Publications

2025

----	Malavasi, V., Pusztai, M., Jankowska, K., Zakryś, B. & Škaloud, P. (2025) Revisiting Chrysococcus (Chrysophyceae): new phylogenetic evidence and evolutionary implications. Fottea (accepted).
	Jadrná, I. & Škaloud, P. (2025) Exploring the factors shaping microscopic morphological traits: insights from thechrysophycean genus Synura (Stramenopiles). European Journal of Phycology 60: 67-83.

2024

	Nemcova, Y., Knotek, P., Jadrná, I., Černajová, I. & Škaloud, P. (2024) Nanopatterns on silica scales of Mallomonas (Chrysophyceae, Stramenopiles): Unraveling UV resistance potential and diverse response to UVA and UVB radiation. Journal of Phycology 60: 1256-1272.
	Tedersoo, L., Moghaddam, M.S.H., Mikryukov, V., Hakimzadeh, A., Bahram, M., Nilsson, R.H., Yatsiuk, I., Geisen, S., Schwelm, A., Piwosz, K., Prous, M., Sildever, S., Chmolowska, D., Rueckert, S., Skaloud, P., Laas, P., Tines, M., Jung, J.-H., Choi, J.H., Alkahtani, S. & Anslan, S. (2024) EUKARYOME: the rRNA gene reference database for identification of all eukaryotes. Database 2024: baae043.
	Puginier,C., Libourel, C., Otte, J., Škaloud, P., Haon, M., Grisel, S., Petersen, M., Berrin, J.G., Delaux, P.M., Dal Grande, F. & Keller, J. (2024) Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae. Nature Communications 15: 4452.
	Malavasi, V., Pusztai, M., Jadrná, I., Škvorová, Z. & Škaloud, P. (2024) Morphological diversity and phylogeny of palmelloid Chrysophyte genera Chrysotilos and Globulochrysis, gen. nov. European Journal of Phycology (published online).
	Veselá, V., Malavasi, V. & Škaloud, P. (2024) A synopsis of green-algal lichen symbionts with an emphasis on their free-living lifestyle. Phycologia 63: 317-338.
	del Campo, J., Carlos-Oliveira, M., Čepička, I., Hehenberger,E., Horák, A., Karnkowska, A., Kolisko, 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 32:128-131.
	Škaloud, P., Jadrná, I., Dvořák, P., Škvorová, Z., Pusztai, M., Čertnerová, D., Bestová, H. & Rengefors, K. (2024) Rapid diversification of a free-living protist is driven by adaptation to climate and habitat. Current Biology 34: 92-105.

2023

	Kotyk, M., Bourland, W.A., Soviš, M., Méndez-Sánchez, D., Škaloud, P., Kotyková Varadínová, Z. & Čepička, I. (2023) 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 zlad154.
	Knotek, P. & Škaloud, P. (2023) The effect of patterned structures on the mechanical resistance of microscopic silica scales. Fottea 23: 190-200.
	Pusztai, M., Jadrná, I. & Škaloud, P. (2023) Elucidating the phylogeny and taxonomic position of the genus Spiniferomonas Takahashi (Chrysophyceae). Fottea 23: 217-222.
	Škaloud, P., Škaloudová, M., Jadrná, I., Pilátová, J., Shin, W. & Kopecký, J. (2023) Unravelling the hidden complexity in diversity and pigment composition of a colonial flagellate Synura sphagnicola (Chrysophyceae, Stramenopiles). Fottea 23: 149-163.
	Němcová, Y., Faturová, J. & Škaloud, P. (2023) Comparing continental and local distribution patterns of protists: A case study of silica-scaled chrysophytes. Fottea 23: 177-189.
	Sharma, B., Fatima, S., Rajeshkumar, K.C., Škaloud, P., Divakar, P.K., Gaikwad, S., Ansil, P.A., Mohan, A.S. & Sequeira, S. (2023) Molecular studies of Flavopunctelia and Punctelia species and their Trebouxia photobiont from the Himalayas, India. Mycotaxon 137: 853-869.
	Elster, J., Souquieres, C.-E., Jadrná, I., Škaloud, P., Søreide, J.E. & Kvíderová, J. (2023) Invasive Vaucheria aff. compacta (Xanthophyceae) and its distribution over a high arctic tidal flat in Svalbard. Estuarine, Coastal and Shelf Science 281: 108206.

2022

	Malavasi, V. & Škaloud, P. (2022) Insert a new Chapter E in Division II on a Code of Ethics. Taxon 71: 1343-1344.
	Černajová, I., Steinová, J., Škvorová, Z. & Škaloud, P. (2022) The curious case of Cladonia luteoalba: no support for its distinction. The Lichenologist 54: 345-354.
	Stanojković, A., Skoupý, S., Škaloud, P. & Dvořák, P.(2022) High genomic differentiation and limited gene flow indicate recent cryptic speciation within the genus Laspinema (cyanobacteria). Frontiers in Microbiology 13: 977454.
	Barcytė, D., Zátopková, M., Němcová, Y., Richtář, M., Yurchenko, T., Jaške, K., Fawley, K.P, Škaloud, P., Ševčíková, T., Fawley, M.W. & Eliáš, M. (2022) Redefining Chlorobotryaceae as one of the principal and most diverse lineages of eustigmatophyte algae. Molecular Phylogenetics and Evolution: 107607.
	Malavasi, V., Škvorová, Z., Němcová, Y. & Škaloud, P. (2022) Laetitia sardoa gen. & sp. nov., a new member of the Chlorellales (Trebouxiophyceae, Chlorophyta) isolated from Sardinia Island. Phycologia 61: 375-383.
	Malavasi, V., Klimešová, M., Lukešová, A. & Škaloud, P. (2022) Rindifilum ramosum gen. nov., sp. nov., a new freshwater genus within the Ulvales (Ulvophyceae, Chlorophyta). Cryptogamie, Algologie 43: 125-133.
	De Araújo, C.B., Bicudo, C.E.M., Da Silva, T.G., Šťastný, J., Trumhová, K. & Škaloud, P. (2022) Hidden generic diversity in desmids: description of Pseudomicrasterias gen. nov. (Desmidiaceae, Zygnematophyceae). Phycologia 61: 227-240.
	Čertnerová, D., Čertner, M. & Škaloud, P. (2022) Alternating nuclear DNA content in chrysophytes provides evidence of their isomorphic haplo-diploid life cycle. Algal Research 64: 102707.
	Černajová, I., Schiefelbein, U. & Škaloud, P. (2022) Lichens from the littoral zone host diverse ulvophycean photobionts. Journal of Phycology 58: 267-280.
	Peksa, O., Gebouská, T., Škvorová, Z., Vančurová, L. & Škaloud, P. (2022) The guilds in green algal lichens—an insight into the life of terrestrial symbiotic communities. FEMS Microbiology Ecology 98: 1-17.
	Steinová, J., Holien, H., Košuthová, A. & Škaloud, P. (2022) An exception to the rule? Could photobiont identity be a better predictor of lichen phenotype than mycobiont odentity? Journal of Fungi 8: 275.
	Barcytė, D., Pusztai, M., Škaloud, P. & Eliáš, M. (2022) When you like other algae: Adglutina synurophila gen. et sp. nov. (Moewusinia, Chlorophyceae), a clingy green microalga associated with Synura colonies. Protist 173: 125858.
	Pusztai, M. & Škaloud, P. (2022) Species delimitation within the colonial flagellates Uroglena, Uroglenopsis and Urostipulosphaera (Chrysophyceae). European Journal of Phycology 57: 79-95.
	Škvorová, Z., Černajová, I., Steinová, J., Peksa, O., Moya, P. & Škaloud, P. (2022) Promiscuity in lichens follows clear rules: partner switching in Cladonia is regulated by climatic factors and soil chemistry. Frontiers in Microbiology 12: 781585.
	Čertnerová, D. (2022) Meet the challenges of analyzing small genomes using flow cytometry (commentary). Cytometry 101: 707-709.

2021

	Vančurová, L., Malíček, J., Steinová, J. & Škaloud, P. (2021) Choosing the right life partner: Ecological drivers of lichen symbiosis. Frontiers in Microbiology 12: 769304.
	Moya, P., Molins, A., Škaloud, P., Divakar, P.K., Chiva, S., Dumitru, C., Molina, M.C., Crespo, A. & Barreno, E. (2021) Biodiversity patterns and ecological preferences of the photobionts associated with the lichen-forming genus Parmelia. Frontiers in Microbiology 12: 765310.
	Bestová, H., Segrestin, J., von Schwartzenberg, K., Škaloud, P., Lenormand, T. & Violle, C. (2021) Biological scaling in green algae: the role of cell size and geometry. Scientific Reports 11: 14425.
	Kosecka, M., Guzow-Krzemińska, B., Černajová, I., Škaloud, P., Jabłońska, A. & Kukwa, M. (2021) New lineages of photobionts in Bolivian lichens expand our knowledge on habitat preferences and distribution of Asterochloris algae. Scientific Reports 11: 8701.
	Galbraith, D., Loureiro, J., Antoniadi, I., Bainard, J., Bureš, P., Cápal, P., Castro, M., Castro, S., Čertner, M., Čertnerová, D. et al. (2021) Best practices in plant cytometry. Cytometry 99: 311-317.
	Čertnerová, D. & Galbraith, D.W. (2021) Best practices in the flow cytometry of microalgae. Cytometry 99: 359-364.
	Čertnerová, D. (2021) Nuclei isolation protocols for flow cytometry allowing nuclear DNA content estimation in problematic microalgal groups. Journal of Applied Phycology 33: 2057-2067.
	Jadrná, I., Siver, P.A. & Škaloud, P. (2021) Morphological evolution of silica scales in the freshwater genus Synura (Stramenopiles). Journal of Phycology 57: 355-369.

2020

	Černajová, I. & Škaloud, P. (2020) Lessons from culturing lichen soredia. Symbiosis 82: 109-122.
	Čertnerová, D. & Škaloud, P. (2020) Substantial intraspecific genome size variation in golden-brown algae and its phenotypic consequences. Annals of Botany 126: 1077-1087.
	Vančurová, L., Kalníková, V., Peksa, O., Škvorová, Z., Malíček, J., Moya, P., Chytrý, K., Černajová, I. & Škaloud, P. (2020) Symbiosis between river and dry lands: Phycobiont dynamics on river gravel bars. Algal Research 51: 102062.
	Škaloud, P., Škaloudová, M., Jadrná, I., Bestová, H., Pusztai, M., Kapustin, D. & Siver, P.A. (2020) Comparing morphological and molecular estimates of species diversity in the freshwater genus Synura (Stramenopiles): a model for understanding diversity of eukaryotic microorganisms. Journal of Phycology 56: 574-591.
	Del Cortona, A., Jackson, C.J., Bucchini, F, Van Bel, M., D’hondt, S., Škaloud, P., Delwiche, C.W., Knoll, A.H., Raven, J.A., Verbruggen, H., Vandepoele, K., De Clerck, O. & Leliaert, F. (2020) Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds. Proceedings of the National Academy of Sciences 117: 2551-2559.

2019

	Stancheva, R., Škaloud, P., Pusztai, M., Loflen, C.L. & Sheath, R.G. (2019) First record of the rare freshwater alga Tetrasporopsis fuscescens (Chrysomerophyceae, Ochrophyta) in North America. Fottea 19: 163-174.
	Pusztai, M. & Škaloud, P. (2019) Elucidating the evolution and diversity of Uroglena-like colonial flagellates (Chrysophyceae), polyphyletic origin of the morphotype. European Journal of Phycology 54: 404-416.
	Čertnerová, D., Čertner, M. & Škaloud, P. (2019) Molecular phylogeny and evolution of phenotype in silica-scaled chrysophyte genus Mallomonas. Journal of Phycology 55: 912-923.
	Černajová, I. & Škaloud, P. (2019) The first survey of Cystobasidiomycete yeasts in the lichen genus Cladonia; with the description of Lichenozyma pisutiana gen. nov., sp. nov. Fungal Biology 123: 625-637.
	Škaloud, P., Škaloudová, M., Doskočilová, P., Kim, J.I., Shin, W. & Dvořák, P. (2019) Speciation in protists: Spatial and ecological divergence processes cause rapid species diversification in a freshwater chrysophyte. Molecular Ecology 28: 1084-1095.
	Steinová, J., Škaloud, P., Yahr, R., Bestová, H. & Muggia, L. (2019) Reproductive and dispersal strategies shape the diversity of mycobiont-photobiont association in lichen symbioses. Molecular Phylogenetics and Evolution 134: 226-237.
	Klimešová, M., Rindi, F. & Škaloud, P. (2019) There is more than meets the eye: DNA cloning demonstrates high genetic heterogeneity in populations of the subaerial green alga Trentepohlia (Trentepohliales, Chlorophyta). Journal of Phycology 55: 224-235.
	Kim, J.I., Shin, H., Škaloud, P., Jung, J., Yoon, H.S., Archibald, J.M. (2019) Comparative plastid genomics of Synurophyceae: inverted repeat dynamics and gene content variation. BMC Evolutionary Biology 19: 20.

2018

	Vančurová, L., Muggia, L., Peksa, O., Řídká, T. & Škaloud, P. (2018) The complexity of symbiotic interactions influences the ecological amplitude of the host: a case study in Stereocaulon (lichenized Ascomycota). Molecular Ecology 27: 3016-3033.
	Škaloud, P., Moya, P., Molins, A., Peksa, O., Santos-Guerra, A. & Barreno, E. (2018) Untangling the hidden intrathalline microalgal diversity in Parmotrema pseudotinctorum: Trebouxia crespoana sp. nov. The Lichenologist 50: 357-369.
	Moya, P., Chiva, S., Molins, A., Jadrná, I., Škaloud, P., Peksa, O. & Barreno, E. (2018) Myrmecia israeliensis as the primary symbiotic microalga in squamulose lichens growing in European and Canarian terricolous communities. Fottea 18: 72-85.
	Bestová, H., Munoz, F., Svoboda, P., Škaloud, P.& Violle, C. (2018) Ecological and biogeographical drivers of freshwater green algae biodiversity: from local communities to large-scale species pools of desmids. Oecologia 186: 1017-1030.
	Gusev, E.S., Čertnerová, D., Škaloudová, M. & Škaloud, P. (2018) Exploring cryptic diversity and distribution patterns in the Mallomonas kalinae/rasilis species complex with a description of a new taxon – Mallomonas furtiva sp. nov. Journal of Eukaryotic Microbiology 65: 38-47.

2017

	Donner, A., Ryšánek, D., Mikhailyuk, T. & Karsten, U. (2017) Ecophysiological traits of various genotypes of a green key alga in biological soil crusts from the semi-arid Colorado Plateau, USA. Journal of Applied Phycology 29: 2911-2923.
	Pierangelini, M., Ryšánek, D., Lang, I., Adlassnig, W. & Holzinger, A. (2017) Terrestrial adaptation of green algae Klebsormidium and Zygnema (Charophyta) involves diversity in photosynthetic traits but not in CO2 acquisition. Planta 246: 971-986.
	Rindi, F., Ryšánek, D. & Škaloud, P. (2017) Problems of epitypification in morphologically simple green microalgae: a case study of two widespread species of Klebsormidium (Klebsormidiophyceae, Streptophyta). Fottea 17: 78-88.

2016

	Ryšánek, D., Elster, J., Kováčik, L. & Škaloud, P. (2016) Diversity and dispersal capacities of a terrestrial algal genus Klebsormidium (Streptophyta) in polar regions. FEMS Microbiology Ecology 92: fiw039.
	Pusztai, M., Čertnerová, D., Škaloudová, M. & Škaloud, P. (2016) Elucidating the phylogeny and taxonomic position of the genus Chrysodidymus Prowse (Chrysophyceae, Synurales) Cryptogamie, Algologie 37: 297-307.
	Jo, B.Y., Kim, J.I., Škaloud, P., Siver, P.A. & Shin, W. (2016) Multigene phylogeny of Synura (Synurophyceae) and descriptions of four new species based on morphological and DNA evidence. European Journal of Phycology 51: 413-430.
	Škaloud, P., Friedl, T., Hallmann, C., Beck, A. & Dal Grande, F. (2016) Taxonomic revision and species delimitation of coccoid green algae currently assigned to the genus Dictyochloropsis (Trebouxiophyceae, Chlorophyta). Journal of Phycology 52: 599-617.
	Ryšánek, D., Holzinger, A. & Škaloud, P. (2016) Influence of substrate and pH on the diversity of aeroterrestrial alga Klebsormidium (Klebsormidiales, Streptohyta): a potentially important factor for sympatric speciation. Phycologia 55: 347-358.
	Malavasi, V., Škaloud, P., Rindi, F., Tempesta, S., Paoletti, M. & Pasqualetti, M. (2016) DNA-based taxonomy in ecologically versatile microalgae: A re-evaluation of the species concept within the coccoid green algal genus Coccomyxa (Trebouxiophyceae, Chlorophyta) PLoS ONE 11: e0151137.

2015

	Yahr, R., Florence, A., Škaloud, P. & Voytsekhovich, A. (2015) Molecular and morphological diversity in photobionts associated with Micarea s. str. (Lecanorales, Ascomycota). The Lichenologist 47: 403-414.
	Wierzchos, J., DiRuggiero, J., Vítek., P., Artieda, O., Souza-Egipsy, V., Škaloud, P., Tisza, M., Davila, A.F., Vílchez, C., Garbayo, I. & Ascaso, C. (2015) Adaptation strategies of endolithic chlorophototrophs to survive the hyperarid and extreme solar radiation environment of the Atacama Desert. Frontiers in Microbiology 6: 934.
	Moya, P., Škaloud, P., Chiva, S., García-Breijo, F.J., Reig-Armiñana, J. Vančurová, L. & Barreno, E. (2015) Molecular phylogeny and ultrastructure of the lichen microalga Asterochloris mediterranea sp. nov. from Mediterranean and Canary Islands ecosystems. International Journal of Systematic and Evolutionary Microbiology 65: 1838-1854.
	Vančurová, L., Peksa, O., Němcová, Y. & Škaloud, P. (2015) Vulcanochloris (Trebouxiales, Trebouxiophyceae), a new genus of lichen photobiont from La Palma, Canary Islands, Spain. Phytotaxa 219: 118-132.
	Škaloud, P., Steinová, J., Řídká, T., Vančurová, L. & Peksa, O. (2015) Assembling the challenging puzzle of algal biodiversity: species delimitation within the genus Asterochloris (Trebouxiophyceae, Chlorophyta). Journal of Phycology 51: 507-527.
	Ryšánek, D., Hrčková, K. & Škaloud, P. (2015) Global ubiquity and local endemism of free-living terrestrial protists: Phylogeographic assessment of the streptophyte alga Klebsormidium. Environmental Microbiology 17: 689-698. - see also the ‘Highlight’ piece on this article by Christopher J. van der Gast (Microbial biogeography: the end of the ubiquitousdispersal hypothesis?)

2014

	Neustupa, J., Šťastný, J. & Škaloud, P. (2014) Splitting of Micrasterias fimbriata (Desmidiales, Viridiplantae) into two monophyletic species and description of Micrasterias compereana sp. nov. Plant Ecology and Evolution 147: 405-411.
	Škaloud, P., Lukešová, A., Malavasi, V., Ryšánek, D., Hrčková, K. & Rindi, F. (2014) Molecular evidence for the polyphyletic origin of low pH adaptation in the genus Klebsormidium (Klebsormidiophyceae, Streptophyta). Plant Ecology and Evolution 147: 333-345.
	Fučíková, K., Leliaert, F., Cooper, E.D., Škaloud, P., D'Hondt, S., De Clerck, O., Gurgel, C.F.D, Lewis, L.A., Lewis, P.O., Lopez-Bautista, J.M., Delwiche, C.F. & Verbruggen, H. (2014) New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data. Frontiers in Ecology and Evolution 2: 63.
	Jurdíková, K., Kulichová, J., Bestová, H., Leliaert, F. & Škaloud, P. (2014) Exploration of nuclear DNA markers and population structure assessment in desmid species Micrasterias rotata (Zygnematophyceae, Streptophyta). Journal of Eukaryotic Microbiology 61: 509-519.
	Kulichová, J., Škaloud, P. & Neustupa, J. (2014) Molecular diversity of green corticolous microalgae from two submediterranean European localities. European Journal of Phycology 49: 345-355.
	Drahota, P., Škaloud, P., Nováková, B. & Mihaljevič, M. (2014) Comparison of Pb, Zn, Cd, As, Cr, Mo and Sb adsorption onto natural surface coatings in a stream draining natural as geochemical anomaly. Bulletin of Environmental Contamination and Toxicology 93: 311-315.
	Škaloud, P., Škaloudová, M., Procházková, A. & Němcová, Y. (2014) Morphological delineation and distribution patterns of four newly described species within the Synura petersenii species complex (Chrysophyceae, Stramenopiles). European Journal of Phycology 49: 213-229.
	Škaloud, P., Němcová, Y., Pytela, J., Bogdanov, N.I., Bock, C. & Pickinpaugh, S.H. (2014) Planktochlorella nurekis, gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel coccoid green alga carrying significant biotechnological potential. Fottea 14: 53-62.
	Poulíčková, A., Mazalová, P., Vašut, R.J., Šarhanová, P., Neustupa, J. & Škaloud, P. (2014) DNA content variation and its significance in the evolution of the genus Micrasterias (Desmidiales, Streptophyta). Plos ONE 9: e86247.

2013

	Škaloud, P., Škaloudová, M., Pichrtová, M., Němcová, Y., Kreidlová, J. & Pusztai, M. (2013) www.chrysophytes.eu – a database on distribution and ecology of silica-scaled chrysophytes in Europe. Nova Hedwigia, Beiheft 142: 141-146.
	Pichrtová, M., Němcová, Y., Škaloud, P. & Rott, E. (2013) Silica-scaled chrysophytes from North Tyrol (Austria) including a description of Mallomonas tirolensis sp. nov. Nova Hedwigia, Beiheft 142: 69-85..
	Škaloudová, M. & Škaloud, P. (2013) A new species of Chrysosphaerella (Chrysophyceae: Chromulinales), Chrysosphaerella rotundata, sp. nov., from Finland. Phytotaxa 130: 34-42.
	Steinová, J., Stenroos, S., Grube, M. & Škaloud, P. (2013) Genetic diversity and species delimitation of the zeorin-containing red-fruited Cladonia species (lichenized Ascomycota) assessed with ITS rDNA and β-tubulin data. The Lichenologist 45: 665-684.
	Škaloud, P., Nedbalová, L., Elster, J. & Komárek, J. (2013) A curious occurrence of Hazenia broadyi spec. nova in Antarctica, and the review of the genus Hazenia (Ulotrichales, Chlorophyceae). Polar Biology 36: 1281-1291.
	Neustupa, J., Němcová, Y., Veselá, J., Steinová, J. & Škaloud, P. (2013) Parachloroidium gen. nov. (Trebouxiophyceae, Chlorophyta), a novel genus of coccoid green algae from subaerial corticolous biofilms. Phycologia 52: 411-421.
	Škaloud, P., Kristiansen, J. & Škaloudová, M. (2013) Developments in the taxonomy of silica-scaled chrysophytes - from morphological and ultrastructural to molecular approaches (review). Nordic Journal of Botany 31: 385-402.
	Muggia, L., Vančurová, L., Škaloud, P., Peksa, O., Wedin, M. & Grube, M. (2013) The symbiotic playground of lichen thalli – a highly flexible photobiont association in rock-inhabiting lichens. FEMS Microbiology Ecology 85:313–323.
	Gaysina, L., Němcová, Y., Škaloud, P., Ševčíková, T. & Eliáš, M. (2013) Chloropyrula uraliensis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a new green coccoid alga with a unique ultrastructure, isolated from soil in South Urals. Journal of Systematics and Evolution 51: 476-484.
	Škaloud, P. & Rindi, F. (2013) Ecological differentiation of cryptic species within an asexual protist morphospecies: a case study of filamentous green alga Klebsormidium (Streptophyta). Journal of Eukaryotic Microbiology 60: 350-362.
	Šťastný, J., Škaloud, P., Langenbach, D., Nemjová, K. & Neustupa, J. (2013) Polyphasic evaluation of Xanthidium antilopaeum and Xanthidium cristatum (Zygnematophyceae, Streptophyta) species complex. Journal of Phycology 49: 401-416.
	Škaloud, P., Kalina, T., Nemjová, K., De Clerck, O. & Leliaert, F. (2013) Morphology and phylogenetic position of the freshwater green microalgae Chlorochytrium (Chlorophyceae) and Scotinosphaera (Scotinosphaerales, ord. nov., Ulvophyceae). Journal of Phycology 49: 115-129.
	Eliáš, M., Neustupa, J., Pažoutová, M. & Škaloud, P. (2013) A case of taxonomic inflation in coccoid algae: Ellipsoidion parvum and Neocystis vischeri are conspecific with Neocystis (=Nephrodiella) brevis (Chlorophyta, Trebouxiophyceae). Phytotaxa 76: 15-27.
	Neustupa, J., Němcová, Y., Veselá, J., Steinová, J. & Škaloud, P. (2013) Leptochlorella corticola gen. et sp. nov. and Kalinella apyrenoidosa sp. nov.: two new Chlorella-like green microalgae (Trebouxiophyceae, Chlorophyta) from subaerial habitats. International Journal of Systematic and Evolutionary Microbiology 63: 377-387.

2012

	Škaloud, P., Šťastný, J., Nemjová, K., Mazalová, P., Poulíčková, A. & Neustupa, J. (2012) Molecular phylogeny of baculiform desmid taxa (Zygnematophyceae). Plant Systematics and Evolution 298: 1281-1292.
	Škaloud, P., Kynčlová, A., Benada, O., Kofroňová, O. & Škaloudová, M. (2012) Towards a revision of the genus Synura, section Petersenianae (Synurophyceae, Heterokontophyta): morphological characterization of six pseudo-cryptic species. Phycologia 51: 303-329.

2011

	Škaloud, P., Nemjová, K., Veselá, J., Černá, K. & Neustupa, J. (2011) A multilocus phylogeny of the desmid genus Micrasterias (Streptophyta): evidence for the accelerated rate of morphological evolution in protists. Molecular Phylogenetics and Evolution 61: 933-943.
	Veselá, J., Škaloud, P., Urbánková, P., Škaloudová, M. & Kalina, T. (2011) The CAUP image database. Fottea 11: 313-316.
	Peksa, O. & Škaloud, P. (2011) Do photobionts influence the ecology of lichens? A case study of environmental preferences in symbiotic green alga Asterochloris (Trebouxiophyceae). Molecular Ecology 20: 3936-3948. - see also the ‘Perspectives’ piece on this article by M. Piercey-Normore and C. Deduke (Fungal farmers or algal escorts: lichen adaptation from the algal perspective)
	Němcová, Y., Eliáš, M., Škaloud, P., Neustupa, J. & Hodač, L. (2011) Jenufa gen. nov.:  a new genus of coccoid green algae (Chlorophyceae, incertae sedis) previously recorded by environmental sequencing. Journal of Phycology 47: 928-938.
	Nemjová, J., Neustupa, J., Šťastný, J., Škaloud, P. & Veselá, J. (2011) Species concept and morphological differentiation of strains traditionally assigned to Micrasterias truncata. Phycological Research 59: 208-220.
	Neustupa, J., Šťastný, J., Nemjová, K., Mazalová, P., Goodyer, E., Poulíčková, A. & Škaloud, P. (2011) A novel, combined approach to assessing species delimitation and biogeography within the well-known desmid species Micrasterias fimbriata and M. rotata (Desmidiales, Steptophyta. Hydrobiologia 667: 223-239.
	Neustupa, J., Eliáš, M., Škaloud, P., Němcová, Y. & Šejnohová, L. (2011) Xylochloris irregularis, gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga. Phycologia 50: 57-66.

2010

	Neustupa, J., Škaloud, P. & Šťastný, J. (2010) The molecular phylogenetic and geometric morphometric evaluation of Micrasterias crux-melitensis / M. radians species complex. Journal of Phycology 46: 703-714.
	Kynčlová, A., Škaloud, P. & Škaloudová, M. (2010) Unveiling hidden diversity in the Synura petersenii species complex (Synurophyceae, Heterokontophyta). Nova Hedwigia, Beiheft 136: 283-298.
	Eliáš, M., Němcová, Y., Škaloud, P., Neustupa, J., Kaufnerová, V. & Šejnohová, L. (2010) Hylodesmus singaporensis gen. et sp. nov., a novel autosporic subaerial green alga (Scenedesmaceae, Chlorophyta) from Singapore. International Journal of Systematic and Evolutionary Microbiology 60: 1224-1235.
	Poulíčková, A., Veselá, J., Neustupa, J. & Škaloud, P. (2010) Pseudocryptic diversity versus cosmopolitanism in diatoms: a case study on Navicula cryptocephala Kütz. (Bacillariophyceae) and morphologically similar taxa. Protist 161: 353-369.
	Neustupa, J. & Škaloud, P. (2010) Diversity of subaerial algae and cyanobacteria growing on bark and wood in the lowland tropical forests of Singapore. Plant Ecology and Evolution 143: 51-62.
	Bačkor, M., Peksa, O., Škaloud, P. & Bačkorová, M. (2010) Photobiont diversity in lichens from metal-rich substrata based on ITS rDNA sequences. Ecotoxicology and Environmental Safety 73: 603-612.
	Pažoutová, M., Škaloud, P. & Nemjová, K. (2010) Phylogenetic position of Ooplanctella planoconvexa gen. et comb. nova and Echinocoleum elegans(Oocystaceae, Trebouxiophyceae, Chlorophyta). Fottea 10: 75-82.
	Skaloud, P. & Peksa, O. (2010) Evolutionary inferences based on ITS rDNA and actin sequences reveal extensive diversity of the common lichen alga Asterochloris (Trebouxiophyceae, Chlorophyta). Molecular Phylogenetics and Evolution 54: 36-46.

2005 - 2009

	Neustupa, J., Němcová, Y., Eliáš, M. & Škaloud, P. (2009) Kalinella bambusicola gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel coccoid Chlorella-like subaerial alga from Southeast Asia. Phycological Research 57: 159-169.
	Škaloud, P. (2009) Species composition and diversity of aero-terrestrial algae and cyanobacteria of the Boreč Hill ventaroles. Fottea 9: 65-80.
	Poulíčková, A., Neustupa, J., Špačková, J. & Škaloud, P. (2009) Distribution of epipelic diatoms in artificial fishponds along environmental and spatial gradients. Hydrobiologia 624: 81-90.
	Eliáš, M., Neustupa, J. & Škaloud, P. (2008) Elliptochloris bilobata var. corticola var. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccal green alga. Biologia 63: 787-794.
	Neustupa, J. & Škaloud, P. (2008) Diversity of subaerial algae and cyanobacteria on tree bark in tropical mountain habitats. Biologia 63: 802-808.
	Peksa, O. & Škaloud, P. (2008) Changes in chloroplast structure in lichenized algae. Symbiosis 46: 153-160.
	Škaloud, P. & Peksa, O. (2008) Comparative study of chloroplast morphology and ontogeny in Asterochloris (Trebouxiophyceae, Chlorophyta). Biologia 63: 869-876.
	Neustupa, J. & Škaloud, P. (2007) Geometric morphometrics and qualitative patterns in the morphological variation of five species of Micrasterias (Zygnemophyceae, Viridiplantae). Preslia 79: 401-417.
	Pichrtová, M., Řezáčová-Škaloudová, M. & Škaloud, P. (2007) The silica-scaled chrysophytes of the Czech-Moravian Highlands. Fottea 7(1): 43-48.
	Škaloud, P. (2006) Variation and taxonomic significance of some morphological features in European strains of Klebsormidium (Klebsormidiophyceae, Streptophyta). Nova Hedwigia 83(3-4): 533-550.
	Škaloud, P., Řezáčová, M. & Ellegaard, M. (2006) Spatial distribution of phytoplankton in Spring 2004 along a transect in the eastern part of the North Sea. Journal of Oceanography 62(5): 717-729.
	Řezáčová, M. & Škaloud, P. (2005) Silica-scaled chrysophytes of Ireland. With an appendix: Geographic variation of scale shape of Mallomonas caudata. Nova Hedwigia, Beiheft 128: 101-124.
	Škaloud, P., Neustupa, J., Radochová, B., Kubínová, L. (2005) Confocal microscopy of chloroplast morphology and ontogeny in three strains of Dictyochloropsis (Trebouxiophyceae, Chlorophyta). Phycologia 44: 261-269.

Books, book chapters

Kaštovský, J., Hauer, T., Geriš, R., Chattová, B., Juráň, J., Lepšová-Skácelová, O., Pitelková, P., Puzstai, P., Škaloud, P., Šťastný, J., Čapková, K., Bohunická, M. & Mühlsteinová, R. (2018) Atlas sinic a řas ČR, Powerprint. - 864 pp. - 1st part - 2nd part

Škaloud, P., Rindi, F., Boedeker, C. & Leliaert, F. (2018) Freshwater Flora of Central Europe, Vol 13: Chlorophyta: Ulvophyceae, Springer Spektrum. - 289 pp.

Kristiansen, J. & Škaloud, P. (2017) Chrysophyta. In: Archibald, J.M., Simpson, A.G.B., Slamovits C.H. (eds.), Handbook of the Protists, Second Edition. - pp. 331-366, Springer International Publishing.

Řídká, T., Peksa, O., Rai, H., Upreti, D.K. & Škaloud, P. (2014) Photobiont diversity in Indian Cladonia lichens, with special emphasis on the geographical patterns. In: Rai, H. & Upreti, D.K. (eds.), Terricolous lichens in India. - pp. 53-71, Springer, New York.

Neustupa, J. & Škaloud, P. (2004) Contribution to the knowledge of soil algae of two abandoned industrial sedimentation basins in Eastern Bohemia. In: Kovář, P. (ed.), Natural recovery of man-made deposits in landscape (Biotic interactions and ore/ash-slag artificial ecosystems). - pp. 188-192, Academia, Praha.

Papers in non-impacted journals

	Malavasi, V. & Škaloud, P. (2022) A taxonomic note on the genus Rindifilum Malavasi, Klimešová, Lukešová & Škaloud (Ulvales, Ulvophyceae). Notulae Algarum 245: 1-3.
	Škaloud, P. & Leliaert, F. (2017) Validation of the genus Hazenia H.C.Bold 1958 (Ulvophyceae). Notulae Algarum 41: 1-4.
	Neustupa, J., Škaloud, P., Peksa, O., Kubátová, A., Soldán, Z., Černá, K., Prášil, K., Bukovská, P., Vojta, J., Pažoutová, M., Veselá, J. & Škaloudová, M. (2008) The biological soil crusts in Central European ecosystems, with special reference to taxonomic structure and ecology of the surface crusts at Czech ore-waste and ash-slag sedimentation industrial basins. Novitates Botanicae Universitatis Carolinae 19: 1-96.
	Řezáčová, M. & Škaloud, P. (2004) A contribution to the knowledge of the silica-scaled chrysophytes in eastern Hungary. Czech Phycology 4: 67-73.
	Škaloud, P. & Radochová, B. (2004) Confocal microscopy of the green-algal chloroplast. Czech Phycology 4: 183-190.
	Šejnohová, L., Škaloud, P., Neustupa, J., Nováková, S., Řezáčová, M. & Ošlejšková, L. (2003) Algae and cyanoprokaryotic species from peat bog, streams, ponds and aerial biotopes in the region of South Šumava Mts. Czech Phycology 3: 41-52.
	Neustupa, J., Nováková, S., Šejnohová, L., Škaloud, P. & Řezáčová, M. (2002) Algae from the aquatic, peat bog and aerial biotopes in the tributary of Křemelná river in Šumava National Park. Czech Phycology 2: 47-61.

Popularizational papers

Škaloud, P. (2007) Chloroplasty řas v konfokálním mikroskopu. Živa 55(1): 3-5.