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2017


Sato Y, Ling EYS, Turaev D, Laffy P, Weynberg KD, Rattei T et al. Unraveling the microbial processes of black band disease in corals through integrated genomics. Scientific Reports. 2017 Jan 17;7:40455. doi: 10.1038/srep40455

Weynberg KD, Laffy PW, Wood-Charlson EM, Turaev D, Rattei T, Webster NS et al. Coral-associated viral communities show high levels of diversity and host auxiliary functions. PeerJ. 2017;5:e4054. doi: 10.7717/peerj.4054

Capel E, Barnier J-P, Zomer AL, Bole-Feysot C, Nussbaumer T, Jamet A et al. Peripheral blood vessels are a niche for blood-borne meningococci. Virulence. 2017;8(8):1808–1819. Epub 2017 Nov 27. doi: 10.1080/21505594.2017.1391446

2016


Diesner SC, Bergmayr C, Pfitzner B, Assmann V, Krishnamurthy D, Starkl P et al. A distinct microbiota composition is associated with protection from food allergy in an oral mouse immunization model. Clinical Immunology. 2016 Dec;173:10–18. doi: 10.1016/j.clim.2016.10.009

Eder T, Grebien F, Rattei T. NVT: a fast and simple tool for the assessment of RNA-Seq normalization strategies. Bioinformatics. 2016 Aug 11;32(23):3682-3684. doi: 10.1093/bioinformatics/btw521

Weinmaier T, Platzer A, Frank J, Hellinger H-J, Tischler P, Rattei T. ConsPred - a rule-based (re-)annotation framework for prokaryotic genomes. Bioinformatics. 2016 Jul 4;32(21):3327-3329. doi: 10.1093/bioinformatics/btw393

Bulat T, Smidak R, Sialana FJ, Jung G, Rattei T, Bilban M et al. Transcriptomic and Proteomic Analysis of Arion vulgaris-Proteins for Probably Successful Survival Strategies? PLoS ONE. 2016 Mar;11(3):e0150614. doi: 10.1371/journal.pone.0150614

Maixner F, Krause-Kyora B, Turaev D, Herbig A, Hoopmann MR, Hallows JL et al. The 5300-year-old Helicobacter pylori genome of the Iceman. Science. 2016 Jan 8;351(6269):162-165. doi: 10.1126/science.aad2545

Eichinger V, Nussbaumer T, Platzer A, Jehl M-A, Arnold R, Rattei T. EffectiveDB-updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. Nucleic Acids Research. 2016 Jan 4;44(D1):D669–D674. doi: 10.1093/nar/gkv1269

Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research. 2016 Jan 4;44(D1):D286–D293. doi: 10.1093/nar/gkv1248

Capel E, Zomer AL, Nussbaumer T, Bole C, Izac B, Frapy E et al. Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization. mBio. 2016;7(4):e01173-16. doi: 10.1128/mBio.01173-16

Laffy PW, Wood-Charlson EM, Turaev D, Weynberg KD, Botté ES, van Oppen MJH et al. HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts. Frontiers in Microbiology. 2016;7:822. doi: 10.3389/fmicb.2016.00822

2015


Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M et al. Complete nitrification by Nitrospira bacteria. Nature. 2015 Dec 24;528(7583):504–509. doi: 10.1038/nature16461

Weinmaier T, Probst AJ, La Duc MT, Ciobanu D, Cheng J-F, Ivanova N et al. A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses. Microbiome. 2015 Dec 8;3:62. 62. doi: 10.1186/s40168-015-0129-y

Feldbauer R, Schulz F, Horn M, Rattei T. Prediction of microbial phenotypes based on comparative genomics. BMC Bioinformatics. 2015 Oct 2;16 (14):S1. doi: 10.1186/1471-2105-16-S14-S1

Muller C, Cacaci M, Sauvageot N, Sanguinetti M, Rattei T, Eder T et al. The Intraperitoneal Transcriptome of the Opportunistic Pathogen Enterococcus faecalis in Mice. PLoS ONE. 2015 May 15;10(5):e0126143. 0126143. doi: 10.1371/journal.pone.0126143