- Šobotník , Hanus R., Kalinová B., Piskorski R., Cvačka J., Bourguignon T. & Roisin Y. 2008: (E,E)-alpha-farnesene, the alarm pheromone of Prorhinotermes canalifrons (Isoptera: Rhinotermitidae). Journal of Chemical Ecology 34: 478-486.
- Bourguignon T., Šobotník J., Lepoint G., Martin -M. & Roisin Y. 2009: Niche differentiation among Neotropical soldierless soil-feeding termites revealed by stable isotope ratios. Soil Biology & Biochemistry 41: 2038-2043.
- Hanus R., Vrkoslav V., Hrdý I., Cvačka J. & Šobotník J. 2010: Beyond cuticular hydrocarbons: evidence of proteinaceous secretion specific to termite kings and queens. Proceedings of the Royal Society B, Biological Sciences 277: 995-1002.
- Šobotník J., Jirošová A. & Hanus R. 2010: Chemical warfare in termites. Journal of Insect Physiology 56: 1012-1021. (Invited Review)
- Bourguignon T., Šobotník J., Lepoint G., Martin J.-M., Hardy O.J., Dejean A. & Roisin 2011: Feeding ecology and phylogenetic structure of a complex neotropical termite assemblage, revealed by nitrogen stable isotope ratios. Ecological Entomology 36: 261-269.
- Šobotník J., Bourguignon T., Hanus R., Demianová Z., Pytelková J., Mareš M., Foltýnová P., Preisler J., Cvačka J., Krasulová J. & Roisin Y. 2012: Explosive backpacks in old termite workers. Science 337: 436. (Rated by Science editors among Top 10 most interesting papers in 2012)
- Bourguignon T., Lo N., Cameron S.L., Šobotník J., Hayashi Y., Shigenobu S., Watanabe D., Roisin Y., Miura T. & Evans T.A. 2015: The evolutionary history of termites as inferred from 66 mitochondrial genomes. Molecular Biology and Evolution 32: 406-421.
- Billen J. & Šobotník J. 2015: Insect exocrine glands. Arthropod Structure & Development 44: 399-400.
- Bourguignon T., Šobotník J., Brabcová J., Sillam-Dusses D., Buček A., Krasulová J., Vytisková B., Demianová Z., Mareš M., Roisin Y. & Vogel H. 2016: Molecular mechanism of the two-component suicidal weapon of Neocapritermes taracua old workers. Molecular Biology and Evolution 33: 809-819.
- Bourguignon T., Lo N., Šobotník J., Ho S.Y.W., Iqbal N., Coissac E., An M.L., Jendryka M., Sillam-Dusses D., Křížková B., Roisin Y. & Evans T.A. 2017: Mitochondrial phylogenomics resolves the global spread of higher termites, ecosystem engineers of the tropics. Molecular Biology and Evolution 34: 589-597.
- Wen X.-L., Wen P., Dahlsjö C.A.L., Sillam-Dusses D. & Šobotník J. 2017: Breaking the cipher: ant eavesdropping on the variational trail pheromone of its termite prey. Proceedings of the Royal Society B, Biological Sciences 284: 20170121.
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Bourguignon T., Lo N., Dietrich C., Šobotník J., Sidek S., Roisin Y., Brune A. & Evans T.A. 2018: Rampant host switching shaped the termite gut microbiome. Current Biology 28: 649-654.
Veškeré publikace zde nebo na ResearchGate
Kapitoly v knihách
- Šobotník J. & Dahlsjö C.A.L. 2017: Isoptera. In: Reference Module in Life Sciences, Elsevier, ISBN 9780128096338, více zde
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Ulyshen M. & Šobotník J. 2018: An Introduction to the Diversity, Ecology, and Conservation of Saproxylic Insects. In: Saproxylic Insects. Diversity, Ecology and Conservation, Ulyshen M. (Ed.). Springer, Cham, Switzerland, pp.1-47. více zde