Škaloud, P., Šťastný, J., Nemjová, K., Mazalová, P., Poulíčková, A. & Neustupa, J. (2012)
Molecular phylogeny of baculiform desmid taxa (Zygnematophyceae).
Plant Systematics and Evolution (in press)

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.

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.

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)
Microspeciation 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.

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.

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.

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.

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.

Škaloud, P. & Řezáčová, M. (2004)
Spatial distribution of phytoplankton in the eastern part of the North Sea.
Fagprojekt in marine phytoplankton, Københavns Universitet, Denmark, 46 pp.

Řezáčová, M. & Škaloud, P. (2004)
Silica-scaled chrysophytes of Ireland.
Biologisk projektarbejde, Københavns Universitet, Denmark, 53 pp.

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.

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

Vančurová, L., Muggia, L., Škaloud, P., Peksa, O. & Grube, M. (2012)
Are long-living lichen thalli an arena for photobiont variation?
7th IAL Symposium: Lichens: from genome to ecosystems in a changing world. Bangkok, Thailand.

Škaloud, P., Nemjová, K., Veselá, J., Černá, K. & Neustupa, J. (2011)
A multilocus phylogeny of the desmid genus Micrasterias: Accelerated rate of morphological evolution in protists.
Fifth European Phycological Congress, Rhodes, Greece. Eur. J. Phycol. 46(1), Suppl.: 100-101.

Škaloud, P. & Rindi, F. (2011)
Ecological differentiation of cryptic species within an asexual protist morphospecies.
Fifth European Phycological Congress, Rhodes, Greece. Eur. J. Phycol. 46(1), Suppl.: 187-188.

Škaloud, P., Peksa, O. & Rindi, F. (2011)
Ecological differentiation of cryptic species in green microalgae.
Joint Meeting of the PSA/ISOP, Seattle, USA.

Škaloud, P. & Rindi, F. (2010)
More species than expected? Ecological differentiation of cryptic species within an asexual protist morphospecies.
60th annual meeting of the International Society of Protistologists, Canterbury, England.

Škaloud, P., Neustupa, J., Veselá, J., Nemjová, K. & Šťastný, J. (2009)
Molecular phylogeny and cryptic diversity of Micrasterias (Zygnematophyceae, Streptophyta).
9th International Phycological Congress, Tokyo, Japan.

Peksa, O. & Škaloud, P. (2008)
Photobiont diversity in the Lepraria neglecta group (Lecanorales, Stereocaulaceae).
6th IAL Symposium and Annual ABLS Meeting: Biology of lichens and bryophytes, California, USA.

Škaloud, P. & Peksa, O. (2008)
Phylogeny, morphology and taxonomic revision of the symbiotic alga Asterochloris (Trebouxiophyceae, Chlorophyta).
Algal Culture Collections 2008, Dunstaffnage Marine Laboratory, UK.

Škaloud, P., Neustupa, J., Veselá, J., Eliáš, M. & Škaloudová, M. (2008)
Algal culture collection in Prague - CAUP. A platform for education and taxonomic research.
Algal Culture Collections 2008, Dunstaffnage Marine Laboratory, UK.

Kynčlová, A., Škaloud, P. & Řezáčová-Škaloudová, M. (2008)
Molecular diversity and species concept in Synura petersenii (Synurophyceae, Heterokontophyta).
Algal Culture Collections 2008, Dunstaffnage Marine Laboratory, UK.
Seventh International Chrysophyte Symposium, Connecticut College, USA.

Pažoutová, M. & Škaloud, P. (2008)
Phylogeny and the generic concept of capsal green algae, family Radiococcaceae.
Algal Culture Collections 2008, Dunstaffnage Marine Laboratory, UK.

Škaloud, P., Friedl, T. & Neustupa, J. (2007)
Morphology, molecular phylogeny and taxonomy of green algal genera Aerosphaera and Dictyochloropsis (Trebouxiophyceae, Chlorophyta).
European Phycological Congress, Oviedo. EPC4 Programme, Eur. J. Phycol. 42(1), Suppl.: 107-108.

Škaloud, P. & Peksa, O. (2007)
Taxonomic study of Asterochloris (Trebouxiophyceae) based on comparative morphology of chloroplast structure and ITS sequences.
European Phycological Congress, Oviedo. EPC4 Programme, Eur. J. Phycol. 42(1), Suppl.: 108.

Neustupa, J., Škaloud, P., Šťastný, J. & Hodač, L. (2007)
Patterns of morphological variation in the genus Micrasterias (Desmidiales) - applications of geometric morphometrics.
European Phycological Congress, Oviedo. EPC4 Programme, Eur. J. Phycol. 42(1), Suppl.: 104.

Peksa, O. & Škaloud, P. (2007)
Changes of chloroplast structure in lichenized algae observed by confocal microscopy.
European Phycological Congress, Oviedo. EPC4 Programme, Eur. J. Phycol. 42(1), Suppl.: 147.

Neustupa, J., Škaloud, P., Šťastný, J. & Hodač, L. (2007)
Molecular diversity and phylogeny of tropical aerophytic green algae.
Biology and taxonomy of green algae V, Programme & Abstracts: 19.

Eliáš, M., Hodač, L., Škaloud, P., Němcová, Y. & Neustupa, J. (2007)
Molecular diversity and phylogeny of tropical aerophytic green algae.
Biology and taxonomy of green algae V, Programme & Abstracts: 19.

Neustupa, J., Škaloud, P. & Šťastný, J. (2007)
Geometric morphometrics of Micrasterias (Desmidiales) - infrageneric differentiation and pattern of morphological variation.
Biology and taxonomy of green algae V, Programme & Abstracts: 50.

Neustupa, J. & Škaloud, P. (2007)
Diversity of subaerial algae on tree bark in tropical mountain habitats.
Biology and taxonomy of green algae V, Programme & Abstracts: 51.

EU 7th Framework Programme: Development of an innovative, completely automated antifouling test system for professional examinations of marine coatings. Leader of the Czech team.

Higher Education Development Fund: Educational algal web-database of silica-scaled chrysophytes. Project leader.

AKTION Czech Republic - Austria (bilateral cooperation in sciences at university level): Symbiotic selection arenas in lichens. Leader of the Czech team.

Czech Science Foundation: Species concept and molecular diversity of green aerophytic algae. Project leader.

Czech Science Foundation: Cryptic and pseudocryptic species differentiation in desmids (Desmidiales, Viridiplantae). Researcher, Project leader: Jiří Neustupa.

Higher Education Development Fund: Educational algal web-database of permanent slides and herbarium specimens. Researcher, Project leader: Jana Veselá.

Czech Science Foundation: Diversity, ecological preferences and reproductive biology of freshwater epipelic diatoms. Researcher, Project leader: Aloisie Poulíčková.

Grant Agency of Charles University: Phylogeny and taxonomy of aerophytic green algae from the morphologically defined family Radiococcaceae. Researcher, Project leader: Marie Pažoutová.

Grant Agency of Charles University: Confocal microscopy and phylogeny of lichenized Trebouxia species. Project leader.

Czech Science Foundation: Integrated research of biodiversity and taxonomy of aerophytic green algae in tropic rainforest ecosystems. Researcher, Project leader: Jiří Neustupa.

Czech Ministry of Environment: Ecological boundary: interaction of biotic and abiotic in the surface microecosystems of soil and antropogenic substrates. Researcher, Project leader: Zdeněk Soldán.

Higher Education Development Fund: Confocal microscopy of the green-algal chloroplast. Researcher, Project leader: Jiří Neustupa.

Grant Agency of Charles University: Aerophytic epiphylic algae of the tropic rainforest ecosystems. Researcher, Project leader: Jiří Neustupa.

Grant Agency of Charles University: Eustigmatophyceae and Xanthophyceae on terrestrial biotopes. Researcher, Project leader: Jiří Neustupa.