{"id":230,"date":"2022-08-08T23:31:06","date_gmt":"2022-08-08T23:31:06","guid":{"rendered":"http:\/\/demon-protists.eu\/?page_id=230"},"modified":"2024-01-25T12:40:41","modified_gmt":"2024-01-25T11:40:41","slug":"publications","status":"publish","type":"page","link":"https:\/\/demon-protists.eu\/?page_id=230","title":{"rendered":"Publications"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"230\" class=\"elementor elementor-230\">\n\t\t\t\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-2aaa160 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"2aaa160\" data-element_type=\"section\" data-settings=\"{&quot;_ha_eqh_enable&quot;:false}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-bb5a4e3\" data-id=\"bb5a4e3\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-962f4d3 elementor-widget elementor-widget-heading\" data-id=\"962f4d3\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<style>\/*! elementor - v3.6.8 - 27-07-2022 *\/\n.elementor-heading-title{padding:0;margin:0;line-height:1}.elementor-widget-heading .elementor-heading-title[class*=elementor-size-]>a{color:inherit;font-size:inherit;line-height:inherit}.elementor-widget-heading .elementor-heading-title.elementor-size-small{font-size:15px}.elementor-widget-heading .elementor-heading-title.elementor-size-medium{font-size:19px}.elementor-widget-heading .elementor-heading-title.elementor-size-large{font-size:29px}.elementor-widget-heading .elementor-heading-title.elementor-size-xl{font-size:39px}.elementor-widget-heading .elementor-heading-title.elementor-size-xxl{font-size:59px}<\/style><h2 class=\"elementor-heading-title elementor-size-default\">Relevant Publications<\/h2>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-ef71424 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"ef71424\" data-element_type=\"section\" data-settings=\"{&quot;_ha_eqh_enable&quot;:false}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-f7b6dbd\" data-id=\"f7b6dbd\" data-element_type=\"column\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t\t\t<div class=\"elementor-element elementor-element-11fa8f6 elementor-widget elementor-widget-heading\" data-id=\"11fa8f6\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h4 class=\"elementor-heading-title elementor-size-default\">Consortium Publications<\/h4>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-18b68d1 elementor-widget elementor-widget-text-editor\" data-id=\"18b68d1\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<style>\/*! elementor - v3.6.8 - 27-07-2022 *\/\n.elementor-widget-text-editor.elementor-drop-cap-view-stacked .elementor-drop-cap{background-color:#818a91;color:#fff}.elementor-widget-text-editor.elementor-drop-cap-view-framed .elementor-drop-cap{color:#818a91;border:3px solid;background-color:transparent}.elementor-widget-text-editor:not(.elementor-drop-cap-view-default) .elementor-drop-cap{margin-top:8px}.elementor-widget-text-editor:not(.elementor-drop-cap-view-default) .elementor-drop-cap-letter{width:1em;height:1em}.elementor-widget-text-editor .elementor-drop-cap{float:left;text-align:center;line-height:1;font-size:50px}.elementor-widget-text-editor .elementor-drop-cap-letter{display:inline-block}<\/style>\t\t\t\t<ul>\n<li style=\"\" aria-level=\"1\">Del Campo, J., Carlos-Oliveira, M., \u010cepi\u010dka, I., Hehenberger, E., Hor\u00e1k, A., Karnkowska, A., Kol\u00edsko, M., Lara, E., Luke\u0161 J., P\u00e1nek, T., Piwosz, K., Richter, D., \u0160kaloud, P., Sutak, R., Tachezy, J., Hampl, V. (2024). The protist cultural renaissance. Trends in Microbiology, in press.<br><\/li>\n<\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8064e81 elementor-widget elementor-widget-heading\" data-id=\"8064e81\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h4 class=\"elementor-heading-title elementor-size-default\">Metabarcoding<\/h4>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-56a7051 elementor-widget elementor-widget-text-editor\" data-id=\"56a7051\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Flegontova O, Flegontov P, Malviya S, Audic S, Wincker P, de Vargas C, Bowler C, Luke\u0161 J, Hor\u00e1k A. Extreme Diversity of Diplonemid Eukaryotes in the Ocean. Curr Biol. 2016 Nov 21;26(22):3060-3065. doi: 10.1016\/j.cub.2016.09.031<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">del Campo, J., Kolisko, M., Boscaro, V., Santoferrara, L. F., Nenarokov, S., Massana, R., Guillou, L., Simpson, A. G. B., Berney, C., de Vargas, C., Brown, M. W., Keeling, P. J., &amp; Wegener Parfrey, L. (2018). EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. <\/span><i><span style=\"font-weight: 400;\">PLOS Biology<\/span><\/i><span style=\"font-weight: 400;\">, <\/span><i><span style=\"font-weight: 400;\">16<\/span><\/i><span style=\"font-weight: 400;\">(9), e2005849. https:\/\/doi.org\/10.1371\/journal.pbio.2005849<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Metz S, Singer D, Domaizon I, Unrein F, Lara E. Global distribution of Trebouxiophyceae diversity explored by high-throughput sequencing and phylogenetic approaches. Environ Microbiol. 2019 Oct;21(10):3885-3895. doi: 10.1111\/1462-2920.14738<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Flegontova O., Flegontov P., Casta\u0148eda Londo\u0148o P., Walczowski W., \u015aanti\u0107 D., Edgcomb V., Luke\u0161 J., Hor\u00e1k A. (2020) Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans Environmental Microbiology 22: 4014\u20134031. doi: 10.1111\/1462-2920.15190<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Flegontova O., Flegontov P., Malviya S., Poulain J., de Vargas C., Bowler C., Luke\u0161 J., Hor\u00e1k A. (2018) Neobodonids are dominant kinetoplastids in the global ocean Environmental Microbiology 20: 878-889. doi:\u00a0 10.1111\/1462-2920.14034<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Luke\u0161ov\u00e1 S, Karlicki M, Tome\u010dkov\u00e1 Hadariov\u00e1 L, Szabov\u00e1 J, Karnkowska A, Hampl V. Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments. Environ Microbiol Rep. 2020 Feb;12(1):78-91. doi: 10.1111\/1758-2229.12817<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Singer D, Seppey CVW, Lentendu G, Dunthorn M, Bass D, Belbahri L, Blandenier Q, Debroas D, de Groot GA, de Vargas C, Domaizon I, Duckert C, Izaguirre I, Koenig I, Mataloni G, Schiaffino MR, Mitchell EAD, Geisen S, Lara E. Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems. Environ Int. 2021 Jan;146:106262. doi: 10.1016\/j.envint.2020.106262<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">del Campo, J., Heger, T. J., Rodr\u00edguez-Mart\u00ednez, R., Worden, A. Z., Richards, T. A., Massana, R., Keeling, P. J., del Campo, J., Heger, T. J., Rodr\u00edguez-Mart\u00ednez, R., Worden, A. Z., Richards, T. A., Massana, R., &amp; Keeling, P. J. (2019). Assessing the diversity and distribution of apicomplexans in host and free-living environments using high-throughput amplicon data and a phylogenetically informed reference framework. <\/span><i><span style=\"font-weight: 400;\">Frontiers in Microbiology<\/span><\/i><span style=\"font-weight: 400;\">, <\/span><i><span style=\"font-weight: 400;\">10<\/span><\/i><span style=\"font-weight: 400;\">(OCT), 1\u201315. https:\/\/doi.org\/10.3389\/fmicb.2019.02373<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Piwosz, K., Ca\u0142kiewicz, J., Go\u0142\u0119biewski, M., and Creer, S. (2018) Diversity and community composition of pico- and nanoplanktonic protists in the Vistula River estuary (Gulf of Gda\u0144sk, Baltic Sea). Estuar Coast Shelf Sci 207: 242-249<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">P\u00e1nek T, T\u00e1borsk\u00fd P, Pachiadaki MG, Hroudov\u00e1 M, Vl\u010dek \u010c, Edgcomb VP, \u010cepi\u010dka I. Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage. Front Microbiol. 2015 Nov 18;6:1288. doi: 10.3389\/fmicb.2015.01288<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Kolisko M, Flegontova O, Karnkowska A, Lax G, Maritz JM, P\u00e1nek T, T\u00e1borsk\u00fd P, Carlton JM, \u010cepi\u010dka I, Hor\u00e1k A, Luke\u0161 J, Simpson AGB, Tai V. EukRef-excavates: seven curated SSU ribosomal RNA gene databases. Database (Oxford). 2020 Nov 20;2020:baaa080. doi: 10.1093\/database\/baaa080<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">\u0141ukomska-Kowalczyk M, Karnkowska A, Krupska M, Milanowski R, Zakry\u015b B. DNA barcoding in autotrophic euglenids: evaluation of COI and 18s rDNA. J Phycol. 2016 Dec;52(6):951-960. doi: 10.1111\/jpy.12439<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Piwosz K, Shabarova T, Pernthaler J, Posch T, \u0160imek K, Porcal P, Salcher MM. Bacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological Interpretations. mSphere. 2020 Mar 4;5(2):e00052-20. doi: 10.1128\/mSphere.00052-20<\/span><\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-dd03b47 elementor-widget elementor-widget-heading\" data-id=\"dd03b47\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Ecology, Biogeography<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-96b9773 elementor-widget elementor-widget-text-editor\" data-id=\"96b9773\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Flegontova O, Flegontov P, Malviya S, Audic S, Wincker P, de Vargas C, Bowler C, Luke\u0161 J, Hor\u00e1k A. Extreme Diversity of Diplonemid Eukaryotes in the Ocean. Curr Biol. 2016 Nov 21;26(22):3060-3065. doi: 10.1016\/j.cub.2016.09.031<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Singer D, Mitchell EAD, Payne RJ, Blandenier Q, Duckert C, Fern\u00e1ndez LD, Fournier B, Hern\u00e1ndez CE, Granath G, Rydin H, Bragazza L, Koronatova NG, Goia I, Harris LI, Kajuka\u0142o K, Kosakyan A, Lamentowicz M, Kosykh NP, Vellak K, Lara E. Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists. Mol Ecol. 2019 Jun;28(12):3089-3100. doi: 10.1111\/mec.15117<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Prokopchuk, G., Koryt\u00e1\u0159, T., Juricov\u00e1, V. Majstorovi\u0107, J., Hor\u00e1k, A., \u0160imek, K., Luke\u0161, J. 2022. Trophic flexibility of marine diplonemids &#8211; switching from osmotrophy to bacterivory. ISME J. https:\/\/doi.org\/10.1038\/s41396-022-01192-0<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Malych R, Stopka P, Mach J, Kotabov\u00e1 E, Pr\u00e1\u0161il O, Sutak R. Flow cytometry-based study of model marine microalgal consortia revealed an ecological advantage of siderophore utilization by the dinoflagellate <\/span><i><span style=\"font-weight: 400;\">Amphidinium carterae<\/span><\/i><span style=\"font-weight: 400;\">. Comput Struct Biotechnol J. 2021 Dec 20;20:287-295. doi: 10.1016\/j.csbj.2021.12.023<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Kotabova E, Malych R, Pierella Karlusich JJ, Kazamia E, Eichner M, Mach J, Lesuisse E, Bowler C, Pr\u00e1\u0161il O, Sutak R. Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability. mSystems. 2021 Feb 9;6(1):e00738-20. doi: 10.1128\/mSystems.00738-20<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Flegontova O., Flegontov P., Casta\u0148eda Londo\u0148o P., Walczowski W., \u015aanti\u0107 D., Edgcomb V., Luke\u0161 J., Hor\u00e1k A. (2020) Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans Environmental Microbiology 22: 4014\u20134031. doi: 10.1111\/1462-2920.15190<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Flegontova O., Flegontov P., Malviya S., Poulain J., de Vargas C., Bowler C., Luke\u0161 J., Hor\u00e1k A. (2018) Neobodonids are dominant kinetoplastids in the global ocean Environmental Microbiology 20: 878-889. doi:\u00a0 10.1111\/1462-2920.14034<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Janou\u0161kovec J., Hor\u00e1k A., Barott K., Rohwer F., Keeling P. (2012) Global analysis of plastid diversity reveals apicomplexan-related lineages in coral reefs. Current Biology 22: R518\u2013R519. doi: 10.1016\/j.cub.2012.04.047<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Janou\u0161kovec J., Hor\u00e1k A., Barott K., Rohwer F., Keeling P. (2013) Environmental distribution of coral-associated relatives of apicomplexan parasites. ISME journal 7: 444-447. doi: 10.1038\/ismej.2012.129<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Singer, D., Kosakyan, A., Seppey, C.V.W., Pillonel, A., Fernandez, L.D., Fontaneto, D., Mitchell, E.A.D., Lara, E., 2018. Environmental filtering and phylogenetic clustering correlate with the distribution patterns of cryptic protist species. Ecology 99, 904-914.\u00a0<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">\u0160kaloud, P., \u0160kaloudov\u00e1, M., Dosko\u010dilov\u00e1, P., Kim, J.I., Shin, W., Dvo\u0159\u00e1k, P., 2019. Speciation in protists: Spatial and ecological divergence processes cause rapid species diversification in a freshwater chrysophyte. Mol Ecol 28:,1084-1095<\/span><\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-f328eb3 elementor-widget elementor-widget-heading\" data-id=\"f328eb3\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Genomics, Transcriptomics<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-8ec2194 elementor-widget elementor-widget-text-editor\" data-id=\"8ec2194\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Rotterov\u00e1 J, Salomaki E, P\u00e1nek T, Bourland W, \u017dihala D, T\u00e1borsk\u00fd P, Edgcomb VP, Beinart RA, Kol\u00edsko M, \u010cepi\u010dka I. Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis. Curr Biol. 2020 Jun 8;30(11):2037-2050.e6. doi: 10.1016\/j.cub.2020.03.064<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">\u017d\u00e1rsk\u00fd V, Klime\u0161 V, Pa\u010des J, Vl\u010dek \u010c, Hradilov\u00e1 M, Bene\u0161 V, N\u00fdvltov\u00e1 E, Hrd\u00fd I, Pyrih J, Mach J, Barlow L, Stairs CW, Eme L, Hall N, Eli\u00e1\u0161 M, Dacks JB, Roger A, Tachezy J. The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba. Mol Biol Evol. 2021 May 19;38(6):2240-2259. doi: 10.1093\/molbev\/msab020<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Karnkowska A, Vacek V, Zub\u00e1\u010dov\u00e1 Z, Treitli SC, Petr\u017eelkov\u00e1 R, Eme L, Nov\u00e1k L, \u017d\u00e1rsk\u00fd V, Barlow LD, Herman EK, Soukal P, Hroudov\u00e1 M, Dole\u017eal P, Stairs CW, Roger AJ, Eli\u00e1\u0161 M, Dacks JB, Vl\u010dek \u010c, Hampl V. A Eukaryote without a Mitochondrial Organelle. Curr Biol. 2016 May 23;26(10):1274-84. doi: 10.1016\/j.cub.2016.03.053<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Woo Y., Ansari H., Otto T.D., Klinger C., Kol\u00edsko M., Mich\u00e1lek J., Saxena A., Shanmugam D., Tayyrov A., Veluchamy A., Ali S., Bernal A., Del C., Cihl\u00e1\u0159 J., Flegontov P., Gornik S., Hajdu\u0161kov\u00e1 E., Hor\u00e1k A., Janou\u0161kovec J., Katris N., Mast F., Miranda-Saavedra D., Mourier T., Naeem R., Nair M., Panigrahi A., Rawlings N., Regelado E., Ramaprasad A., Samad N., Tom\u010dala A., Wilkes J., Neafsey D., Doerig C., Bowler C., Keeling P., Roos D., Dacks J., Templeton T., Waller R., Luke\u0161 J., Oborn\u00edk M., Pain A. (2015) &#8220;Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites &#8221; eLife 4: e06974. doi: 10.7554\/eLife.06974<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">\u0160kodov\u00e1-Sver\u00e1kov\u00e1 I., Z\u00e1honov\u00e1 K., Juricov\u00e1 V., Danchenko M., Moos M., Bar\u00e1th P., Prokopchuk G., Butenko A., Luk\u00e1\u010dov\u00e1 V., Koh\u00fatov\u00e1 L., Bu\u010dkov\u00e1 B., Hor\u00e1k A., Faktorov\u00e1 D., Horv\u00e1th A., \u0160imek P., Luke\u0161 J. (2021) Highly flexible metabolism of the marine euglenozoan protist \/Diplonema papillatum\/. BMC Biology 19: 251. doi: 10.1186\/s12915-021-01186-y<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Treitli SC, Pe\u00f1a-Diaz P, Ha\u0142akuc P, Karnkowska A, Hampl V. High quality genome assembly of the amitochondriate eukaryote <\/span><i><span style=\"font-weight: 400;\">Monocercomonoides exilis<\/span><\/i><span style=\"font-weight: 400;\">. Microb Genom. 2021 Dec;7(12):000745. doi: 10.1099\/mgen.0.000745<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Soukal P, Hrd\u00e1 \u0160, Karnkowska A, Milanowski R, Szabov\u00e1 J, Hradilov\u00e1 M, Strnad H, Vl\u010dek \u010c, \u010cepi\u010dka I, Hampl V. Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology. Sci Rep. 2021 Jun 22;11(1):13070. doi: 10.1038\/s41598-021-92174-3<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Albanaz ATS, Gerasimov ES, Shaw JJ, S\u00e1dlov\u00e1 J, Luke\u0161 J, Volf P, Opperdoes FR, Kostygov AY, Butenko A, Yurchenko V. Genome Analysis of <\/span><i><span style=\"font-weight: 400;\">Endotrypanum<\/span><\/i><span style=\"font-weight: 400;\"> and <\/span><i><span style=\"font-weight: 400;\">Porcisia<\/span><\/i><span style=\"font-weight: 400;\"> spp., Closest Phylogenetic Relatives of <\/span><i><span style=\"font-weight: 400;\">Leishmania<\/span><\/i><span style=\"font-weight: 400;\">, Highlights the Role of Amastins in Shaping Pathogenicity. Genes (Basel). 2021 Mar 20;12(3):444. doi: 10.3390\/genes12030444<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Gerasimov ES, Gasparyan AA, Afonin DA, Zimmer SL, Kraeva N, Luke\u0161 J, Yurchenko V, Kolesnikov A. Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non-canonical mitochondrial RNA editing events. Nucleic Acids Res. 2021 Apr 6;49(6):3354-3370. doi: 10.1093\/nar\/gkab114<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Kayama M, Maciszewski K, Yabuki A, Miyashita H, Karnkowska A, Kamikawa R (2020). Highly reduced plastid genomes of the non-photosynthetic dictyochophyceans <\/span><i><span style=\"font-weight: 400;\">Pteridomonas <\/span><\/i><span style=\"font-weight: 400;\">spp. (Ochrophyta, SAR) are retained for tRNA-Glu-based organellar heme biosynthesis. <\/span><i><span style=\"font-weight: 400;\">Front Plant Sci<\/span><\/i><span style=\"font-weight: 400;\">, doi: 10.3389\/fpls.2020.602455<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Baku\u0142a Z, Gromadka R, Gawor J, Siedlecki P, Pomorski J, Maciszewski K, Gromadka A, Karnkowska A, Jagielski T (2020) Sequencing and analysis of the complete organellar genomes of <\/span><i><span style=\"font-weight: 400;\">Prototheca wickerhamii<\/span><\/i><span style=\"font-weight: 400;\">. <\/span><i><span style=\"font-weight: 400;\">Frontiers in Plant Science<\/span><\/i><span style=\"font-weight: 400;\">:\u00a0 doi: 10.3389\/fpls.2020.01296<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Han KY, Maciszewski K, Graf L, Yang JH, Andersen RA, Karnkowska A, Yoon HS. Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization. J Phycol. 2019 Oct;55(5):1166-1180. doi: 10.1111\/jpy.12904<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Opperdoes FR, Butenko A, Zakharova A, Gerasimov ES, Zimmer SL, Luke\u0161 J, Yurchenko V. The Remarkable Metabolism of <\/span><i><span style=\"font-weight: 400;\">Vickermania ingenoplastis<\/span><\/i><span style=\"font-weight: 400;\">: Genomic Predictions. Pathogens. 2021 Jan 14;10(1):68. doi: 10.3390\/pathogens10010068<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Leger MM, Kolisko M, Kamikawa R, Stairs CW, Kume K, \u010cepi\u010dka I, Silberman JD, Andersson JO, Xu F, Yabuki A, Eme L, Zhang Q, Takishita K, Inagaki Y, Simpson AGB, Hashimoto T, Roger AJ. Organelles that illuminate the origins of <\/span><i><span style=\"font-weight: 400;\">Trichomonas<\/span><\/i><span style=\"font-weight: 400;\"> hydrogenosomes and <\/span><i><span style=\"font-weight: 400;\">Giardia<\/span><\/i><span style=\"font-weight: 400;\"> mitosomes. Nat Ecol Evol. 2017 Apr 1;1(4):0092. doi: 10.1038\/s41559-017-0092<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Hehenberger E, Tikhonenkov DV, Kolisko M, Del Campo J, Esaulov AS, Mylnikov AP, Keeling PJ. Novel Predators Reshape Holozoan Phylogeny and Reveal the Presence of a Two-Component Signaling System in the Ancestor of Animals. Curr Biol. 2017 Jul 10;27(13):2043-2050.e6. doi: 10.1016\/j.cub.2017.06.006<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Boscaro V, Kolisko M, Felletti M, Vannini C, Lynn DH, Keeling PJ. Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nat Ecol Evol. 2017 Aug;1(8):1160-1167. doi: 10.1038\/s41559-017-0237-0. Epub 2017 Jul 21<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Mathur V, Kol\u00edsko M, Hehenberger E, Irwin NAT, Leander BS, Kristmundsson \u00c1, Freeman MA, Keeling PJ. Multiple Independent Origins of Apicomplexan-Like Parasites. Curr Biol. 2019 Sep 9;29(17):2936-2941.e5. doi: 10.1016\/j.cub.2019.07.019<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Salas-Leiva DE, Tromer EC, Curtis BA, Jerlstr\u00f6m-Hultqvist J, Kolisko M, Yi Z, Salas-Leiva JS, Gallot-Lavall\u00e9e L, Williams SK, Kops GJPL, Archibald JM, Simpson AGB, Roger AJ. Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist. Nat Commun. 2021 Oct 14;12(1):6003. doi: 10.1038\/s41467-021-26077-2. Erratum in: Nat Commun. 2021 Dec 16;12(1):7350<\/span><\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-7d9112b elementor-widget elementor-widget-heading\" data-id=\"7d9112b\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Phylogenomics<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-d3ebce1 elementor-widget elementor-widget-text-editor\" data-id=\"d3ebce1\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Tice AK, \u017dihala D, P\u00e1nek T, Jones RE, Salomaki ED, Nenarokov S, Burki F, Eli\u00e1\u0161 M, Eme L, Roger AJ, Rokas A, Shen XX, Strassert JFH, Kol\u00edsko M, Brown MW. PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. PLoS Biol. 2021 Aug 6;19(8):e3001365. doi: 10.1371\/journal.pbio.3001365<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AG, Roger AJ. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic &#8220;supergroups&#8221;. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3859-64. doi: 10.1073\/pnas.0807880106<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Janou\u0161kovec J., Hor\u00e1k A., Oborn\u00edk M., Luke\u0161 J., Keeling P. (2010) A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. Proceedings of the National Academy of Sciences of the United States of America 107: 10949\u201310954. DOI: 10.1073\/pnas.1003335107<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Kostygov AY, Karnkowska A, Vot\u00fdpka J, Tashyreva D, Maciszewski K, Yurchenko V, Luke\u0161 J. Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses. Open Biol. 2021 Mar;11(3):200407. doi: 10.1098\/rsob.200407<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Butenko A, Hammond M, Field MC, Ginger ML, Yurchenko V, Luke\u0161 J. Reductionist Pathways for Parasitism in Euglenozoans? Expanded Datasets Provide New Insights. Trends Parasitol. 2021 Feb;37(2):100-116. doi: 10.1016\/j.pt.2020.10.001<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Butenko A, Opperdoes FR, Flegontova O, Hor\u00e1k A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Luke\u0161 J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol. 2020 Mar 2;18(1):23. doi: 10.1186\/s12915-020-0754-1.<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">\u0160ev\u010d\u00edkov\u00e1 T., Hor\u00e1k A., Klime\u0161 V., Zbr\u00e1nkov\u00e1 V., Demir-Hilton E., Sudek S., Jenkins J., Schmutz J., P\u0159ibyl P., Vl\u010dek \u010c., Lang B., Oborn\u00edk M., Worden A., Eli\u00e1\u0161 M. (2015) Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? Scientific Reports 5: 10134. doi: 10.1038\/srep10134<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Gentekaki E, Kolisko M, Gong Y, Lynn D. Phylogenomics solves a long-standing evolutionary puzzle in the ciliate world: The subclass Peritrichia is monophyletic. Mol Phylogenet Evol. 2017 Jan;106:1-5. doi: 10.1016\/j.ympev.2016.09.016<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Salomaki ED, Eme L, Brown MW, Kolisko M. Releasing uncurated datasets is essential for reproducible phylogenomics. Nat Ecol Evol. 2020 Nov;4(11):1435-1437. doi: 10.1038\/s41559-020-01296-w<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Heiss AA, Kolisko M, Ekelund F, Brown MW, Roger AJ, Simpson AGB. Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes. R Soc Open Sci. 2018 Apr 4;5(4):171707. doi: 10.1098\/rsos.171707<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Lynn DH, Kolisko M, Bourland W. Phylogenomic Analysis of Nassula variabilis n. sp., Furgasonia blochmanni, and Pseudomicrothorax dubius Confirms a Nassophorean Clade. Protist. 2018 Apr;169(2):180-189. doi: 10.1016\/j.protis.2018.02.002<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Lynn DH, Kolisko M. Molecules illuminate morphology: phylogenomics confirms convergent evolution among &#8216;oligotrichous&#8217; ciliates. Int J Syst Evol Microbiol. 2017 Sep;67(9):3676-3682. doi: 10.1099\/ijsem.0.002060<\/span><\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-bbd5676 elementor-widget elementor-widget-heading\" data-id=\"bbd5676\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Single-cell<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-151c9f4 elementor-widget elementor-widget-text-editor\" data-id=\"151c9f4\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Treitli SC, Kolisko M, Husn\u00edk F, Keeling PJ, Hampl V. Revealing the metabolic capacity of <\/span><i><span style=\"font-weight: 400;\">Streblomastix strix<\/span><\/i><span style=\"font-weight: 400;\"> and its bacterial symbionts using single-cell metagenomics. Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19675-19684. doi: 10.1073\/pnas.1910793116<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Beinart RA, Rotterov\u00e1 J, \u010cepi\u010dka I, Gast RJ, Edgcomb VP. The genome of an endosymbiotic methanogen is very similar to those of its free-living relatives. Environ Microbiol. 2018 Jul;20(7):2538-2551. doi: 10.1111\/1462-2920.14279<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Gawryluk, R. M. R., del Campo, J., Okamoto, N., Strassert, J. F. H., Luke\u0161, J., Richards, T. A., Worden, A. Z., Santoro, A. E., &amp; Keeling, P. J. (2016). Morphological Identification and Single-Cell Genomics of Marine Diplonemids. <\/span><i><span style=\"font-weight: 400;\">Current Biology<\/span><\/i><span style=\"font-weight: 400;\">, <\/span><i><span style=\"font-weight: 400;\">26<\/span><\/i><span style=\"font-weight: 400;\">(22), 3053\u20133059. ttps:\/\/doi.org\/10.1016\/j.cub.2016.09.013<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Strassert JFH, Karnkowska A, Hehenberger E, Del Campo J, Kolisko M, Okamoto N, Burki F, Janou\u0161kovec J, Poirier C, Leonard G, Hallam SJ, Richards TA, Worden AZ, Santoro AE, Keeling PJ. Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. ISME J. 2018 Jan;12(1):304-308. doi: 10.1038\/ismej.2017.167<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Z\u00e1honov\u00e1 K, Lax G, Sinha SD, Leonard G, Richards TA, Luke\u0161 J, Wideman JG. Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans. BMC Biol. 2021 May 17;19(1):103. doi: 10.1186\/s12915-021-01035-y<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">\u200b\u200bSalomaki ED, Terpis KX, Rueckert S, Kotyk M, Varad\u00ednov\u00e1 ZK, \u010cepi\u010dka I, Lane CE, Kolisko M. Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans. BMC Biol. 2021 Apr 16;19(1):77. doi: 10.1186\/s12915-021-01007-2<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Lax G, Kolisko M, Eglit Y, Lee WJ, Yubuki N, Karnkowska A, Leander BS, Burger G, Keeling PJ, Simpson AGB. Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Mol Phylogenet Evol. 2021 Jun;159:107088. doi: 10.1016\/j.ympev.2021.107088<\/span><\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-eaf4e76 elementor-widget elementor-widget-heading\" data-id=\"eaf4e76\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Taxonomy, Diversity, Cultivation of New Lineage<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-ae83506 elementor-widget elementor-widget-text-editor\" data-id=\"ae83506\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Lahr DJG, Kosakyan A, Lara E, Mitchell EAD, Morais L, Porfirio-Sousa AL, Ribeiro GM, Tice AK, P\u00e1nek T, Kang S, Brown MW. Phylogenomics and Morphological Reconstruction of Arcellinida Testate Amoebae Highlight Diversity of Microbial Eukaryotes in the Neoproterozoic. Curr Biol. 2019 Mar 18;29(6):991-100<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Stairs CW, T\u00e1borsk\u00fd P, Salomaki ED, Kolisko M, P\u00e1nek T, Eme L, Hradilov\u00e1 M, Vl\u010dek \u010c, Jerlstr\u00f6m-Hultqvist J, Roger AJ, \u010cepi\u010dka I. Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes. Curr Biol. 2021 Dec 20;31(24):5605-5612.e5. doi: 10.1016\/j.cub.2021.10.010<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Luke\u0161 J, Tesa\u0159ov\u00e1 M, Yurchenko V, Vot\u00fdpka J. Characterization of a new cosmopolitan genus of trypanosomatid parasites, Obscuromonas gen. nov. (Blastocrithidiinae subfam. nov.). Eur J Protistol. 2021 Jun;79:125778. doi: 10.1016\/j.ejop.2021.125778<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Kostygov AY, Frolov AO, Malysheva MN, Ganyukova AI, Chistyakova LV, Tashyreva D, Tesa\u0159ov\u00e1 M, Spodareva VV, Re\u017enarov\u00e1 J, Macedo DH, Butenko A, d&#8217;Avila-Levy CM, Luke\u0161 J, Yurchenko V. Vickermania gen. nov., trypanosomatids that use two joined flagella to resist midgut peristaltic flow within the fly host. BMC Biol. 2020 Dec 2;18(1):187. doi: 10.1186\/s12915-020-00916-y<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Kr\u00e1lov\u00e1 J, Grybchuk-Ieremenko A, Vot\u00fdpka J, Novotn\u00fd V, Kment P, Luke\u0161 J, Yurchenko V, Kostygov AY. Insect trypanosomatids in Papua New Guinea: high endemism and diversity. Int J Parasitol. 2019 Dec;49(13-14):1075-1086. doi: 10.1016\/j.ijpara.2019.09.004<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Prokopchuk G, Tashyreva D, Yabuki A, Hor\u00e1k A, Masa\u0159ov\u00e1 P, Luke\u0161 J. Morphological, Ultrastructural, Motility and Evolutionary Characterization of Two New Hemistasiidae Species. Protist. 2019 Jul;170(3):259-282. doi: 10.1016\/j.protis.2019.04.001<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Okamoto N, Gawryluk RMR, Del Campo J, Strassert JFH, Luke\u0161 J, Richards TA, Worden AZ, Santoro AE, Keeling PJ. A Revised Taxonomy of Diplonemids Including the Eupelagonemidae n. fam. and a Type Species, Eupelagonema oceanica n. gen. &amp; sp. J Eukaryot Microbiol. 2019 May;66(3):519-524. doi: 10.1111\/jeu.12679<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Jagielski T, Baku\u0142a Z, Gawor J, Maciszewski K, Kusber W-H, Dyl\u0105g M, Nowakowska J, Gromadka R, Karnkowska A (2019)\u00a0 <\/span><i><span style=\"font-weight: 400;\">Prototheca<\/span><\/i><span style=\"font-weight: 400;\"> (Trebouxiophyceae, Chlorophyta) revisited: Implications from molecular taxonomic studies. <\/span><i><span style=\"font-weight: 400;\">Algal Research<\/span><\/i><span style=\"font-weight: 400;\">, 43: 101639.<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">\u0141ukomska-Kowalczyk M, Karnkowska A, Milanowski R, \u0141ach \u0141, Zakry\u015b B. Delimiting species in the Phacus longicauda complex (Euglenida) through morphological and molecular analyses. J Phycol. 2015 Dec;51(6):1147-57. doi: 10.1111\/jpy.12352<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Karnkowska A, Bennett MS, Watza D, Kim JI, Zakry\u015b B, Triemer RE. Phylogenetic Relationships and Morphological Character Evolution of Photosynthetic Euglenids (Excavata) Inferred from Taxon-rich Analyses of Five Genes. J Eukaryot Microbiol. 2015 May-Jun;62(3):362-73. doi: 10.1111\/jeu.12192<\/span><\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1f6a6e2 elementor-widget elementor-widget-heading\" data-id=\"1f6a6e2\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Metagenomics, Metatranscriptomics<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-bed416d elementor-widget elementor-widget-text-editor\" data-id=\"bed416d\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Karlicki M, Antonowicz S, Karnkowska A. Tiara: Deep learning-based classification system for eukaryotic sequences. Bioinformatics. 2021 Sep 27;38(2):344\u201350. doi: 10.1093\/bioinformatics\/btab6725.<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Durante IM, Butenko A, Ra\u0161kov\u00e1 V, Charyyeva A, Svobodov\u00e1 M, Yurchenko V, Hashimi H, Luke\u0161 J. Large-Scale Phylogenetic Analysis of Trypanosomatid Adenylate Cyclases Reveals Associations with Extracellular Lifestyle and Host-Pathogen Interplay. Genome Biol Evol. 2020 Dec 6;12(12):2403-2416. doi: 10.1093\/gbe\/evaa226<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Nenarokova A, Z\u00e1honov\u00e1 K, Krasilnikova M, Gahura O, McCulloch R, Z\u00edkov\u00e1 A, Yurchenko V, Luke\u0161 J. Causes and Effects of Loss of Classical Nonhomologous End Joining Pathway in Parasitic Eukaryotes. mBio. 2019 Jul 16;10(4):e01541-19. doi: 10.1128\/mBio.01541-19<\/span><\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-3fbc8fc elementor-widget elementor-widget-heading\" data-id=\"3fbc8fc\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">Soil Biology<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-c2bc557 elementor-widget elementor-widget-text-editor\" data-id=\"c2bc557\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Jassey VEJ, Walcker R, Kardol P, Geisen S, Heger T, Lamentowicz M, Hamard S, Lara E. Contribution of soil algae to the global carbon cycle. New Phytol. 2022 Feb 1. doi: 10.1111\/nph.17950<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Geisen S, Mitchell EAD, Adl S, Bonkowski M, Dunthorn M, Ekelund F, Fern\u00e1ndez LD, Jousset A, Krashevska V, Singer D, Spiegel FW, Walochnik J, Lara E. Soil protists: a fertile frontier in soil biology research. FEMS Microbiol Rev. 2018 May 1;42(3):293-323. doi: 10.1093\/femsre\/fuy006<\/span><\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4fc308b elementor-widget elementor-widget-heading\" data-id=\"4fc308b\" data-element_type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">FISH, CARD-FISH<\/h3>\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-643a856 elementor-widget elementor-widget-text-editor\" data-id=\"643a856\" data-element_type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Piwosz, K. (2019) Weekly dynamics of abundance and size structure of specific nanophytoplankton lineages in coastal waters (Baltic Sea). Limnol Oceanogr 64: 2172-2186.\u00a0 https:\/\/doi.org\/10.1002\/lno.11177<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Piwosz K, Kownacka J, Ameryk A, Zalewski M, Pernthaler J. Phenology of cryptomonads and the CRY1 lineage in a coastal brackish lagoon (Vistula Lagoon, Baltic Sea). J Phycol. 2016 Aug;52(4):626-37. doi: 10.1111\/jpy.12424<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Piwosz K, Mukherjee I, Salcher MM, Gruj\u010di\u0107 V, \u0160imek K. CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology. Front Microbiol. 2021 Mar 4;12:640066. doi: 10.3389\/fmicb.2021.640066<\/span><\/li><li style=\"font-weight: 400;\" aria-level=\"1\"><span style=\"font-weight: 400;\">Piwosz K, Wiktor JM, Niemi A, Tatarek A, Michel C. Mesoscale distribution and functional diversity of picoeukaryotes in the first-year sea ice of the Canadian Arctic. ISME J. 2013 Aug;7(8):1461-71. doi: 10.1038\/ismej.2013.39<\/span><\/li><\/ul>\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Relevant Publications Consortium Publications Del Campo, J., Carlos-Oliveira, M., \u010cepi\u010dka, I., Hehenberger, E., Hor\u00e1k, A., Karnkowska, A., Kol\u00edsko, M., Lara, E., Luke\u0161 J., P\u00e1nek, T., Piwosz, K., Richter, D., \u0160kaloud, P., Sutak, R., Tachezy, J., Hampl, V. (2024). The protist cultural renaissance. Trends in Microbiology, in press. Metabarcoding Flegontova O, Flegontov P, Malviya S, Audic &hellip;<\/p>\n<p class=\"read-more\"> <a class=\"\" href=\"https:\/\/demon-protists.eu\/?page_id=230\"> <span class=\"screen-reader-text\">Publications<\/span> Read More &raquo;<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"site-sidebar-layout":"no-sidebar","site-content-layout":"page-builder","ast-global-header-display":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"disabled","ast-breadcrumbs-content":"","ast-featured-img":"disabled","footer-sml-layout":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","footnotes":""},"_links":{"self":[{"href":"https:\/\/demon-protists.eu\/index.php?rest_route=\/wp\/v2\/pages\/230"}],"collection":[{"href":"https:\/\/demon-protists.eu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/demon-protists.eu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/demon-protists.eu\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/demon-protists.eu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=230"}],"version-history":[{"count":20,"href":"https:\/\/demon-protists.eu\/index.php?rest_route=\/wp\/v2\/pages\/230\/revisions"}],"predecessor-version":[{"id":869,"href":"https:\/\/demon-protists.eu\/index.php?rest_route=\/wp\/v2\/pages\/230\/revisions\/869"}],"wp:attachment":[{"href":"https:\/\/demon-protists.eu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=230"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}