Články v mezinárodních impaktovaných a neimpaktovaných časopisech:
Nežerková P., Hejcman M., Camara A.A., Antonínová M., Pavlů V., Černý T., Bâ A.T. (2005). Analysis of herbaceous undergrowth in woody savannah in the Fathala Reserve, Delta du Saloum National Park, Senegal. – Belgian J. Bot. 138: 119–128.
Černý T., Petřík P., Boublík K. & Kolbek J. (2006) Habitat requirements of Cardaminopsis petraea – rare and relict species of the Czech Republic. – Biologia 61: 51–61.
Černý T. & Neuhäuslová Z. (2006). The "Thymo-Festucetum ovinae" complex and similar subthermophilous communities in the Czech Republic. – Polish Bot. Stud. 22: 137–148.
Boublík K. & Černý T. (2006). Dry psammophytic non-forest vegetation of the Třeboňsko Biosphere Reserve (Czech Republic). – Linzer Biol. Beiträge 38: 1269–1287.
Černý T., Petřík P., Boublík K. & Kolbek J. (2007). Vegetation with Aira praecox in the Czech Republic compared to its variability in Western Europe. – Phytocoenologia 37: 115–134.
Boublík K., Petřík P., Sádlo J., Hédl R., Willner W., Černý T. & Kolbek J. (2007). Calcicolous beech forests and related vegetation in the Czech Republic: a comparison of formalized classifications. – Preslia 79: 141–161.
Doležal J., Song J.-S., Altman J., Janeček Š., Černý T., Šrůtek M. & Kolbek J. (2009). Postlogging regeneration, tree growth and competition in mixed-oak Quercus mongolica forest in Korea. – Ecological Research, 24: 281–290.
Dijk P., Kirschner J., Štěpánek J., Baitulin I.O. & Černý T. (2010). Taraxacum koksaghyz Rodin definitely is not an example of overcollecting in the past. A reply to S. Volis et al. (2009). – J. Appl. Bot. Food Qual. 83: 217–219.
Černý T., Petřík P., Boublík K., Kolbek J. & Adámek M. (2011). Vegetation with Gagea bohemica in the landscape context. – Plant Biosystems 145: 570–583.
Petřík P., Černý T. & Boublík K. (2011). Impact of hoofed game and weather on the vegetation of endangered dry grasslands in the Křivoklátsko Biosphere Reserve (Czech Republic). – Tuexenia 31: 283–299
Černý, T. , Šrůtek, M., Petřík, P., Song, J.-S. & Valachovič, M. 2012. Korean forest database. – Biodiversity & Ecology 4: 300–301.
Doležal J., Altman J., Kopecký M., Černý T., Janeček Š, Bartoš M., Petřík P., Šrůtek M., Lepš J. & Song J.S. (2012). Plant diversity changes during the postglacial in East Asia: insights from forest refugia on Halla Volcano, Jeju Island. – PLoS ONE 7(3): e33065. [doi:10.1371/journal.pone.0033065]
Altman J., Doležal J., Černý T. & Song J.-S. (2013). Forest response to increasing typhoon activity on the Korean peninsula: evidence from oak tree-rings. – Global Change Biology 19: 498–504.
Janeček Š., de Bello F., Horník J., Bartoš M., Černý T., Doležal J., Dvorský M., Fajmon K., Janečková P., Jiráská Š., Mudrák O., Klimešová J. (2013). Effects of land-use changes on plant functional and taxonomic diversity along a productivity gradient in wet meadows. – Journal of Vegetation Science 24: 898–909.
Černý T., Doležal J., Janeček Š., Šrůtek M., Valachovič M., Altman J., Petřík P., Bartoš M. & Song J.S. (2013). Environmental correlates of plant diversity in Korean temperate forests. – Acta Oecologica 47: 37–45.
Kirschner J., Štěpánek J., Černý T., De Heer P. & Dijk P. (2013). Available ex-situ germplasm of the potential rubber crop Taraxacum koksaghyz belongs to a poor rubber producer, T. brevicorniculatum (Compositae – Crepidinae). – Genet. Resour. Crop. Evol. 60: 455–471.
Černý T., Kopecký M., Petřík P., Song J.-S., Šrůtek M., Valachovič M., Altman J. & Doležal J. (2015). Classification of Korean forests: patterns along geographic and environmental gradients. – Appl. Veg. Sci. 18: 5–22.
Odborné články ostatní (výběr):
Šrůtek M., Horák T., Černý T., Petřík P. (2012). Korea – stromy, lesy, kláštery a lidé. Vesmír 91: 706–712.
Černý T. (2012). Pampeliška koksaghyz (Taraxacum koksaghyz) – alternativa ke kaučukovníku. Živa 6/2012: 279–284.
