Hellebuyck, T., Kotyk, M., Solanes VIilanova, F. & Čepička, I. (2024). The association of bacterial agents and flagellated protozoans in the etiopathogenesis of subspectacular abscesses in snakes. Veterinary Ophthalmology, in press.
Lukeš, L., Čepička, I. & Kolísko, M. (2024). Evolution: No end in sight for novel incredible (heterotrophic) protists. Current Biology, 34(2), R55-R58.
Rotterová, J., Pánek, T., Salomaki, E.D., Kotyk, M., Táborský, P., Kolísko, M. & Čepička, I. (2024). Single cell transcriptomics reveals UAR codon reassignment in Palmarella salina (Metopida, Armophorea) and confirms Armophorida belongs to APM clade. Molecular Phylogenetics and Evolution, 191, 107991.
Foučková, M., Uhrová, K., Kubánková, A., Pánek, T. & Čepička, I. (2024). Lighting lantern above Psalteriomonadidae: Unveiling novel diversity within the genus Psalteriomonas (Discoba: Heterolobosea). European Journal of Protistology, 93, 126052.
del Campo, J., Carlos-Oliveira, M., Čepička, I., Hehenberger, E., Horák, A., Karnkowska, A., Kolísko, M., Lara, E., Lukeš, J., Pánek, T., Piwosz, K., Richter, D.J., Škaloud, P., Sutak, R., Tachezy, J. & Hampl, V. (2024). The protist cultural renaissance. Trends in Microbiology, 32(2), 128-131.
Feng, X., Méndez-Sánchez, D., Zhuang, W., Li, R., Pomahač, O., Čepička, I., Rotterová, J. & Hu, X. (2024). Morphology, morphogenesis, and molecular characterization of Castula specialis sp. nov. (Ciliophora, Armophorea, Metopida). Journal of Eukaryotic Microbiology, 71(2), e13014.
Pavlátová, M., Hanousková, P. & Čepička, I. (2024). Anaeramoeba pumila sp. nov. and Anaeramoeba sp. OCE22C represent two novel types of symbiosis of Anaeramoebae and prokaryotes. Journal of Eukaryotic Microbiology, 71: e13008.
Kotyk, M., Bourland, W.A., Soviš, M., Méndez-Sánchez, D., Škaloud, P., Kotyková Varadínová, Z. & Čepička, I. (2024). Morphology matters: congruence of morphology and phylogeny in the integrative taxonomy of Clevelandellidae (Ciliophora: Armophorea) with description of six new species. Zoological Journal of the Linnean Society, in press.
Gallot-Lavallée, L., Jerlström-Hultqvist, J, Zegarra-Vidarte, P., Salas-Leiva, D.E., Stairs, C.W., Čepička, I., Roger, A.J. & Archibald, J.M. (2023) Massive intein content in Anaeramoeba reveals aspects of intein mobility in eukaryotes. Proceedings of the National Academy of Sciences of the United States of America, 120 (49), e2306381120.
Mazancová, E., Zadrobílková, E., Yubuki, N. & Čepička, I. (2023) Phylogenetic and morphological diversity of free-living diplomonads. European Journal of Protistology, 91, 126024.
Záhonová, K., Füssy Z., Stairs, C.W., Legerm M.M., Tachezy, J, Čepička, I., Roger, A.J. & Hampl, V. (2023). Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans. Microbial Genomics, 9(11), 001143.
Treitli, S., Hanousková, P., Beneš, V., Brune, A., Čepička, I. & Hampl, V. (2023). Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti. The ISME Journal, 17, 1884-1894.
Poláková, K., Bourland, W. A., & Čepička, I. (2023). Anaerocyclidiidae fam. nov. (Oligohymenophorea, Scuticociliatia): A newly recognized major lineage of anaerobic ciliates hosting prokaryotic symbionts. European Journal of Protistology, 90, 126009.
Venkatachalam, A. K. S. B., Čepička, I., Hrazdilová, K., & Svobodová, M. (2023). Host specificity of passerine Lankesterella (Apicomplexa: Coccidia). European Journal of Protistology, 90, 126007.
Barmshuri, M., Pomahač, O., & Bourland, W. (2023). Enchelyothrix muria n. gen, n. sp., (Ciliophora, Litostomatea, Spathidiida), an extreme halotroph spathidiid from Maharloo Lake, Iran. European Journal of Protistology, 126005.
Jerlström-Hultqvist, J., Gallot-Lavallée, L., Salas-Leiva, D. E., Curtis, B. A., Záhonová, K., Čepička, I., Stairs, C. W., Pipaliya, S., Dacks, J. B., Archibald, J. M., & Roger, A. J. (2023). A unique symbiosome in an anaerobic single-celled eukaryote. bioRxiv, 2023-03.
Pomahač, O., Méndez-Sánchez, D., Poláková, K., Müller, M., Solito, M. M., Bourland, W. A., & Čepička, I. (2023). Rediscovery of remarkably rare anaerobic tentaculiferous ciliate genera Legendrea and Dactylochlamys (Ciliophora: Litostomatea). Biology-Basel, 12(5), 707.
Méndez‐Sánchez, D., Pomahač, O., Rotterová, J., Bourland, W. A., & Čepička, I. (2023). Morphology and phylogenetic position of three anaerobic ciliates from the classes Odontostomatea and Muranotrichea (Ciliophora). Journal of Eukaryotic Microbiology, 70, e12965.
Svobodová, M., Čepička, I., Zídková, L., Kassahun, A., Votýpka, J., Peške, L., Hrazdilová, K., Brzoňová, J., Voříšek, P., Weidinger, K. (2023). Blood parasites (Trypanosoma, Leucocytozoon, Haemoproteus) in the Eurasian sparrowhawk (Accipiter nisus): diversity, incidence and persistence of infection at the individual level. Parasites & Vectors, 16(1), 1-16.
Méndez-Sánchez, D., Pomahač, O., Rotterová, J., Bourland, W., Čepička, I. (2022). Diversity and Phylogenetic Position of Bothrostoma Stokes, 1887 (Ciliophora: Metopida), with Description of Four New Species. Protist, Volume 173, Issue 4,
125887.
Céza V., Kotyk M., Kubánková A., Yubuki N, Šťáhlavský F, Silberman JD, Čepička I. (2022). Free-living trichomonads are unexpectedly diverse. Protist 173: 122833.
Pilátová J, Pánek T., Oborník M., Čepička I., Mojzeš P. (2022). Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes. ISME Journal 16: 2290-2294.
Vargová, R., Hanousková, P., Salamanová, J., Žihala, D., Silberman, JD, Eliáš M., Čepička I. (2022). Evidence for an independent hydrogenosome-to-mitosome transition in the CL3 lineage of fornicates. Frontiers in Microbiology 13: 86645.
Rotterová J., Edgcomb VP, Čepička I., Beinart R. (2022). Anaerobic ciliates as a model group for studying symbioses in oxygen-depleted environments. Journal of Eukaryotic Microbiology 5: e12912.
Pánek, T., Barcytė, D., Treitli, S.C., Záhonová K., Sokol M., Ševčíková T., Zadrobílková E., Jaške K., Yubuki N., Čepička I., Eliáš M. (2022), A new lineage of non-photosynthetic green algae with extreme organellar genomes. BMC Biology 20, 66.
Záhonová, K., Treitli, S. C., Le, T., Škodová-Sveráková, I., Hanousková, P., Čepička, I., ... & Hampl, V. (2022). Anaerobic derivates of mitochondria and peroxisomes in the free-living amoeba Pelomyxa schiedti revealed by single-cell genomics. BMC Biology, 20(1), 1-16.
Bourland, W., Pomahač, O., & Čepička, I. (2022). Morphology and phylogeny of two anaerobic freshwater ciliates: Brachonella comma sp. nov. and the widely distributed but little‐known caenomorphid, Ludio parvulus Penard, 1922. Journal of Eukaryotic Microbiology, 69:3.
Brotánková, A., Fialová, M., Čepička, I., Brzoňová, J., & Svobodová, M. (2022). Trypanosomes of the Trypanosoma theileri group: Phylogeny and new potential vectors. Microorganisms, 10(2), 294.
Santolíková, A., Brzoňová, J., Čepička, I., & Svobodová, M. (2022). Avian Louse Flies and Their Trypanosomes: New Vectors, New Lineages and Host–Parasite Associations. Microorganisms, 10(3), 584.
Pilátová J., Pánek T., Oborník M., Čepička I., Mojzeš P. (2022) Paradigm shift in eukaryotic biocrystallization. bioRxiv: 2022.01.11.475817
STAIRS, C. W., TÁBORSKÝ, P., SALOMAKI, E. D., KOLÍSKO, M., PÁNEK, T., EME, L., ... & ČEPIČKA, I. (2021). Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes. Current Biology, 31(24), 5605-5612.
SOUKAL P, HRDÁ Š, KARNKOWSKA A, MILANOWSKI R, SZABOVÁ J, HRADILOVÁ M, STRNAD H., VLČEK Č, ČEPIČKA I, HAMPL V. 2021. Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology. Scientific Reports 11: 13070
FÜSSY Z, VINOPALOVÁ M, TREITLI SC, PÁNEK T, SMEJKALOVÁ P, ČEPIČKA I, DOLEŽAL P, HAMPL V. 2021. Retortamonads from vertebrate hosts share features of anaerobic metabolism and pre-adaptations to parasitism with diplomonads. Parasitology International 82: 102308
POLÁKOVÁ K, ČEPIČKA I, BOURLAND W. 2021. Phylogenetic position of three well-known ciliates from the controversial order Loxocephalida Jankowski, 1980 (Scuticociliatia, Oligohymenophorea) and Urozona buetschlii (Schewiakoff, 1889) with improved morphological descriptions. Protist 172: 125833
SALOMAKI ED, TERPIS KX, RUECKERT S, KOTYK M, KOTYKOVÁ VARADÍNOVÁ Z, ČEPIČKA I, LANE CE, KOLISKO M. 2021. Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans. BMC Biology 19: 77
PÁNEK T., 2021. Protozoa. In: Encyclopedia of Life Sciences, John Wiley & Sons. (Book chapter).
HORVÁTHOVÁ L., ŽÁRSKÝ V., PÁNEK T., DERELLE R., PYRIH J., MOTYČKOVÁ A., KLÁPŠŤOVÁ V., VINOPALOVÁ M., MARKOVÁ L., VOLEMAN L., KLIMEŠ V., PETRŮ M., VAITOVÁ Z., ČEPIČKA I., HRYZÁKOVÁ K., HARANT K., GRAY M., CHAMI M., GUILVOUT I., FRANCETIC O.B., LANG F., VLČEK Č., TSAOUSIS A., ELIÁŠ M., DOLEŽAL P., 2021. Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. Nature Communications 12: 2947.
PYRIH J., PÁNEK T., DURANTE I., RAŠKOVÁ V., CIMRHANZLOVÁ K., KRIEGOVÁ E., TSAOUSIS A., ELIÁŠ M., LUKEŠ J., 2021. Vestiges of the bacterial signal recognition particle-based protein targeting in mitochondria. Molecular Biology and Evolution Volume 38, Issue 8, August 2021, Pages 3170–3187.
KOLÁTKOVÁ V, ČEPIČKA I, HOFFMAN R, VOHNÍK M. 2021. Marinomyxa gen. nov. (Endomyxa: Phytomyxea) accommodates widespread gall-forming parasites of the tropical to subtropical seagrass genus Halophila. Microbial Ecology 81: 673-686
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 J, ČEPIČKA 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 J, ČEPIČKA 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 J, ČEPIČKA 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 J, ČEPIČKA 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.