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Theriot, E.C., Ashworth, M.P., Nakov, T., Ruck, E. & Jansen, R.K. 2015. Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Molecular Phylogenetics and Evolution, 89:28-36. link

Nakov, T., Ashworth, M., and E.C. Theriot. 2014. Comparative analysis of the interaction between habitat and growth form in diatoms. ISME-J, 9: 246–255. link

Nakov, T., Ruck, E.C., Galachyants, Y., Spaulding, S.A. and E.C. Theriot. 2014 Molecular phylogeny of the Cymbellales (Bacillariophyceae) with a comparison of models for accommodating rate-variation across sites. Phycologia, 53: 359-373. link

Ruck, E. C., Nakov, T., Jansen, R. K., Theriot, E. C. and A. J. Alverson. 2014. Serial gene losses and foreign DNA underlie size and sequence variation in the plastid genomes of diatoms. Genome Biology and Evolution 6: 644-654. link

Jovanovska, E., Buczkó, K., Nakov, T., and Z. Levkov. 2014. Diploneis transylvanica (Bacillariophyceae), a new diatom species from a Neogene fossil deposit in Romania. Nova Hedwigia 98: 3-4. link

Nakov, T., Theriot, E. C., and A. J. Alverson. 2014. Using phylogeny to model the evolution of cell size in marine and freshwater diatoms. Limnology and Oceanography, 59: 79-86. link

Jovanovska, E., Buczko, K., Ognjanova-Rumenova, N.G., Nakov, T & Levkov, Z. 2013. Identity and typification of Diploneis ostracodarum, Diploneis budayana and Diploneis praeclara (Bacillariophyta). Phytotaxa 137, 15–26. link

Ashworth, M.P., Nakov, T & Theriot, E.C. 2013. Revisiting Ross and Sims (1971): Towards a molecular phylogeny of the Biddulphiaceae and Eupodiscaceae (Bacillariophyceae). Journal of Phycology, 6: 1207-1222.link

Jovanovska, E., Nakov, T & Z. Levkov. 2013. Observations of the genus Diploneis from Lake Ohrid, Macedonia. link

Theriot, E.C., E.C. Ruck, M.P. Ashworth, Nakov, T. & R.K. Jansen. 2011. Status of the pursuit of the diatom phylogeny: Are traditional views and new molecular paradigms really that different?  In: J. Seckbach & J.P. Kociolek (eds.). The Diatom World Cellular Origins, Life in Extreme Environments.  CRC Press. pp 119-142.

Theriot, E.C., E.C. Ruck, M.P. Ashworth, Nakov, T. & R.K. Jansen. 2010. The diatom phylogeny: status and prospects. Plant Evolution and Ecology, 278–296. pdf

Pavlov, A., Nakov, T., Levkov, Z., Furey, P., Lowe, R. & Ector, L. 2009. Luticola grupcei *(Bacillaryophyceae) – a new freshwater diatom from Mointain Baba (Macedonia) and Great Smoky Mountains National Park (U.S.A): comparison with the type material of *L. goeppertiana (Bleisch) D.G.Mann. Nova Hedwigia, 89: 147-164.

Levkov, Z., Saul, B., Krstic, S., Nakov, T. & Ector, L. (2008) Ecoloy of benthic diatoms from Lake Prespa, Macedonia. Archiv für Hydrobiologie Supplement/Algological Studies, 124: 71-83.

Levkov, Z., Edlund M.B. & Nakov, T. (2008). “The identity, distribution and lectotypification of Navicula hasta (Bacillariophyceae). Phycological Research, 56: 47-57.

Levkov, Z., Krstic, S., Metzeltin, D. & Nakov, T. (2007). Diatoms of Lakes Prespa and Ohrid (Macedonia). Iconographia Diatomologica 16: 603 pp.

Levkov, Z., Krstic, S. & Nakov, T. (2006). A new Gyrosigma species from Lakes Prespa and Ohrid, Republic of Macedonia. In: Ognjanova-Rumenova N. & Manoylov K. (eds). *Fossil and Recent Phycological Studies. *Pensoft, Sofia.139-145.

Levkov Z., Nakov, T. & Metzeltin, D. (2006). New species and combination from genus Sellaphora *Mereschkowsky (Bacillariophyceae) from Macedonia. *Diatom Research, 21: 297-312.

Edlund, M.B.,Brant, L.A.,Levkov, Z. & Nakov, T. (2006). An emended description of Decussata (Patrick) Lange-Bertalot & Metzeltin that includes protoplast organization. Diatom Research, 21: 297-310.

Levkov, Z., Krstic, S., Nakov, T. & Melovski, Lj. (2005). Diatom assemblages on Shara and Nidze Mountains, Macedonia. Nova Hedwigia, 81 (3-4): 501-538.