Škaloud, P., Kynčlová, A., Benada, O., Kofroňová, O. & Škaloudová, M. (2012)
Toward a revision of the genus Synura, section Petersenianae (Synurophyceae, Heterokontophyta): morphological characterization of six pseudo-cryptic species.
Phycologia 51: 303-329.

Přibyl, P., Eliáš, M., Cepák, V., Lukavský, J., Kaštánek, P. (2012)
Zoosporogenesis, morphology, ultrastructure, pigment composition, and phylogenetic position of Trachydiscus minutus (Eustigmatophyceae, Heterokontophyta).
Journal of Phycology 48: 231-242.

Banks, J.A., Nishiyama, T., Hasebe M. + 100 additional authors incl. Elias, M. (2011)
The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.
Science 332: 960-963.

Němcová, Y., Bulant, P. & Kristiansen, J. (2011)
Mallomonas solea-ferrea and Mallomonas siveri (Chrysophyceae/Synurophyceae): two new taxa from the
Western Cape (South Africa).
Nova Hedwigia 93: 375-384.

Němcová, Y., Eliáš, M., Škaloud, P., Hodač, L. & Neustupa, J. (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, K., 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., Černá, K. & Šťastný, J. (2011)
The effects of aperiodic desiccation on the diversity of benthic desmid assemblages in a lowland peat bog.
Biodiversity and Conservation 20: 1695-1711.

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., 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.

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.

Pichrtová, M. & Němcová, Y. (2011)
Effect of temperature on size and shape of silica scales in Synura petersenii and Mallomonas tonsurata
(Stramenopiles).
Hydrobiologia 673: 1-11.

Pichrtová, M., Janatková, K. & Němcová, Y. (2011)
Silica-scaled chrysophytes from Abisko (Swedish Lapland).
Nordic Journal of Botany 29: 112-118.

Škaloud, O., 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.

Sucgang, C. et al. incl. Eliáš, M. (2011)
Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.
Genome Biology 12: R20.

Svoboda, D., Peksa, O. & Veselá, J. (2011)
Analysis of the species composition of epiphytic lichens in Central European oak forests.
Preslia 83: 129-144.

Veselá, J., Škaloud, P., Urbánková, P., Škaloudová, M. & Kalina, T. (2011)
The CAUP image database.
Fottea 11: 313-316.

Vlahou, G., Eliáš, M., von Kleist-Retzov, J.C., Wiesner, R.J. & Rivero, F. (2011)
The Ras related GTPase Miro is not required for mitochondrial transport in Dictyostelium discoideum.
European Journal of Cell Biology 90: 342-355.

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.

Černá, K. (2010)
Small-scale spatial variation of benthic algal assemblages in a peat bog.
Limnologica 40: 315-321.

Černá, K. & Neustupa, J. (2010)
The pH-related morphological variations of two acidophilic species of Desmidiales (Viridiplantae) isolated from a lowland peat bog, Czech Republic.
Aquatic Ecology 44: 409-419.

Cock, J.M., Sterck, L., Rouzé, P., Scornet, D. + 70 additional authors incl. Elias, M. (2010)
The Ectocarpus genome and the independent evolution of multicellularity in brown algae.
Nature 465: 617-621.

Elias, M. (2010)
Patterns and processes in the evolution of the eukaryotic endomembrane system.
Molecular Membrane Biology 27: 469-489.

Eliáš, M., Němcová, Y., Škaloud, P., Neustupa, J., Kaufnerová, V. & Šejnohová, L. (2010)
Hylodesmus singaporensis gen. et sp. nov., a new autosporic subaerial green alga (Scenedesmaceae, Chlorophyta) from Singapore.
International Journal of Systematic and Evolutionary Microbiology 60: 1224-1235.

Kynčlová, A., Škaloud, P. & Škaloudová, M. (2010)
Unveiling hidden diversity in the Synura petersenii species complex (Synurophyceae, Heterokontophyta).
Nova Hedwigia, Beiheft 136: 283-298.

Němcová, Y. (2010)
Diversity and ecology of silica-scaled chrysophytes (Synurophyceae, Chrysophyceae) in the National Nature Monument Swamp and Brehynsky Pond, Czech Republic
Cryptogamie, Algologie 31: 229-243.

Němcová, Y., Neustupa, J., Kvíderová, J. & Řezáčová-Škaloudová, M. (2010)
Morphological plasticity of silica scales of Synura echinulata (Synurophyceae) in crossed gradients of light and temperature – a geometric morphometric approach.
Nova Hedwigia, Beiheft 136: 21-32.

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.

Neustupa, J., Řezáčová-Škaloudová, M. & Němcová, Y. (2010)
Shape variation of the silica scales of Mallomonas kalinae (Mallomonadales, Synurophyceae) in relation to their position on the cell body.
Nova Hedwigia, Beiheft 136: 33-42.

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.

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.

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.

Řezáčová-Škaloudová, M., Neustupa, J. & Němcová, Y. (2010)
Effect of temperature on the variability of silicate structures in Mallomonas kalinae and Synura curtispina (Synurophyceae).
Nova Hedwigia, Beiheft 136: 55-70.

Savriama, Y., Neustupa, J. & Klingenberg, C.P. (2010)
Geometric morphometrics of symmetry and allometry in Micrasterias rotata (Zygnemophyceae, Viridiplantae).
Nova Hedwigia, Beiheft 136: 43-54.

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.

Šťastný, J. (2010)
Desmids (Conjugatophyceae, Viridiplantae) from the Czech Republic; new and rare taxa, distribution, ecology.
Fottea 10: 1-74.

Svoboda, D., Peksa, O. & Veselá, J. (2010)
Epiphytic lichen diversity in Central European oak forests: Assessment of the effects of natural environmental factors and human influences.
Environmental Pollution 158: 812-819.

Elias, M. & Archibald, J.M. (2009)
Sizing up the genomic footprint of endosymbiosis
BioEssays 31: 1273-1279.

Elias, M. & Archibald, J.M. (2009)
The RJL family of small GTPases is an ancient eukaryotic invention probably functionally associated with the flagellar apparatus.
Gene 442: 63-72.

Eliáš, M. & Neustupa, J. (2009)
Pseudomarvania, gen. nov. (Chlorophyta, Trebouxiophyceae), a new genus for “budding” subaerial green algae Marvania aerophytica Neustupa et Šejnohová and Stichococcus ampulliformis Handa.
Fottea 9: 169-177.

Elias, M., Patron, N.J. & Keeling, P.J. (2009)
The RAB family GTPase Rab1A from Plasmodium falciparum defines a unique paralog shared by chromalveolates and Rhizaria.
Journal of Eukaryotic Microbiology 56: 348-356.

Fránková, M., Poulíčková, A., Neustupa, J., Pichrtová, M. & Marvan, P. (2009)
Geometric morphometrics - a sensitive method to distinguish diatom morphospecies: a case study on the sympatric populations of Reimeria sinuata and Gomphonema tergestinum (Bacillariophyceae) from the River Bečva, Czech Republic
Nova Hedwigia 88: 81-95.

Janatková, K. & Němcová, Y. (2009)
Silica-scaled chrysophytes of Southern Bohemian water bodies, including Mallomonas conspersa Dürrschmidt with occurrence so far reported from Japan and New Zealand
Fottea 9: 93-99.

Ma, L.J., Ibrahim, A.S., Skory, C., Grabherr, M.G., Burger, G., Butler, M., Elias, M. et al. (2009)
Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication.
PLoS Genetics 5: e1000549.

Machová-Černá, K., Neustupa, J. (2009)
Spatial distribution of algal assemblages in a temperate lowland peat bog.
International Review of Hydrobiology 94: 40-56.

Němcová, Y. & Pichrtová, M. (2009)
The rare species Synura lapponica (Synurophyceae) new to the Czech Republic, local vs. global diversity in colonial synurophytes.
Biologia 64: 1070-1075.

Nemjová, K. & Kaufnerová, V. (2009)
New reports of Vaucheria species (Vaucheriales, Xanthophyceae, Heterokontophyta) from the Czech Republic.
Fottea 9: 53-57.

Neustupa, J., Černá, K. & Šťastný, J. (2009)
Diversity and morphological disparity of desmid assemblages in Central European peatlands.
Hydrobiologia 630: 243-256.

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.

Pichrtová, M. & Veselá, J. (2009)
The silica-scaled chrysophytes of the Elbe Sandstone Region, Czech Republic.
Fottea 9: 101-106.

Píšková, A., Grygar, T., Veselá, J. & Oberhänsli, H. (2009)
Diatom assemblage variations in the Aral Sea core C2/2004 over the past two millennia.
Fottea 9: 333-342.

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.

Prášil, O., Bína, D., Medová, H., Řeháková, K., Zapomělová, E., Veselá, J. & Oren, A. (2009)
Emission spectroscopy and kinetic fluorometry studies of the phototrophic microbial communities along the salinity gradient in the solar saltern evaporation ponds of Eilat, Israel.
Aquatic Microbial Ecology 56: 285-296.

Řeháková, K., Zapomělová, E., Prášil, O., Veselá, J., Medová, H. & Oren, A. (2009)
Composition changes of phototrophic microbial communities along the salinity gradient in the solar saltern evaporation ponds of Eilat, Israel.
Hydrobiologia 636: 77-88.

Škaloud, P. (2009)
Species composition and diversity of aero-terrestrial algae and cyanobacteria of the Boreč Hill ventaroles.
Fottea 9: 65-80.

Šťastný, J. (2009)
The desmids of the Swamp Nature Reserve (North Bohemia, Czech Republic) and a small neighbouring bog: species composition and ecological condition of both sites.
Fottea 9: 135-148.

Veselá, J. (2009)
Spatial heterogeneity and ecology of algal communities in an ephemeral sandstone stream in the Bohemian Switzerland National Park, Czech Republic.
Nova Hedwigia 88: 531-547.

Veselá, J. & Johansen, J. (2009)
The diatom flora of ephemeral headwater streams in the Elbsandsteingebirge region of the Czech Republic.
Diatom Research 24: 443-477.

Veselá, J., Neustupa, J., Pichrtová, M. & Poulíčková A. (2009)
Morphometric study of Navicula morphospecies (Bacillariophyta) with respect to diatom life cycle.
Fottea 9: 307-316.