Mgr. Aleš Horák, Ph.D.

Job Position: Group leader - Laboratory of Evolutionary Protistology

Contact details

Phone: +420 387775449
Room: THS 5.11


In my recent research I focus mainly on different aspects of evolutionary biology of Protists. It could be divided into two areas. First deals with the biodiversity and evolutionary history of various groups of protists, ranging from katablepharids (Okamoto et al. 2009, PloS One), dinoflagellates (Okamoto et al., in prep.), colpodellids and apicomplexans (Howe et al., in prep.; Janouskovec et al., in prep) to leishmanias (Lukes et al. 2007, P.N.A.S.) or parabasalid termite-gut endosymbionts (Carpenter et al., 2010, Protist). In these projects, I've been  responsible mainly for describing and quantifiyng diversity and finding hierarchy in studied taxa using molecular markers (i.e. phylogenetic and population genetic analyses). Second part of my work have been so far dedicated to uncovering macroevolutionary processes shaping up eukaryotic Tree of Life. I am part of annotating team for the genome projects of Guillardia theta (Cryptophyta) and Bigellowiela natans (Chlorarachniophyta), two non-relative alga important by the presence of remnant endosymbiont genome called nucleomorph. I've also worked on comparative genomics of four nucleomorph genomes (Horak, in. prep) and comparative genomics of plastids of Chromera velia and relative algal lineage CCMP3155 (Janouskovec at al. 2010, P.N.A.S).

Curriculum vitae


Education and employment

  • 2011-present research scientist at Department of Moleculary Biology, University of South Bohemia, Faculty of Science
  • 2010-present post-doctoral fellow at Laboratory of Molecular Taxonomy, Institute of Parasitology Academy of Sciences of the Czech Republic
  • 2007-2010 post-doctoral fellow at University of British Columbia, Dept. of Botany, Keeling lab.
  • 2000 – 2007 (with exclusion of 2003 - 2004 when absolved Civil service) PhD student at Department of Zoology, Faculty of Sciences, University of South Bohemia.
  • 1994 – 2000 Student (Msc.) Faculty of Biological Sciences, University of South Bohemia

Courses and Workshops

  • June 2011 EuPathDB Workshop, UGA, Athens, GA, USA
  • June 2010 CIFAR Eukaryotic Genome Annotation Workshop, Dalhousie, Halifax, NS, Canada
  • May 2010 CIFAR BigData Workshop, UBC, Vancouver, BC, Canada
  • May 2008 IMG Microbial Genomics Workshop, JGI, Walnut Creek, CA, USA


  • Rector Award of the Best Publication of the Year 2010


Total found: 58 records
del Campo J., Carlos-Oliveira M., Čepička I., Hehenberger E., Horák A., Karnkowska A., Kolísko M., Lara E., Lukeš J., Pánek T., Piwosz K., Richter D.J., Škaloud P., Šuťák R., Tachezy J., Hampl V. (2024) The protist cultural renaissance Trends in Microbiology 32 : 128-131.
DOI: 10.1016/j.tim.2023.11.010

Documents to download:
delCampo_2024_TrendsParasitol (pdf)
Flegontova O., Flegontov P., Jachníková N., Lukeš J., Horák A. (2023) Water masses shape pico-nano eukaryotic communities of the Weddell Sea Communications Biology 6 : 64.
DOI: 10.1038/s42003-023-04452-7

Documents to download:
Flegontova_2023_CommBiol (pdf)
Flegontova O., Lukeš J., Horák A. (2023) Intragenomic diversity of the V9 hypervariable domain in eukaryotes has little effect on metabarcoding iScience 26 : 107291.
DOI: 10.1016/j.isci.2023.107291

Documents to download:
Flegontova_2023_iScience (pdf)
Lampe R.H., Coale T.H., Forsch K.O., Jabre L.J., Kekuewa S., Bertrand E.M., Horák A., Oborník M., Rabines A.J., Rowland E., Zheng H., Andersson A.J., Barbeau K.A., Allen A.E. (2023) Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton Nature Communications 14 : 7215.
DOI: 10.1038/s41467-023-42949-1
Richtová J., Bazalová O., Horák A., Tomčala A., Gonepogu V., Oborník M., Doležel D. (2023) Circadian rhythms and circadian clock gene homologs of complex alga Chromera velia Frontiers in Plant Science 14 : 1226027.
DOI: 10.3389/fpls.2023.1226027
Rudenko N., Golovchenko M., Horák A., Grubhoffer L., Mongodin E.F., Fraser C.M., Qiu W., Luft B., Morgan R.G., Casjens S.R., Schutzer S. (2023) Genomic confirmation of Borrelia garinii in the USA Emerging Infectious Diseases 29 : 1.
DOI: 10.3201/eid2901.220930
Tashyreva D., Týč J., Horák A., Lukeš J. (2023) Ultrastructure and 3D reconstruction of a diplonemid protist (Diplonemea) and its novel membranous organelle. mBio 14 : e01921-23.
DOI: 10.1128/mbio.01921-23

Documents to download:
Tashyreva_2023_MBio (pdf)
George E.E., Tashyreva D., Kwong W.K., Okamoto N., Horák A., Husník F., Lukeš J., Keeling P. (2022) Gene transfer agents in bacterial endosymbionts of microbial eukaryotes Genome Biology and Evolution 14 : evac099.
DOI: 10.1093/gbe/evac099

Documents to download:
George_2022_GBE (pdf)
Prokopchuk G., Korytář T., Juricová V., Horák A., Majstorović J., Šimek K., Lukeš J. (2022) Trophic flexibility of marine diplonemids - switching from osmotrophy to bacterivory The ISME Journal 16 : 1409–1419.
DOI: 10.1038/s41396-022-01192-0

Documents to download:
Prokopchuk_2022_ISMEJ (pdf)
Tashyreva D., Simpson A., Prokopchuk G., Škodová-Sveráková I., Butenko A., Hammond M., George E.E., Flegontova O., Záhonová K., Faktorová D., Yabuki A., Horák A., Keeling P., Lukeš J. (2022) Diplonemids - A Review on "New" Flagellates on the Oceanic Block Protist 173 : 125868.
DOI: 10.1016/j.protis.2022.125868

Documents to download:
Tashyreva_2022_Protist (pdf)
Barcytė D., Eikrem W., Engesmo A., Seoane S., Wohlmann J., Horák A., Yurchenko T., Eliáš M. (2021) Olisthodiscus represents a new class of Ochrophyta Journal of Phycology 57 : 1094–1118.
DOI: 10.1111/jpy.13155
Škodová-Sveráková I., Záhonová K., Juricová V., Danchenko M., Moos M., Baráth P., Prokopchuk G., Butenko A., Lukáčová V., Kohútová L., Bučková B., Horák A., Faktorová D., Horváth A., Šimek P., Lukeš J. (2021) Highly flexible metabolism of the marine euglenozoan protist /Diplonema papillatum/. BMC Biology 19 : 251.
DOI: 10.1186/s12915-021-01186-y

Documents to download:
Skodova-Sverakova_2021_BMCBiol (pdf)
Turnšek J., Brunson J.K., Viedma M.D.P.M., Deerinck T.J., Horák A., Oborník M., Bielinski V.A., Allen A.E. (2021) Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway eLife 10 : e52770.
DOI: 10.7554/eLife.52770
Butenko A., Opperdoes F.R., Flegontova O., Horák A., Hampl V., Keeling P., Gawryluk R., Tikhonenkov D.V., Flegontov P., Lukeš J. (2020) Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids BMC biology 18 : 23.
DOI: 10.1186/s12915-020-0754-1

Documents to download:
Butenko_BMC-Biology_2020 (pdf)
Flegontova O., Flegontov P., Castaňeda Londoňo P., Walczowski W., Śantić D., Edgcomb V., Lukeš J., Horák A. (2020) Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans Environmental Microbiology 22 : 4014–4031.
DOI: 10.1111/1462-2920.15190

Documents to download:
Flegontova_2020_EnvMicrob (pdf)
George E.E., Husník F., Tashyreva D., Prokopchuk G., Horák A., Kwong W.K., Lukeš J., Keeling P. (2020) Highly Reduced Genomes of Protist Endosymbionts Show Evolutionary Convergence Current Biology 30 : 925-933.
DOI: 10.1016/j.cub.2019.12.070

Documents to download:
George_2020_CurrentBiology (pdf)
Horák A., Allen A.E., Oborník M. (2020) Common origin of ornithine–urea cycle in opisthokonts and stramenopiles Scientific Reports 10 : 16687.
DOI: 10.1038/s41598-020-73715-8
Kolísko M., Flegontova O., Karnkowska A., Lax G., Maritz J.M., Pánek T., Táborský P., Carlton J.M., Čepička I., Horák A., Lukeš J., Simpson A., Tai V. (2020) EukRef-excavates: seven curated SSU ribosomal RNA gene databases Database 2020 : baaa080.
DOI: 10.1093/database/baaa080

Documents to download:
Kolisko_2020_Database (pdf)
Smýkal V., Pivarči M., Provazník J., Bazalová O., Jedlička P., Lukšan O., Horák A., Vaněčková H., Beneš V., Fiala I., Hanus R., Doležel D. (2020) Complex evolution of insect insulin receptors and homologous decoy receptors, and functional significance of their multiplicity. Molecular Biology and Evolution 37 : 1775-1789.
DOI: 10.1093/molbev/msaa048
Coale T.H., Moosburner M., Horák A., Oborník M., Barbeau K.A., Allen A.E. (2019) Reduction-dependent siderophore assimilation in a model pennate diatom Proceedings of the National Academy of Sciences of United States of America 116 : 23609-23617.
DOI: 10.1073/pnas.1907234116

More publications


Biology Centre CAS
Institute of Parasitology
Branišovská 1160/31
370 05 České Budějovice

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