Mgr. Aleš Horák, Ph.D.

Job Position: Head of Laboratory - Laboratory of environmental genomics

Contact details

Phone: +420 387775409


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: 46 records
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
Prokopchuk G., Tashyreva D., Yabuki A., Horák A., Masařová P., Lukeš J. (2019) Morphological, ultrastructural, motility and evolutionary characterization of two new Hemistasiidae species Protist 170 : 259–282.
DOI: 10.1016/j.protis.2019.04.001

Documents to download:
Prokopchuk et al._2019_Protist (pdf)
Smith S.R., Dupont C.L., McCarthy J.K., Boddrick J.T., Oborník M., Horák A., Füssy Z., Cihlář J., Kleessen S., Zheng H., McCrow J.P., Hixson K.K., Araújo W.L., Nunes-Nesi A., Fernie A., Nikoloski Z., Palsson B.O., Allen A.E. (2019) Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom Nature Communications 10 : 4552.
DOI: 10.1038/s41467-019-12407-y
Faktorová D., Bär A., Hashimi H., McKenney K., Horák A., Schnaufer A., Rubio M., Alfonzo J., Lukeš J. (2018) TbUTP10, a protein involved in early stages of pre-18S rRNA processing in Trypanosoma brucei Molecular and Biochemical Parasitology 225 : 84–93.
DOI: 10.1016/j.molbiopara.2018.09.003

Documents to download:
Faktorova_et al._2018 (pdf)
Flegontova O., Flegontov P., Malviya S., Poulain J., de Vargas C., Bowler C., Lukeš J., Horák A. (2018) Neobodonids are dominant kinetoplastids in the global ocean Environmental Microbiology 20 : 878-889.
DOI: 10.1111/1462-2920.14034

Documents to download:
Flegontova_et.al_2018 (pdf)
McQuaid J.B., Kustka A.B., Oborník M., Horák A., Mccrow J., Karas B.J., Zheng H., Kindeberg T., Andersson A.J., Barbeau K.A., Allen A. (2018) Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms Nature 555 : 534-537.
DOI: 10.1038/nature25982
Tashyreva D., Prokopchuk G., Votýpka J., Yabuki A., Horák A., Lukeš J. (2018) Life cycle, ultrastructure, and phylogeny of new diplonemids and their endosymbiotic bacteria mBio 9 : e02447-17.
DOI: 10.1128/mBio.02447-17

Documents to download:
Tashyreva et al. 2018 mBio (pdf)
Tashyreva D., Prokopchuk G., Yabuki A., Kaur B., Faktorová D., Votýpka J., Kusaka Ch., Fujikura K. , Shiratori T., Ishida K., Horák A., Lukeš J. (2018) Phylogeny and morphology of new diplonemids from Japan Protist 169 : 158–179.
DOI: 10.1016/j.protis.2018.02.001

Documents to download:
Tashyreva_et.al_Protist_2018 (pdf)
Rueckert S., Horák A. (2017) Archigregarines of the English Channel revisited: new molecular data on Selenidium species including early described and new species and the uncertainties of phylogenetic relationships Plos ONE 12 : e0187430.
DOI: 10.1371/journal.pone.0187430
Sobotka R., Esson H. J., Koník P., Trsková E., Moravcová L., Horák A., Dufková P., Oborník M. (2017) Extensive gain and loss of photosystem I subunits in chromerid algae, photosynthetic relatives of apicomplexans Scientific Reports 7 : 13214.
Cihlář J., Füssy Z., Horák A., Oborník M. (2016) Evolution of the Tetrapyrrole Biosynthetic Pathway in Secondary Algae: Conservation, Redundancy and Replacement PLoS ONE 11 : e0166338.
DOI: 10.1371/journal.pone.0166338
Flegontova O., Flegontov P., Malviya S., Audic S., Wincker P., de Vargas C., Bowler C., Lukeš J., Horák A. (2016) Extreme diversity of diplonemid eukaryotes in the ocean Current Biology 26 : 3060-3065.
DOI: 10.1016/j.cub.2016.09.031

Documents to download:
Flegontova et al. 2016 CB (pdf)
de Vargas C., Audic S., Henry N., Decelle J., Mahé F., Logares R., Lara E., Berney C., Le Bescot N., Probert I., Carmichael M., Poulain J., Romac S., Colin S., Aury J., Bittner L., Chaffron S., Dunthorn M., Engelen S., Flegontova O., Guidi L., Horák A., Jaillon O., Lima-Mendez G., Lukeš J., Malviya S., Morard R., Mulot M., Scalco E., Siano R., Vincent F., Zingone A., Dimier C., Picheral M., Searson S., Kandels-Lewis S., Coordinators T., Acinas S., Bork P., Bowler C., Gorsky G., Grimsley N., Hingamp P., Iudicone D., Not F., Ogata H., Pesant S., Raes J., Sieracki M., Speich S., Stemmann L., Sunagawa S., Weissenbach J., Wincker P., Karsenti E. (2015) Eukaryotic plankton diversity in the sunlit ocean Science 348 : 1261605.
DOI: 10.1126/science.1261605

Documents to download:
deVargas-et-al_Science_2015 (pdf)

More publications


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

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