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Predl, M., Mießkes, M., Rattei, T., & Zanghellini, J. (2024). PyCoMo: a python package for community metabolic model creation and analysis. Bioinformatics (Oxford, England), 40(4), [btae153]. https://doi.org/10.1093/bioinformatics/btae153

Esser, S. P., Rahlff, J., Zhao, W., Predl, M., Plewka, J., Sures, K., Wimmer, F., Lee, J., Adam, P. S., McGonigle, J., Turzynski, V., Banas, I., Schwank, K., Krupovic, M., Bornemann, T. L. V., Figueroa-Gonzalez, P. A., Jarett, J., Rattei, T., Amano, Y., ... Probst, A. J. (2023). A predicted CRISPR-mediated symbiosis between uncultivated archaea. Nature Microbiology, 8(9), 1619-1633. https://doi.org/10.1038/s41564-023-01439-2

Collingro, A., Köstlbacher, S., Siegl, A., Toenshoff, E. R., Schulz, F., Mitchell, S. O., Weinmaier, T., Rattei, T., Colquhoun, D. J., & Horn, M. (2023). The Fish Pathogen "Candidatus Clavichlamydia salmonicola"-A Missing Link in the Evolution of Chlamydial Pathogens of Humans. Genome Biology and Evolution, 15(8), [evad147]. https://doi.org/10.1093/gbe/evad147

Herrera, P., Schuster, L., Zojer, M., Na, H., Schwarz, J., Wascher, F., Kempinger, T., Regner, A., Rattei, T., & Horn, M. (2023). Genome Dynamics and Temperature Adaptation During Experimental Evolution of Obligate Intracellular Bacteria. Genome Biology and Evolution, 15(8), [evad139]. https://doi.org/10.1093/gbe/evad139

Olmo, R., Wetzels, S. U., Berg, G., Cocolin, L., Hartmann, M., Hugas, M., Kostic, T., Rattei, T., Ruthsatz, M., Rybakova, D., Sessitsch, A., Shortt, C., Timmis, K., Selberherr, E., & Wagner, M. (2023). Food systems microbiome-related educational needs. Microbial Biotechnology, 16(7), 1412-1422. https://doi.org/10.1111/1751-7915.14263

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), [e04353-22]. https://doi.org/10.1128/spectrum.04353-22, 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

Viljakainen, L., Fürst, M. A., Grasse, A. V., Jurvansuu, J., Oh, J., Tolonen, L., Eder, T., Rattei, T., & Cremer, S. (2023). Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology, 14, [1119002]. https://doi.org/10.3389/fmicb.2023.1119002

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

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

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

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