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Graffius, S., Garzón, J. F. G., Zehl, M., Pjevac, P., Kirkegaard, R., Flieder, M., Loy, A., Rattei, T., Ostrovsky, A., & Zotchev, S. B. (2023). Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris. Microbiology Spectrum, 11(2), e0435322. https://doi.org/10.1128/spectrum.04353-22

Tveit, A. T., Söllinger, A., Rainer, E. M., Didriksen, A., Hestnes, A. G., Motleleng, L., Hellinger, H-J., Rattei, T., & Svenning, M. M. (2023). Thermal acclimation of methanotrophs from the genus Methylobacter. The ISME Journal, 17(4), 502-513. https://doi.org/10.1038/s41396-023-01363-7

Lüftinger, L., Májek, P., Rattei, T., & Beisken, S. (2023). Metagenomic Antimicrobial Susceptibility Testing from Simulated Native Patient Samples. Antibiotics, 12(2), [366]. https://doi.org/10.3390/antibiotics12020366

Halter, T., Köstlbacher, S., Rattei, T., Hendrickx, F., Manzano-Marín, A., & Horn, M. (2023). One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus. Microbial genomics, 9(2), [000943]. https://doi.org/10.1101/2022.05.31.494226, https://doi.org/10.1099/mgen.0.000943

Doncheva, N. T., Morris, J. H., Holze, H., Kirsch, R., Nastou, K. C., Cuesta-Astroz, Y., Rattei, T., Szklarczyk, D., von Mering, C., & Jensen, L. J. (2023). Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks. Journal of Proteome Research, 22(2), 637-646. https://doi.org/10.1021/acs.jproteome.2c00651

Hernández-Plaza, A., Szklarczyk, D., Botas, J., Cantalapiedra, C. P., Giner-Lamia, J., Mende, D. R., Kirsch, R., Rattei, T., Letunic, I., Jensen, L. J., Bork, P., von Mering, C., & Huerta-Cepas, J. (2023). eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research, 51(D1), D389-D394. https://doi.org/10.1093/nar/gkac1022

Kennedy, K. M., de Goffau, M. C., Perez-Muñoz, M. E., Arrieta, M-C., Bäckhed, F., Bork, P., Braun, T., Bushman, F. D., Dore, J., de Vos, W. M., Earl, A. M., Eisen, J. A., Elovitz, M. A., Ganal-Vonarburg, S. C., Gänzle, M. G., Garrett, W. S., Hall, L. J., Hornef, M. W., Huttenhower, C., ... Walter, J. (2023). Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature, 613(7945), 639-649. https://doi.org/10.1038/s41586-022-05546-8

Tocino Márquez, I., Zehl, M., Pjevac, P., Kirkegaard, R., Flieder, M., Loy, A., Rattei, T., & Zotchev, S. (2022). Developing co-cultures of bacterial isolates from the bryozoan Cristatella mucedo for the discovery of novel secondary metabolites. Planta Medica, 88(15), 1438-1438.

Sekurova, O. N., Zehl, M., Predl, M., Hunyadi, P., Rattei, T., & Zotchev, S. B. (2022). Targeted Metabolomics and High-Throughput RNA Sequencing-Based Transcriptomics Reveal Massive Changes in the Streptomyces venezuelae NRRL B-65442 Metabolism Caused by Ethanol Shock. Microbiology Spectrum, 10(6), [e0367222]. https://doi.org/10.1128/spectrum.03672-22

Bernard, C., Locard-Paulet, M., Noël, C., Duchateau, M., Giai Gianetto, Q., Moumen, B., Rattei, T., Hechard, Y., Jensen, L. J., Matondo, M., & Samba-Louaka, A. (2022). A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. Nature Communications, 13(1), [4104]. https://doi.org/10.1038/s41467-022-31832-0

Maixner, F., Sarhan, M. S., Huang, K. D., Tett, A., Schoenafinger, A., Zingale, S., Blanco-Míguez, A., Manghi, P., Cemper-Kiesslich, J., Rosendahl, W., Kusebauch, U., Morrone, S. R., Hoopmann, M. R., Rota-Stabelli, O., Rattei, T., Moritz, R. L., Oeggl, K., Segata, N., Zink, A., ... Kowarik, K. (2021). Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Current Biology, 31(23), 5149-5162. https://doi.org/10.1016/j.cub.2021.09.031

Majek, P., Lueftinger, L., Beisken, S., Rattei, T., & Materna, A. (2021). Genome-Wide Mutation Scoring for Machine-Learning-Based Antimicrobial Resistance Prediction. International Journal of Molecular Sciences, 22(23), [13049]. https://doi.org/10.3390/ijms222313049

Flieder, M., Buongiorno, J., Herbold, C. W., Hausmann, B., Rattei, T., Lloyd, K. G., Loy, A., & Wasmund, K. (2021). Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling. The ISME Journal, 15(11), 3159-3180. https://doi.org/10.1038/s41396-021-00992-0

Hanson, B. T., Dimitri Kits, K., Löffler, J., Burrichter, A. G., Fiedler, A., Denger, K., Frommeyer, B., Herbold, C. W., Rattei, T., Karcher, N., Segata, N., Schleheck, D., & Loy, A. (2021). Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. The ISME Journal, 15(9), 2779-2791. https://doi.org/10.1038/s41396-021-00968-0

Lueftinger, L., Ferreira, I., Frank, B. J. H., Beisken, S., Weinberger, J., von Haeseler, A., Rattei, T., Hofstaetter, J. G., Posch, A. E., & Materna, A. (2021). Predictive Antibiotic Susceptibility Testing by Next-Generation Sequencing for Periprosthetic Joint Infections: Potential and Limitations. Biomedicines, 9(8), [910]. https://doi.org/10.3390/biomedicines9080910

Wasmund, K., Pelikan, C., Schintlmeister, A., Wagner, M., Watzka, M., Richter, A., Bhatnagar, S., Noel, A., Hubert, C. R. J., Rattei, T., Hofmann, T., Hausmann, B., Herbold, C. W., & Loy, A. (2021). Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments. Nature Microbiology, 6(7), 885-898. https://doi.org/10.1038/s41564-021-00917-9

Gerner, S. M., Graf, A. B., & Rattei, T. (2021). Tamock: simulation of habitat-specific benchmark data in metagenomics. BMC Bioinformatics, 22(1), [227]. https://doi.org/10.1186/s12859-021-04154-z

Lüftinger, L., Majek, P., Beisken, S., Rattei, T., & Posch, A. E. (2021). Learning From Limited Data: Towards Best Practice Techniques for Antimicrobial Resistance Prediction From Whole Genome Sequencing Data. Frontiers in Cellular and Infection Microbiology, 11, [610348]. https://doi.org/10.3389/fcimb.2021.610348

Walliser, B., Lucaciu, C. R., Molitor, C., Marinovic, S., Nitarska, D. A., Aktas, D., Rattei, T., Kampatsikas, I., Stich, K., Haselmair-Gosch, C., & Halbwirth, H. (2021). Dahlia variabilis cultivar 'Seattle' as a model plant for anthochlor biosynthesis. Plant Physiology and Biochemistry, 159, 193-201. https://doi.org/10.1016/j.plaphy.2020.12.016

Feldbauer, R., Gosch, L., Lüftinger, L., Hyden, P., Flexer, A., & Rattei, T. (2020). DeepNOG: Fast and accurate protein orthologous group assignment. Bioinformatics, 36(22-23), 5304-5312. https://doi.org/10.1093/bioinformatics/btaa1051