Publications | Microbial Single Cell Genomics

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Porcel Sanchis, D.; Pola, M.; Engelberts, J. P.; Guerra Font, O.; Messer, L.; Alberola Mora, I.; Escobar Sáez, L.; Pérez Gómez, N.; Portolés Campo, Á.; Valero Tebar, J.; Naya Garmendia, L. M.; Preciado Barahona, J. C.; Gil García, R.; Arnau, V.; McIlroy, S. J.; Džunková, M. (2026). Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs. Microbiome, 14(1), 184. DOI: 10.1186/s40168-026-02456-z

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Hug, L. A.; Hatzenpichler, R.; Moraru, C.; Soares, A.; Meyer, F.; Heyder, A.; The Data Reuse Consortium (including M. Džunková); Probst, A. (2025). A roadmap for equitable reuse of public microbiome data. Nature Microbiology, 10(10), 2384–2395. DOI: 10.1038/s41564-025-02116-2

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Arnau, V.; Ortiz Maiques, A.; Valero Tebar, J.; Mora Quilis, L.; Kurmauskaite, V.; Campos Dopazo, L.; Domingo-Calap, P.; Džunková, M. (2025). CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics. ISME Communications, 5(1), ycaf134. DOI: 10.1093/ismeco/ycaf134

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Alberola Mora, I.; Guerra Font, O.; Espinosa Calderón, O. D.; Galià Camps, C.; Džunková, M. (2025). Combination of Sample Preservation Approaches and DNA Extraction Methods for Long-Read Sequencing of Nudibranchs' Genomes. Ecology and Evolution, 15(4), e71262. DOI: 10.1002/ece3.71262

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Lejri, R.; Mekki, A.; Ellafi, A.; Henchiri, S.; Giner Tarazón, J.; Valero Tebar, J.; D’Auria, G.; Chamkha, M.; Chaieb, M.; Džunková, M.; Ben Younes, S. (2024). Genomic features of metal-resistant bacteria suitable for tannery effluent bioremediation. Journal of Water Process Engineering, 68, 106406. DOI: 10.1016/j.jwpe.2024.106406

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Lejri, R.; Ellafi, A.; Valero Tebar, J.; Chaieb, M.; Mekki, A.; Džunková, M.; Ben Younes, S. (2024). Phenotypic characterization for bioremediation suitability of isolates from Southern Tunisian tannery effluent. Microbiological Research, 285, 127771. DOI: 10.1016/j.micres.2024.127771

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Feješ, A.; Belvončíková, P.; Porcel Sanchis, D.; Borbélyová, V.; Celec, P.; Džunková, M.; Gardlík, R. (2024). The Effect of Cross-Sex Fecal Microbiota Transplantation on Metabolism and Hormonal Status in Adult Rats. International Journal of Molecular Sciences, 25(1), 601. DOI: 10.3390/ijms25010601

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Džunková, M.; Moraru, C.; Anantharaman, K. (2023). Advances in viromics: new tools, challenges, and data towards characterizing human and environmental viromes. Frontiers in Microbiology, 14, 1290062. DOI: 10.3389/fmicb.2023.1290062

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Arnau, V.; Díaz-Villanueva, W.; Mifsut Benet, J.; Villasante, P.; Beamud, B.; Mompó, P.; Sanjuan, R.; González-Candelas, F.; Domingo-Calap, P.; Džunková, M. (2023). Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts. Viruses, 15(5), 1196. DOI: 10.3390/v15051196

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Džunková, M.; La Clair, J. J.; Tyml, T.; Doud, D.; Schulz, F.; Piquer-Esteban, S.; Porcel Sanchis, D.; Osborn, A.; Robinson, D.; Louie, K. B.; Bowen, B. P.; Bowers, R. M.; Lee, J.; Arnau, V.; Díaz-Villanueva, W.; Stepanauskas, R.; Gosliner, T.; Date, S. V.; Northen, T. R.; Cheng, J.-F.; Burkart, M. D.; Woyke, T. (2023). Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium. Microbiome, 11, 130. DOI: 10.1186/s40168-023-01560-8

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Ortiz Maiques, A.; Džunková, M. (2025). Characterization of Microbial Diversity and Mobile Genetics Elements Through Single-Cell Genomics. In Single-Cell Omics in Microbiome Research, pp. 23–41. Springer. DOI: 10.1007/978-3-032-07527-7_3

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Džunková, M. (2022). Single-cell Genomics for Uncovering Relationships between Bacteriophages and their Hosts. In Genetic Diversity – Recent Advances and Applications. IntechOpen. DOI:10.5772/intechopen.108118

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Rinke, C.; Džunková, M. (Eds.). (2025). Single-Cell Omics in Microbiome Research. Springer. DOI: 10.1007/978-3-032-07527-7

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