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Svoboda D., Halda J. P., Malíček J., Palice Z., Šoun J. & Vondrák J. 2014: Lišejníky Českého krasu: shrnutí výzkumů a soupis druhů. Bohemia Centralis 32, 213 - 265.
Leavitt S. D., Fernandez-Mendoza F., Perez-Ortega S., Sohrabi M., Divakar P. K., Vondrák J., Lumbsch H. T. & St. Clair L. L. 2013: Local representation of global diversity in a morphologically cryptic lichen-forming fungal species-complex with a cosmopolitan distribution (Rhizoplaca, Ascomycota). Journal of Biogeography 40, 1792 - 1806. doi:10.1111/jbi.12118
Malíček J., Berger F., Bouda F., Cezanne R., Eichler M., Kocourková J., Müller A., Palice Z., Peksa O., Šoun J. & Vondrák J. 2013: Lichens recorded during the autumnal bryo-lichenological meeting in Novohradské hory Mts in 2012. Bryonora 51, 24 - 35.
Steinová J., Bouda B., Halda J. P., Kukwa M., Malíček J., Müller A., Palice Z., Peksa O., Schiefelbein U., Svoboda D., Syrovátková L., Šoun J., Uhlík P. & Vondrák J. 2013: Lichens recorded during the 16th meeting of the bryological and lichenological section CBS in Slavkovský les mountains, April 2009. Bryonora 51, 1 - 14.
Vondrák J., Frolov I., Arup U. & Khodosovtsev A. 2013: Methods for phenotypic evaluation of crustose lichens with emphasis on Teloschistaceae. Čornomorskij botaničnij žurnal 9, 382 - 405.
Vondrák J., Frolov I., Říha P., Hrouzek P., Palice Z., Nadyeina O., Halici G., Khodosovtsev A. & Roux C. 2013: New crustose Teloschistaceae in Central Europe. Lichenologist 45, 701 - 722. doi:10.1017/S0024282913000455
Vondrák J. & Kubásek J. 2013: Algal stacks and fungal stacks as adaptations to high light in lichens. Lichenologist 45, 115 - 124. doi:10.1017/S0024282912000722
Vondrák J. & Liška J. 2013: Lichens and lichenicolous fungi from the Retezat Mts and overlooked records for the checklist of Romanian lichens. Herzogia 26, 293 - 305.
Vondrák J. & Mayrhofer H. 2013: Caloplaca anularis and Caloplaca scrobiculata are distinct. Herzogia 26, 21 - 29.
Vondrák J., Palice Z., Mareš J. & Kocourková J. 2013: Two superficially similar lichen crusts, Gregorella humida and Moelleropsis nebulosa, and a description of the new lichenicolous fungus Llimoniella gregorellae. Herzogia 26, 31 - 48.
Vondrák J. & Wirth V. 2013: Caloplaca. In: Wirth V., Hauck M. & Schultz M. (eds) Die Flechten Deutschlands. Stuttgart: Ulmer., 262 - 317.
Frolov I. & Vondrák J. 2012: Lishayniki roda Caloplaca (Teloschistales, Ascomycota) s chernimi apotetsiami v stepnoy zone Yuzhnogo Urala i Preduralya. Cibilyev et al. (eds.) Stepi Severnoj Jevrazii - Steppes of northern Eurasia: materialy VI Meždunarodnogo simpoziuma, 770 - 773.
Halici M.G. & Vondrák J. 2012: Towards the Lichen Flora of Turkey. Cibilyev et al. (eds.) Stepi Severnoj Jevrazii - Steppes of northern Eurasia: materialy VI Meždunarodnogo simpoziuma, 847 - 848.
Khodosovtsev A., Vondrák J., Naumovich A., Kocourková J., Vondráková O. & Motiejunaite J. 2012: Three new Pronectria species in terricolous and saxicolous microlichen communities (Bionectriaceae, Ascomycota). Nova Hedwigia 95, 211 - 220. doi:10.1127/0029-5035/2012/0026
Malíček J. & Vondrák J. 2012: Lišejníky NPR Čertoryje v Bílých Karpatech. Bryonora 2012, 8 - 13.
Malíček J. & Vondrák J. 2012: Lišejníky NPR Jazevčí, Porážky a Zahrady pod Hájem v Bílých Karpatech. Acta Musei Richnoviensis 19, 1 - 11.
Powell, M. & Vondrák, J. 2012: Yellow sorediate crusts called Caloplaca citrina in England. British Lichen Society Bulletin 110, 20 - 24.
Powell, M. & Vondrák, J. 2012: Italian balustrade at Cliveden hosts Italian lichens? British Lichen Society Bulletin 110, 11 - 14.
Redchenko O., Vondrák J. & Košnar J. 2012: The oldest sequenced fungal herbarium sample. Lichenologist 44, 715 - 718. doi:10.1017/S002428291200031X
Vondrák J. 2012: [Recenze]: Biomonitoring, ecology, and systematics of lichens. [Bates, S. T.; Bungartz, F.; Lücking, R.; Herrera-Campos, M.; Zambrano, A.: Biomonitoring, ecology, and systematics of lichens.]. The Bryologist 115, 636 - 637. doi:10.1639/BRYOLOGIST-D-12-00046.1