Machado, M.J., Jacinavicius, F.R., Médice, R.V., Dextro, R.B., Feitosa, A.M.T., Weiss, M.B., Pellegrinetti, T.A., Cotta, S.R., Crnkovic, C.M., Fiore, M.F. Genetic and biochemical diversity of terpene biosynthesis in cyanobacterial strains from tropical soda lakes. Frontiers in Microbiology (2025) 16:1582103

Almeida, E.C., Jacinavicius, F.R.,Médice, R.V., Menezes, R.B., Passos, L.S., Anderson, D., Yoon, J., Faria, E.D., Crnkovic, C.M., Fonseca, A.L., Henry, T., Pinto, E. Unraveling the Toxicity of a Non-Microcystin-Producing Strain (CCIBt3106) of Microcystis aeruginosa: Ecotoxicological Effects on Aquatic Invertebrates. Toxins (2025) 17(7):321

Weiss, M.B., Borges, R.M., Sullivan, P., Domingues, J.P.B., Silva, F.H.S., Trindade, V.G.S., Luo, S., Orjala, J., Crnkovic, C.M. Chemical diversity of cyanobacterial natural products. Natural Product Reports (2025) 42(1):6-49

Suzuki, J.Y., Herkenhoff, M.E., Yoon, J., Jesus, L.S., Amaral, S.C., Sartori, A.G.O.; Crnkovic, C.M., Fabi, JP, Saad, S.M.I. Gene expression analysis and metabolomics of red pitaya fermented with probiotic strains: implications for vitamin D receptor and inflammatory pathways. Food Bioscience (2025), 68:106364

Almeida, E.C., Jacinavicius, F.R., Passos, L.S., Médice, R.V., Marques, L.G., Crnkovic, C.M., Marinho, M.M., Gomes, L.C., Pinto, E. Phytoplankton composition and metabolomic profiles in aquaculture systems: A case study in Brazil's natural lakes. Aquaculture (2025), 742135.

Médice, R.V., Arruda, R.N., Yoon, J., Borges, R.M., Noyma, N.P., Lürling, M., Crnkovic, C.M., Marinho, M.M., Pinto, E. Unlocking Biological Activity and Metabolomics Insights: Primary Screening of Cyanobacterial Biomass from a Tropical Reservoir. Environmental Toxicology and Chemistry (2024) 43(10):2222-2231

Campos, T.G.V., Gama, W.A., Geraldes, V., Yoon, J., Crnkovic, C.M., Pinto, E., Jacinavicius, F.R. New records on toxic cyanobacteria from Brazil: Exploring their occurrence and geography. Science of The Total Environment (2024) 931:172689

Michaliski, L.F., Ióca, L.P., Oliveira, L.S., Crnkovic, C.M., Takaki, M., Freire, V., Berlinck, R.G.S. Improvement of Targeted Fungi Secondary Metabolite Production Using a Systematic Experimental Design and Chemometrics Analysis. Methods and Protocols (2023) 6(5):77.

Oliveira, L.S., Crnkovic, C.M., Amorim, M.R., Navarro-Vázquez, A., Paz, T.A., Freire, V., Takaki, M., Venâncio, T., Ferreira, A.G., Saito, R.F., Chammas, R., Berlinck, R.G.S. Phomactinine, the First Nitrogen-Bearing Phomactin, Produced by Biatriospora sp. CBMAI 1333. Journal of Natural Products (2023), 86(8):2065–2072.

Jacinavicius, F.R., Geraldes, V., Fernandes, K., Crnkovic, C.M., Gama, W.A., Pinto, E. Toxicological effects of cyanobacterial metabolites on zebrafish larval development. Harmful Algae (2023) 125:102430

Borges, R. M., das Neves Costa, F., Chagas, F. O., Teixeira, A. M., Yoon, J., Weiss, M. B., Crnkovic, C. M., Pilon, A. C., Garrido, B. C., Betancur, L. A., Forero, A. M., Castellanos, L., Ramos, F. A., Pupo, M. T., Kuhn, S. Data Fusion‐based Discovery (DAFdiscovery) pipeline to aid compound annotation and bioactive compound discovery across diverse spectral data. Phytochemical Analysis (2023) 34(1):48-55

Berlinck, R.G.S., Crnkovic, C.M., Gubiani, J.R., Bernardi, D.I., Ióca, L.P., Quintana-Bulla, J.I. The isolation of water-soluble natural products – challenges, strategies and perspectives. Natural Product Reports (2022) 39:596-669

Tonon, L.A.C, Rua, C., Crnkovic, C.M., Bernardi, D.I., Pires Junior, O.R., Haddad, C.F.B., Pedrosa, C.S.G., Souza, L.R.Q., Rehen, S.K., Azevedo, G.P.R., Thompson, C.C. Thompson, F.L., Berlinck, R.G.S. Microbiome associated with the tetrodotoxin-bearing anuran Brachycephalus pitanga. Toxicon (2021) 203:139-146

Ióca, L.P., Dai, Y., Kunakom, S., Santos Júnior, P.L.T, Diaz-Espinosa, J., Krunic, A., Crnkovic, C.M., Orjala, J., Sanchez, L.M., Ferreira, A. G., Berlinck, R.G.S., Eustáquio, A.S. A novel family of nonribosomal peptides modulate collective behavior in Pseudovibrio bacteria isolated from marine sponges. Angewandte Chemie (2021) 60(29):15891-15898

Costa, J.H., Bazioli, J.M., Barbosa, L.D., Santos Júnior, P.L.T, Reis F.C.G., Klimeck, T., Crnkovic, C.M., Berlinck, R.G.S., Sussulini, A., Rodrigues, M.L., Fill, T.P. Phytotoxic tryptoquialanines produced in vivo by Penicillium digitatum are exported in extracellular vesicles. MBio (2021) 2(1): e03393-20 

Jacinavicius, F.R., Geraldes, V., Crnkovic, C.M., Delbaje, E., Fiori, M., Pinto, E. Effect of ultraviolet radiation on the metabolomic profiles of potentially toxic cyanobacteria. FEMS Microbiology Ecology (2021) 1:fiaa243

May, D.S., Crnkovic, C.M., Krunic, A., Wilson, T.A., Fuchs, J.R., Orjala, J. 15N stable isotope labeling and comparative metabolomics facilitates genome mining in cultured cyanobacteria. ACS Chemical Biology (2020) 15(3):758-765

Crnkovic, C.M., Braesel, J., Krunic, A., Eustáquio, A.S., Orjala, J. Scytodecamide from the Cultured Scytonema sp. UIC 10036 Expands the Chemical and Genetic Diversity of Cyanobactins. ChemBioChem (2020). 21(6):845-852

Prior to Jan, 2020

Guo, Y.*, Crnkovic, C.M.*, Won, K.J., Yang, X., Lee, J.R., Orjala, J., Lee, H., Jeong, H. Commensal gut bacteria convert the immunosuppressant tacrolimus to less potent metabolites. Drug Metabolism and Disposition (2019) 47(3):194-202

Crnkovic, C.M., Krunic, A., May, D.S., Wilson, T.A. Kao, D., Burdette, J.E., Fuchs, J.R., Oberlies, N.H., Orjala, J. Calothrixamides A and B from the cultured cyanobacterium Calothrix sp. UIC 10520. Journal of Natural Products (2018) 81(9):2083-2090

Braesel, J., Crnkovic, C.M., Kunstman, K., Green, S., Maienschein-Cline, M., Orjala, J., Murphy, B.T., Eustaquio, A.S. Complete genome of Micromonospora sp. strain B006 reveals biosynthetic potential of a Lake Michigan actinomycete. Journal of Natural Products (2018) 81(9):2057-2068

Crnkovic, C.M., May, D.S. & Orjala, J. The impact of culture conditions on growth and metabolomic profiles of freshwater cyanobacteria. Journal of Applied Phycology (2018) 30(1):375-384

Crnkovic, C.M, Silva, F.H.S., Amorim, H.M.M. Prospecção de metabólitos secundários bioativos. In: Fiamoncini, J., Demarque, D.P., Crnkovic, C.M. (eds) Fitoquímicos em alimentos, fármacos e medicamentos. Manole, Santana de Parnaíba [SP] (2023), pp 238-261.

Fiamoncini, J., Demarque, D.P., Crnkovic, C.M. Fitoquímicos em alimentos, fármacos e medicamentos. Manole, Santana de Parnaíba [SP] (2023), 326 pp.

Weiss, M.N., Médice, R.V., Jacinavicius, F.R., Pinto, E., Crnkovic, C.M. Metabolomics applied to cyanobacterial toxins and natural products. In: Pacheco Fill, T. (ed) Microbial Natural Products Chemistry. Advances in Experimental Medicine and Biology. Springer, Cham (2023), vol 1439, pp 21–49.

Souza, K.S., Silva, M.R.F., Araújo, L.C.A, Silva, K.C.C., Silva, F.H.S., Crnkovic, C.M., Motteran, F.,Oliveira, M.B.M. Impacts of the Pesticides on Urban Aquatic Ecosystems and Their Regulation Measures. In: Singh, R., Singh, P., Tripathi, S., Chandra, K.K., Bhadouria, R. (eds) Xenobiotics in Urban Ecosystems. Springer, Cham (2023), pp 391–398.

Silva, M.R.F., Souza, K.S., Silva, F.H.S., Crnkovic, C.M., Motteran, F., Araújo, L.C.A, Oliveira, M.B.M. Bioremediation Strategies for Microplastic Removal in Impacted Aquatic Environments. In: Singh, R., Singh, P., Tripathi, S., Chandra, K.K., Bhadouria, R. (eds) Xenobiotics in Urban Ecosystems. Springer, Cham (2023), pp 341–351.

Crnkovic, C.M., Caricati, C.P., Oliveira, R.P.S., Stephano, M.A. Biosafety applied in pharmaceutical and biotechnological processes. In: Pharmaceutical Biotechnology; Pessoa Jr, A., Vitolo, M., Long, P.F., Eds.; CRC Press/Taylor & Francis Group: Boca Raton, 2021; pp 313-324

Protocols, Databases & Software

Yoon, J., Amorim, H.M.M., Andrade, L.S., Bueno, M,G.S., Crnkovic, C.M. Screening natural products against Artemia salina. Protocols.io (2025) dx.doi.org/10.17504/protocols.io.yxmvm9q35l3p/v1

Jesus, L.S., Weiss, M.B., Yoon, J., do Amaral, S.C., Crnkovic, C.M. Prefractionating Cyanobacterial Extracts by Solid-Phase. Protocols.io (2025) dx.doi.org/10.17504/protocols.io.3byl4wdkrvo5/v1

Domingues, J. P. B., Mizuyama, L. A., Ióca, L. P., Eustaquio, A. S., Crnkovic, C. M. BGCpri. GitHub (2025) github.com/LabAzul/BGCpri

Weiss, M.B., Borges, R.M., Domingues, J.P.B., Silva, F.H.S., Crnkovic, C.M. Chemical Diversity of Cyanobacterial Natural Products (2010-2023). Zenodo (2024) https://doi.org/10.5281/zenodo.12627503