Publications

Geijo Fernández JB, Pfundner A, Garcia-Perez CA. Bridging taxonomic gaps in microbial community profiling with LSTM-generated synthetic full-length 16S rRNA sequences. ISME Communications. 2026 Apr 23. doi: 10.1093/ismeco/ycag112

Speth DR, Pullen N, Aroney STN, Coltman BL, Osvatic J, Woodcroft BJ et al. GlobDB: a comprehensive species-dereplicated microbial genome resource. Bioinformatics advances. 2025 Nov 9;5(1):1-4. doi: 10.1093/bioadv/vbaf280

Data Reuse Consortium, Wagner M, Rattei T, Osvatic J, Speth D. A roadmap for equitable reuse of public microbiome data. Nature Microbiology. 2025 Oct;10(10):2384-2395. Epub 2025 Sept 26. doi: 10.1038/s41564-025-02116-2

Tocino-Márquez I, Zehl M, Séneca Cardoso Da Silva J, Pjevac P, Felkl M, Becker CFW et al. The bacterial community of the freshwater bryozoan Cristatella Mucedo and its secondary metabolites production potential. Scientific Reports. 2025 Aug 26;15(1):31456. doi: 10.1038/s41598-025-17084-0

Jain K, Hauschild R, Bochkareva OO, Roemhild R, Tkačik G, Guet CC. Pulsatile basal gene expression as a fitness determinant in bacteria. Proceedings of the National Academy of Sciences of the United States of America. 2025 Apr 7;122(15):e2413709122. doi: 10.1073/pnas.2413709122

Rauchenwald T, Benedikt-Kühnast P, Eder S, Grabner GF, Forstreiter S, Lang M et al. Clearing the path for whole-mount labeling and quantification of neuron and vessel density in adipose tissue. Journal of Cell Science. 2025 Feb 7;138(3):1-11. jcs263438. doi: 10.1242/jcs.263438

Gelabert P, Oberreiter V, Straus LG, Morales MRG, Sawyer S, Marín-Arroyo AB et al. Author Correction: A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain. Nature Communications. 2025 Jan 17;16(1):779. doi: 10.1038/s41467-025-56198-x

Gelabert P, Oberreiter V, Straus LG, Morales MRG, Sawyer S, Marín-Arroyo AB et al. A sedimentary ancient DNA perspective on human and carnivore persistence through the Late Pleistocene in El Mirón Cave, Spain. Nature Communications. 2025 Jan 2;16(1):107. doi: 10.1038/s41467-024-55740-7

Hämmerle M, Guellil M, Trgovec-Greif L, Cheronet O, Sawyer S, Ruiz-Gartzia I et al. Screening great ape museum specimens for DNA viruses. Scientific Reports. 2024 Nov 30;14(1):29806. doi: 10.1038/s41598-024-80780-w

Beikbaghban T, Proietti L, Ebner J, Sango R, Rattei T, Weichhart T et al. Differential regulation of mitochondrial uncoupling protein 2 in cancer cells. Biochimica et Biophysica Acta - Bioenergetics. 2024 Nov;1865(4):149486. doi: 10.1016/j.bbabio.2024.149486

Duller S, Vrbancic S, Szydłowski Ł, Mahnert A, Blohs M, Predl M et al. Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome. Nature Communications. 2024 Aug 31;15(1):1-16. 7593. Epub 2024 Aug 31. doi: 10.1038/s41467-024-52037-7

Oberreiter V, Gelabert P, Brück F, Franz S, Zelger E, Szedlacsek S et al. Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach. Scientific Reports. 2024 Aug 20;14(1):19388. doi: 10.1038/s41598-024-69741-5

Ziveri J, Le Guennec L, dos Santos Souza I, Barnier JP, Walter SM, Diallo Y et al. Angiopoietin-like 4 protects against endothelial dysfunction during bacterial sepsis. Nature Microbiology. 2024 Aug 5;9(9):2434-2447. doi: 10.1038/s41564-024-01760-4

Trgovec-Greif L, Hellinger HJ, Mainguy J, Pfundner A, Frishman D, Kiening M et al. VOGDB-Database of Virus Orthologous Groups. Viruses. 2024 Jul 25;16(8):1191. doi: 10.3390/v16081191

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

Predl M, Gandolf K, Hofer M, Rattei T. ScyNet: Visualizing interactions in community metabolic models. Bioinformatics advances. 2024;4(1):vbae104. doi: 10.1093/bioadv/vbae104

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 Sept. 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