mastigella and Pelomyxa. Protist, 166: 14-41.

 

Chapters in books

WALKER G, ZADROBÍLKOVÁ E, ČEPIČKA I. 2017. Archamoebae. In: Archibald JM, Simpson AGB, Slamovits CH (Eds), Handbook of the Protists, 2nd edition, Springer, 1349-1403.

 

KULDA J, NOHÝNKOVÁ E, ČEPIČKA I. 2017. Retortamonadida (with notes on Carpediemonas-like organisms). In: Archibald JM, Simpson AGB, Slamovits CH (Eds), Handbook of the Protists, 2nd edition, Springer, 1247-1278.

ČEPIČKA I, DOLAN MF, Gile GH. 2017. Parabasalia. In: Archibald JM, Simpson AGB, Slamovits CH (Eds), Handbook of the Protists, 2nd edition, Springer, 1175-1218.

PÁNEK T, ČEPIČKA I. 2012. Diversity of Heterolobosea. In: Caliskan M (Ed.), Genetic Diversity in Microorganisms, InTech, Rijeka, ISBN 979-953-307-161-8, pp. 3-26.

SIMPSON AGB, ČEPIČKA I 2009: Amitochondriate protists (diplomonads, parabasalids and oxymonads). In: Schaechter M (Ed.), Encyclopedia of Microbiology, 3rd edition, Elsevier, Oxford, pp. 545-557.

ČEPIČKA I, LUKEŠ J, VÁVRA J 2007: Protozoologie. In: VOLF P, HORAK P (Eds.), Paraziti a jejich biologie, Triton, Praha, pp. 50-137.

# protistology

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