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Showing entries 1 - 20 out of 161
2024
Sekurova ON, Zehl M, Predl M, Hunyadi P, Rattei T, Zotchev SB. Deletions of conserved extracytoplasmic function sigma factors-encoding genes in Streptomyces have a major impact on secondary metabolism. Microbial Cell Factories. 2024 Jul 18;23(1):201. doi: 10.1186/s12934-024-02479-x
Sudo M, Osvatic J, Taylor JD, Dufour SC, Prathep A, Wilkins LGE et al. SoxY gene family expansion underpins adaptation to diverse hosts and environments in symbiotic sulfide oxidizers. mSystems. 2024 Jun;9(6):e01135-23. Epub 2024 May 15. doi: 10.1128/msystems.01135-23
Predl M, Mießkes M, Rattei T, Zanghellini J. PyCoMo: a python package for community metabolic model creation and analysis. Bioinformatics (Oxford, England). 2024 Apr 1;40(4):btae153. doi: 10.1093/bioinformatics/btae153
2023
Yurtseven A, Buyanova S, Agrawal AA, Bochkareva O, Kalinina O. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 2023 Dec 20;23(1):404. Epub 2023 Sep. doi: 10.1186/s12866-023-03147-7
Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology. 2023 Nov;41(11):1633-1644. Epub 2023 Feb 23. doi: 10.1038/s41587-023-01688-w
Vostokova E, Dranenko N, Gelfand MS, Bochkareva O. Genome rearrangements drive evolution of ANK genes in Wolbachia. bioRxiv : the preprint server for biology. 2023 Oct 27. doi: 10.1101/2023.10.25.563763
Esser SP, Rahlff J, Zhao W, Predl M, Plewka J, Sures K et al. A predicted CRISPR-mediated symbiosis between uncultivated archaea. Nature Microbiology. 2023 Sep 1;8(9):1619-1633. Epub 2023 Sep. doi: 10.1038/s41564-023-01439-2
Collingro A, Köstlbacher S, Siegl A, Toenshoff ER, Schulz F, Mitchell SO et al. The Fish Pathogen "Candidatus Clavichlamydia salmonicola"-A Missing Link in the Evolution of Chlamydial Pathogens of Humans. Genome Biology and Evolution. 2023 Aug 24;15(8):evad147. doi: 10.1093/gbe/evad147
Herrera P, Schuster L, Zojer M, Na H, Schwarz J, Wascher F et al. Genome Dynamics and Temperature Adaptation During Experimental Evolution of Obligate Intracellular Bacteria. Genome Biology and Evolution. 2023 Jul 29;15(8):evad139. doi: 10.1093/gbe/evad139
Olmo R, Wetzels SU, Berg G, Cocolin L, Hartmann M, Hugas M et al. Food systems microbiome-related educational needs. Microbial Biotechnology. 2023 Jul;16(7):1412-1422. doi: 10.1111/1751-7915.14263
Graffius S, Garzón JFG, Zehl M, Pjevac P, Kirkegaard R, Flieder M et al. Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris. Microbiology Spectrum. 2023 Apr 13;11(2):e04353-22. Epub 2023 Feb 2. doi: 10.1128/spectrum.04353-22, 10.1128/spectrum.04353-22
Tveit AT, Söllinger A, Rainer EM, Didriksen A, Hestnes AG, Motleleng L et al. Thermal acclimation of methanotrophs from the genus Methylobacter. The ISME Journal. 2023 Apr 1;17(4):502-513. Epub 2023 Jan 18. doi: 10.1038/s41396-023-01363-7
Viljakainen L, Fürst MA, Grasse AV, Jurvansuu J, Oh J, Tolonen L et al. Antiviral immune response reveals host-specific virus infections in natural ant populations. Frontiers in Microbiology. 2023 Mar 16;14:1119002. doi: 10.3389/fmicb.2023.1119002
Lüftinger L, Májek P, Rattei T, Beisken S. Metagenomic Antimicrobial Susceptibility Testing from Simulated Native Patient Samples. Antibiotics. 2023 Feb 9;12(2):366. doi: 10.3390/antibiotics12020366
Halter T, Köstlbacher S, Rattei T, Hendrickx F, Manzano-Marín A, Horn M. One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus. Microbial genomics. 2023 Feb 9;9(2):000943. doi: 10.1101/2022.05.31.494226, 10.1099/mgen.0.000943
Doncheva NT, Morris JH, Holze H, Kirsch R, Nastou KC, Cuesta-Astroz Y et al. Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks. Journal of Proteome Research. 2023 Feb 3;22(2):637-646. doi: 10.1021/acs.jproteome.2c00651
Valles-Colomer M, Blanco-Míguez A, Manghi P, Asnicar F, Dubois L, Golzato D et al. The person-to-person transmission landscape of the gut and oral microbiomes. Nature. 2023 Feb 2;614(7946):125-135. doi: 10.1038/s41586-022-05620-1
Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta M-C, Bäckhed F, Bork P et al. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature. 2023 Jan 26;613(7945):639-649. doi: 10.1038/s41586-022-05546-8
Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR et al. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research. 2023 Jan 6;51(D1):D389-D394. doi: 10.1093/nar/gkac1022
2022
Tocino Márquez I, Zehl M, Pjevac P, Kirkegaard R, Flieder M, Loy A et al. Developing co-cultures of bacterial isolates from the bryozoan Cristatella mucedo for the discovery of novel secondary metabolites. Planta Medica. 2022 Dec;88(15):1438-1438.