Aleš Horák


email: ogar{at}

phone: (+420)387775428

Education and emplyment

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


Research priorities

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).


List of publications

Valencakova A, Balent P, Ravaszova P, Horak A, Obornik M, Halanova M, Malcekova B, Novotny F, Goldova M. 2011. Molecular identification and genotyping of Microsporidia in selected hosts. Parasitology Research. (in press)

Saldarriaga JF, Gile GH, James ER, Horák A, Scheffrahn RH and Keeling PJ. 2011. Morphology and Molecular Phylogeny of Pseudotrichonympha hertwigi andPseudotrichonympha paulistana (Trichonymphea, Parabasalia) from Neotropical Rhinotermitids. J. Eukaryot. Microbiol. 58: 487–496. doi: 10.1111/j.1550-7408.2011.00575.x

Carpenter K, Horak A, Chow L, Keeling PJ. 2011. Symbiosis, Morphology, and Phylogeny of Hoplonymphidae (Parabasalia) of the Wood-Feeding Roach Cryptocercus punctulatus. J. Eukaryot. Microbiol. (in press)

Cernotikova E, Horak A, Moravec F. 2011. Phylogenetic relationships of some spirurine nematodes (Nematoda: Chromadorea: Rhabditida: Spirurina) parasitic in fishes inferred from SSU rRNA gene sequences. Folia Parasitologica 58(2): 135-148

Allen AE, Dupont CL, Oborník M, Horak A, Numes-Nesi A, McCrow JP, Zheng H, Johnson DA, Hu H, Fernie AR, Bowler C. 2011. Evolution and metabolism significance of the urea cycle in photosynthetic diatoms. Nature 473(7346): 203-207

Stern RF , Horak A, Andrew RL, Coffroth MA , Andersen RA , Kupper FC , Jameson I , Hoppenrath M , Veron B , Kasai F , James ER , Keeling PJ . 2010. Environmental Barcoding Reveals Massive Dinoflagellate Diversity in Marine Environments. PLoS One 5 (11):e13991

Janouskovec, J., Horak A., Obornik, M., Lukes, J., and Keeling, P.J. 2010. A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. P.N.A.S 107(24):10949-10954

Carpenter, K. J., Horak A., and Keeling, P. J. 2010. Phylogenetic position and morphology of Spirotrichosomidae (Parabasalia): new evidence from Leptospironympha of Cryptocercus punctulatus. Protist 161 (1) :122-132

Burki, F., Inagaki, Y., Brate, J., Archibald, J. M., Keeling, P. J., Cavalier-Smith, T., Sakaguchi, M., Hashimoto, T., Horak A., Kumar, S., Klaveness, D., Jakobsen, K. S., Pawkowski, J., & Shalchian-Tabrizi, K. 2009. Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol. Evol. 231-238

Chronakova A., Horak A., Elhottova D. and Kristufek V. 2009. Diverse archaeal community of a bat guano pile in Domica Cave (Slovak Karst, Slovakia). Folia Microbiologica 54 (5): 436-446

Okamoto N., Chantangsi T., Horak A., Leander B.S. and Keeling, P. J. 2009. Molecular phylogenetic position and description of the novel karablepharid Roombia truncata gen. et sp. Nov., and establishment of the Hacrobia taxon nov. PLoS One 4 (9):e7080

Corradi N., Ruffner B., Croll D., Colard A., Horak A. and Sanders IR. 2009. High-Level Molecular Diversity of Copper-Zinc Superoxide Dismutase Genes among and within Species of Arbuscular Mycorrhizal Fungi. Applied and Environmental Microbiology 75 (7):1970-1978

Maletzky A, Mikulicek P, Franzen M, Goldschimdt A, Gruber HJ, Horak A. and Kyek M. 2008. Introgression and hybridization between two species of crested newts (Triturus cristatus, T. carnifex) along contact zones in Germany and Austria: morphological and molecular data. Herpetological Journal 18 (1):1-15

Jiroutova K, Horak A, Bowler C, Obornik M. 2007. Tryptophan synthesis in stramenopiles: replacement of nuclear-encoded genes of plastid (cyanobacterial) origin by eukaryotic homologues from primary and secondary host. J. Mol. Evol. 65 (5): 496-511

Lukes L, Mauricio IS, Schönian G, Dujardin J-C, Soteriadou S, Dedet J-P, Kuhls K, Tintaya QW, Jirku M, Zemanova E, Haralambous C, Pratlong F, Obornik M, Horak A, Ayala FJ, Miles MA. 2007. Multifactorial genetic analysis of the Leishmania donovani complex reveals geographical and evolutionary history, and does not reflect the current taxonomy. P.N.A.S, 104 (22): 9375-9380

Vavra J, Horak A, Modry D, Lukes J, Koudela B. 2006. Trachipleistophora extenrec, n. sp., a new microsporidian (Fungi:Microsporidia) infecting mammals. Journal for Evolutionary Microbiology 53 (6): 464-476

Zemanova E, Jirku M, Mauricio LI, Horak A, Miles M, Lukes J. 2006. Analysis of genetic polymorphism of the Leishmania donovani complex in five metabolic enzymes (ICD, MPI, G6PDH, FH, ME). International Journal for Parasitology 36 (9): 1067-1075

Wijova M, Moravec F, Horak A, Lukes J. 2006. Evolutionary relationships of Spirurina (Nematoda: Chromadorea: Rhabditida) with special emphasis on dracunculoid nematodes inferred from SSU rRNA gene sequences, International Journal for Parasitology, 36 (9): 1067-1075

Lukes J, Horak A, Scholz T. 2005. Helminth genome projects: all or nothing. Trends in Parasitology. 21 (6): 265-26

WijovaM, Moravec F, Horak A, Modry D, Lukes J. 2005. Phylogenetic position of Dracunculus medinensis and some related nematodes inferred from 18S rRNA. Parasitology Research 96 (2): 133-135

Logan FJ, Horak A, Stefka J, Aydogdu A, Scholz T. 2004. The phylogeny of diphyllobothriid tapeworms (Cestoda : Pseudophyllidea) based on ITS-2 rDNA sequences. Parasitology Research 94 (1): 10-15