Publications

Sekurova ON, Zehl M, Predl M, Hunyadi P, Rattei T, Zotchev SB. 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. 2022 Oct 31;10(6):e0367222. doi: 10.1128/spectrum.03672-22

Bernard C, Locard-Paulet M, Noël C, Duchateau M, Giai Gianetto Q, Moumen B et al. A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. Nature Communications. 2022 Jul 14;13(1):4104. doi: 10.1038/s41467-022-31832-0

Sarhan MS, Lehmkuhl A, Straub R, Tett AJ, Wieland G, Franken M et al. Ancient DNA diffuses from human bones to cave stones. iScience. 2021 Dec 17;24(12):103397. 103397. Epub 2021 Nov 23. doi: 10.1016/j.isci.2021.103397

Maixner F, Sarhan MS, Huang KD, Tett A, Schoenafinger A, Zingale S et al. Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Current Biology. 2021 Dec 6;31(23):5149-5162. Epub 2021 Oct 13. doi: 10.1016/j.cub.2021.09.031

Majek P, Lueftinger L, Beisken S, Rattei T, Materna A. Genome-Wide Mutation Scoring for Machine-Learning-Based Antimicrobial Resistance Prediction. International Journal of Molecular Sciences. 2021 Dec 2;22(23):13049. doi: 10.3390/ijms222313049

Flieder M, Buongiorno J, Herbold CW, Hausmann B, Rattei T, Lloyd KG et al. Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling. The ISME Journal. 2021 Nov 1;15(11):3159-3180. Epub 2021 May 12. doi: 10.1038/s41396-021-00992-0

Granehall L, Huang KD, Tett A, Manghi P, Paladin A, O'Sullivan N et al. Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. Microbiome. 2021 Sept 30;9(1):197. doi: 10.1186/s40168-021-01132-8

Tett A, Pasolli E, Masetti G, Ercolini D, Segata N. Prevotella diversity, niches and interactions with the human host. Nature Reviews. Microbiology. 2021 Sept 1;19(9):585–599. Epub 2021 May 28. doi: 10.1038/s41579-021-00559-y

Hanson BT, Dimitri Kits K, Löffler J, Burrichter AG, Fiedler A, Denger K et al. Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. The ISME Journal. 2021 Sept 1;15(9):2779-2791. Epub 2021 Mar 31. doi: 10.1038/s41396-021-00968-0

Lueftinger L, Ferreira I, Frank BJH, Beisken S, Weinberger J, von Haeseler A et al. Predictive Antibiotic Susceptibility Testing by Next-Generation Sequencing for Periprosthetic Joint Infections: Potential and Limitations. Biomedicines. 2021 Jul 29;9(8):910. doi: 10.3390/biomedicines9080910

Wasmund K, Pelikan C, Schintlmeister A, Wagner M, Watzka M, Richter A et al. Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments. Nature Microbiology. 2021 Jul;6(7):885-898. Epub 2021 Jun 14. doi: 10.1038/s41564-021-00917-9

Gerner SM, Graf AB, Rattei T. Tamock: simulation of habitat-specific benchmark data in metagenomics. BMC Bioinformatics. 2021 May 1;22(1):227. Epub 2021 May 1. doi: 10.1186/s12859-021-04154-z

Goettsch W, Beerenwinkel N, Deng L, Dölken L, Dutilh BE, Erhard F et al. Itn—viroinf: Understanding (harmful) virus-host interactions by linking virology and bioinformatics. Viruses. 2021 Apr 27;13(5):1-20. 766. doi: 10.3390/v13050766

Shima K, Kaufhold I, Eder T, Käding N, Schmidt N, Ogunsulire IM et al. Regulation of the mitochondrion-fatty acid axis for the metabolic reprogramming of chlamydia trachomatis during treatment with b-lactam antimicrobials. mBio. 2021 Mar 30;12(2):1-17. e00023-21. doi: 10.1128/mBio.00023-21

Cabal A, Schmid D, Hell M, Chakeri A, Mustafa-Korninger E, Wojna A et al. Isolate-based surveillance of bordetella pertussis, austria, 2018-2020. Emerging infectious diseases. 2021 Mar;27(3):862-871. doi: 10.3201/eid2703.202314

Lüftinger L, Majek P, Beisken S, Rattei T, Posch AE. Learning From Limited Data: Towards Best Practice Techniques for Antimicrobial Resistance Prediction From Whole Genome Sequencing Data. Frontiers in Cellular and Infection Microbiology. 2021 Feb 15;11:610348. doi: 10.3389/fcimb.2021.610348

Walliser B, Lucaciu CR, Molitor C, Marinovic S, Nitarska DA, Aktas D et al. Dahlia variabilis cultivar 'Seattle' as a model plant for anthochlor biosynthesis. Plant Physiology and Biochemistry. 2021 Feb;159:193-201. Epub 2020 Dec 17. doi: 10.1016/j.plaphy.2020.12.016

Feldbauer R, Gosch L, Lüftinger L, Hyden P, Flexer A, Rattei T. DeepNOG: Fast and accurate protein orthologous group assignment. Bioinformatics. 2020 Dec 1;36(22-23):5304-5312. doi: 10.1093/bioinformatics/btaa1051

Steiner PA, Geijo J, Fadeev E, Obiol A, Sintes E, Rattei T et al. Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea. Frontiers in Microbiology. 2020 Nov 16;11:584222. doi: 10.3389/fmicb.2020.584222

Pascelli C, Laffy PW, Botté E, Kupresanin M, Rattei T, Lurgi M et al. Viral ecogenomics across the Porifera. Microbiome. 2020 Oct 2;8(1):144. Epub 2020 Oct 2. doi: 10.1186/s40168-020-00919-5