Tautz, D., Neme, R. & Domazet-Lošo, T. (2013) Evolutionary Origin of Orphan Genes. U: Hildegard Kehrer-Sawatzki (ur.) eLS. Chichester, John Wiley & Sons, str. 1-8.

Tautz, D., Neme, R. & Domazet-Lošo, T. (2013) Evolutionary origin of orphan genes. U: Maccarrone, M. & (ur.) eLS. Chichester, John Wiley & Sons, str. 1-10.

Čorak, N., Anniko, S., Daschkin-Steinborn, C., Krey, V., Koska, S., Futo, M., Široki, T., Woichansky, I., Opašić, L., Kifer, D., Tušar, A., Maxeiner, H., Domazet-Lošo, M., Nicolaus, C. & Domazet-Lošo, T. (2023) Pleomorphic Variants of Borreliella (syn. Borrelia) burgdorferi Express Evolutionary Distinct Transcriptomes. International journal of molecular sciences, 24 (6), 5594, 23 doi:10.3390/ijms24065594.

Futo, M., Široki, T., Koska, S., Čorak, N., Tušar, A., Domazet-Lošo, M. & Tomislav Domazet-Lošo (2022) A novel time-lapse imaging method for studying developing bacterial biofilms. Scientific Reports, 12, 21120, 13 doi:10.1038/s41598-022-24431-y.

Domazet-Lošo, T. (2022) mRNA Vaccines: Why Is the Biology of Retroposition Ignored?. Genes, 13 (5), 719, 24 doi:10.3390/genes13050719.

Futo, M., Opašić, L., Koska, S., Čorak, N., Široki, T., Ravikumar, V., Thorsell, A., Lenuzzi, M., Kifer, D., Domazet-Lošo, M., Vlahoviček, K., Mijakovic, I. & Domazet-Lošo, T. (2021) Embryo-like features in developing Bacillus subtilis biofilms. Molecular biology and evolution, 38 (1), 31-47 doi:10.1093/molbev/msaa217.

Ravikumar, V., Nalpas, N., Anselm, V., Krug, K., Lenuzzi, M., Šestak, M., Domazet-Lošo, T., Mijakovic, I. & Macek, B. (2018) In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins. Scientific Reports, 8 (1), 17246, 11 doi:10.1038/s41598-018-35589-9.

Stancik, I., Sestak, M., Ji, B., Axelson-Fisk, M., Franjevic, D., Jers, C., Domazet- Lošo, T. & Mijakovic, I. (2018) Serine/Threonine protein kinases from bacteria, archaea and eukarya share a common evolutionary origin deeply rooted in the tree of life. Journal of molecular biology, 430 (1), 27-32 doi:10.1016/j.jmb.2017.11.004.

Pozhitkov, A., Neme, R., Domazet-Lošo, T., Leroux, B., Soni, S., Tautz, D. & Noble, P. (2017) Tracing the dynamics of gene transcripts after organismal death. Open Biology, 7 (1), 160267, 25 doi:10.1098/rsob.160267.

Domazet-Lošo, T., Carvunis, A., Mar Albà, M., Sebastijan Šestak, M., Bakarić, R., Neme, R. & Tautz, D. (2017) No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution. Molecular biology and evolution, 34 (4), 843-856 doi:10.1093/molbev/msw284.

Bosch, T., Klimovich, A., Domazet-Lošo, T., Gründer, S., Holstein, T., Jékely, G., Miller, D., Murillo-Rincon, A., Rentzsch, F., Richards, G., Schröder, K., Technau, U. & Yuste, R. (2017) Back to the Basics: Cnidarians Start to Fire. Trends in Neurosciences, 40 (2), 92-105 doi:10.1016/j.tins.2016.11.005.

Domazet-Lošo, M. & Domazet-Lošo, T. (2016) gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances. PLoS One, 11 (11), e0166602-1 doi:10.1371/journal.pone.0166602.

Xu, F., Domazet-Lošo, T., Fan, D., Dunwell, T., Li, L., Fang, X., Zhang, G. & (2016) High expression of new genes in trochophore enlightening the ontogeny and evolution of trochozoans. Scientific Reports, 6, 34664-1 doi:10.1038/srep34664.

Šestak, M. & Domazet-Lošo, T. (2015) Phylostratigraphic Profiles in Zebrafish Uncover Chordate Origins of the Vertebrate Brain. Molecular biology and evolution, 32 (2), 299-312 doi:10.1093/molbev/msu319.

Fuchs, B., Wang, W., Graspeuntner, S., Li, Y., Insua, S., Herbst, E., Dirksen, P., Böhm, A., Hemmrich, G., Sommer, F., Domazet-Lošo, T., C. Klostermeier, U., Anton- Erxleben, F., Rosenstiel, P., C.G. Bosch, T. & Khalturin, K. (2014) Regulation of Polyp-to-Jellyfish Transition in Aurelia aurita. Current biology, 24 (3), 263-273 doi:10.1016/j.cub.2013.12.003.

C. G. Bosch, T., Adamska, M., Augustin, R., Domazet- Lošo, T., Foret, S., Fraune, S., Funayama, N., Grasis, J., Hamada, M., Hatta, M., Hobmayer, B., Kawai, K., Klimovich, A., Manuel, M., Shinzato, C., Technau, Uli, Yum, Seungshic & J. Miller, D. (2014) How do environmental factors influence life cycles and development? An experimental framework for early-diverging metazoans. Bioessays, 36 (12), 1185-1194 doi:10.1002/bies.201400065.

Domazet-Lošo, T., Klimovich, A., Anokhin, B., Anton-Erxleben, F., Hamm, M., Lange, C. & Bosch, T. (2014) Naturally occurring tumours in the basal metazoan Hydra. Nature Communications, 5, 4222-4230 doi:10.1038/ncomms5222.

Šestak, M., Božičević, V., Bakarić, R., Dunjko, V. & Domazet-Lošo, T. (2013) Phylostratigraphic profiles reveal a deep evolutionary history of the vertebrate head sensory systems. Frontiers in Zoology, 10, 18-18 doi:10.1186/1742-9994-10-18.

de Mendoza, A., Sebé-Pedrós, A., Šestak, M., Matejčić, M., Torruella, G., Domazet-Lošo, T. & Ruiz-Trillo, I. (2013) Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proceedings of the National Academy of Sciences of the United States of America, 110 (50), E4858-E4566 doi:10.1073/pnas.1311818110.

McFall-Ngai, M., Hadfield, M., Bosch, T., Carey, H., Domazet-Lošo, T., ... & Wernegreen, J. (2013) Animals in a bacterial world, a new imperative for the life sciences. Proceedings of the National Academy of Sciences of the United States of America, 110 (9), 3229-3236 doi:10.1073/pnas.1218525110.

Zhang G., Fang X., Guo X., Li, L., Luo, R., Xu, F., Yang, P., Zhang, L., Wang, X., Qi, H., Xiong, Z., Que, H., Xie, Y., Holland, P., Paps, J., Zhu, Y., Wu, F., Chen, Y., Wang, J., Peng, C., Meng, J., Yang, L., Liu, J., Wen, B., Zhang, N., Huang, Z., Zhu, Q., Feng, Y., Mount, A., Hedgecock, D., Xu, Z., Liu, Y., Domazet-Lošo, T., Du, Y. & et. al. (2012) The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 490 (7418), 49-54 doi:10.1038/nature11413.

Hemmrich, G., Khalturin, K., Boehm, A., Puchert, M., Anton-Erxleben, F., Wittlieb, J., Klostermeier, U., Rosenstiel, P., Oberg H.H., Domazet-Lošo, T., Sugimoto, T., Niwa, H. & Bosch, T. (2012) Molecular signatures of the three stem cell lineages in hydra and the emergence of stem cell function at the base of multicellularity. Molecular biology and evolution, 29 (11), 3267-3280 doi:10.1093/molbev/mss134.

Franzenburg, S., Fraune, S., Künzel, S., Baines, J., Domazet-Lošo, T. & Bosch, T. (2012) MyD88-deficient Hydra reveal an ancient function of TLR signaling in sensingbacterial colonizers.. Proceedings of the National Academy of Sciences of the United States of America, 109 (47), 19374-19379 doi:10.1073/pnas.1213110109.

Diethard, T. & Domazet-Lošo, T. (2011) The evolutionary origin of orphan genes. Nature reviews genetics, 12 (10), 692-702 doi:10.1038/nrg3053.

Domazet-Lošo, T. & Tautz, D. (2010) A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature, 468 (7325), 815-818 doi:10.1038/nature09632.

Domazet-Lošo, T. & Tautz Diethard (2010) Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa. Bmc biology, 8, 66-66 doi:10.1186/1741-7007-8-66.

Domazet-Lošo, T. & Tautz, D. (2008) An Ancient Evolutionary Origin of Genes Associated with Human Genetic Diseases. Molecular biology and evolution, 25 (12), 2699-2707 doi:10.1093/molbev/msn214.

Domazet-Lošo, T., Brajković, J. & Tautz, D. (2007) A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends in Genetics, 23 (11), 533-539.

Pozhitkov, A., Noble, P., Domazet-Lošo, T., Nolte, A., Staehler, P., Beier, M. & Tautz, D. (2006) Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Research, 34 (9).

Marais, G., Domazet-Lošo, T., Tautz, D. & Charlesworth, B. (2004) Correlated evolution of synonymous and nonsynonymous sites in Drosophila. Journal of molecular evolution, 59, 771-779.

Domazet-Lošo, T. & Diethard, T. (2003) An Evolutionary Analysis of Orphan Genes in Drosophila. Genome Research, 13, 2213-2219.

Široki, T., Koska, S., Čorak, N., Futo, M., Domazet-Lošo, T. & Domazet-Lošo, M. (2019) Correspondence analysis applied to large scale Evo-Devo data. U: Skala, K. (ur.)42th International Convention on Information, Communication and Electronic Technology (MIPRO) - proceedings.

Domazet-Lošo, T. (2003) 'Evolution of orphan genes in Drosophila', doktorska disertacija, Mathematisch-Naturwissenschaftliche Fakultät, Köln.