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Cuénod, Aline; Wüthrich, Daniel; Seth-Smith, Helena M B; Ott, Chantal; Gehringer, Christian; Foucault, Frédéric; Mouchet, Roxanne; Kassim, Ali; Revathi, Gunturu; Vogt, Deborah R; von Felten, Stefanie; Bassetti, Stefano; Tschudin-Sutter, Sarah; Hettich, Timm; Schlotterbeck, Götz; Homberger, Christina; Casanova, Carlo; Moran-Gilad, Jacob; Sagi, Orli; Rodríguez-Sánchez, Belén; ... (2021). Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study. Genome medicine, 13(1), p. 150. BioMed Central 10.1186/s13073-021-00960-5
Dylus, David; Pillonel, Trestan; Opota, Onya; Wüthrich, Daniel; Seth-Smith, Helena M. B.; Egli, Adrian; Leo, Stefano; Lazarevic, Vladimir; Schrenzel, Jacques; Laurent, Sacha; Bertelli, Claire; Blanc, Dominique S.; Neuenschwander, Stefan; Ramette, Alban; Falquet, Laurent; Imkamp, Frank; Keller, Peter M.; Kahles, Andre; Oberhaensli, Simone; Barbié, Valérie; ... (2020). NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test. Frontiers in Microbiology, 11, p. 591093. Frontiers 10.3389/fmicb.2020.591093
Roder, Thomas; Wüthrich, Daniel; Bär, Cornelia; Sattari, Zahra; Ah, Ueli von; Ronchi, Francesca; Macpherson, Andrew; Ganal-Vonarburg, Stephanie C.; Bruggmann, Rémy; Vergères, Guy (2020). In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes. Microorganisms, 8(7) MDPI 10.3390/microorganisms8070966
Machado, Ricardo A. R.; Thönen, Lisa; Arce, Carla C. M.; Theepan, Vanitha; Prada, Fausto; Wüthrich, Daniel; Robert, Christelle A. M.; Vogiatzaki, Evangelia; Shi, Yi-Ming; Schaeren, Olivier P.; Notter, Matheus; Bruggmann, Rémy; Hapfelmeier, Siegfried; Bode, Helge B.; Erb, Matthias (2020). Engineering bacterial symbionts of nematodes improves biocontrol potential of the western corn rootworm. Nature biotechnology, 38(5), pp. 600-608. Nature America 10.1038/s41587-020-0419-1
Troxler, Lukas J.; Werren, Joel P.; Schaffner, Thierry O.; Mostacci, Nadezda; Vermathen, Peter; Vermathen, Martina; Wüthrich, Daniel; Simillion, Cedric; Brugger, Silvio D.; Bruggmann, Rémy; Hathaway, Lucy J.; Furrer, Julien; Hilty, Markus (2019). Carbon source regulates polysaccharide capsule biosynthesis in Streptococcus pneumoniae. Journal of biological chemistry, 294(46), pp. 17224-17238. American Society for Biochemistry and Molecular Biology 10.1074/jbc.RA119.010764
Frazão, Josias B; Colombo, Martino; Simillion, Cedric; Bilican, Adem; Keller, Irene; Wüthrich, Daniel; Zhu, Zhiqing; Okoniewski, Michal J; Bruggmann, Rémy; Condino-Neto, Antonio; Newburger, Peter E (2019). Gene expression in chronic granulomatous disease and interferon-γ receptor-deficient cells treated in vitro with interferon-γ. Journal of cellular biochemistry, 120(3), pp. 4321-4332. Wiley-Blackwell 10.1002/jcb.27718
Allemann, Aurélie; Krämer, Julia G.; Korten, Insa; Ramsey, Kathryn; Casaulta, Carmen; Wüthrich, Daniel; Ramette, Alban Nicolas; Endimiani, Andrea; Latzin, Philipp; Hilty, Markus (2019). Nasal Resistome Development in Infants With Cystic Fibrosis in the First Year of Life. Frontiers in Microbiology, 10(212), p. 212. Frontiers 10.3389/fmicb.2019.00212
Lüdin, Petra; Roetschi, Alexandra; Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Shani, Noam (2018). Update on Tetracycline Susceptibility of Pediococcus acidilactici Based on Strains Isolated from Swiss Cheese and Whey. Journal of food protection, 81(10), pp. 1582-1589. International Association for Food Protection 10.4315/0362-028X.JFP-18-160
Machado, Ricardo A. R.; Wüthrich, Daniel; Kuhnert, Peter; Arce, Carla C. M.; Thönen, Lisa; Ruiz, Celia; Zhang, Xi; Robert, Christelle A. M.; Karimi, Javad; Kamali, Shokoofeh; Ma, Juan; Bruggmann, Rémy; Erb, Matthias (2018). Whole-genome-based revisit of Photorhabdus phylogeny: proposal for the elevation of most Photorhabdus subspecies to the species level and description of one novel species Photorhabdus bodei sp. nov., and one novel subspecies Photorhabdus laumondii subsp. clarkei subsp. nov. International journal of systematic and evolutionary microbiology, 68(8), pp. 2664-2681. Society for General Microbiology SGM 10.1099/ijsem.0.002820
Wüthrich, Daniel; Irmler, Stefan; Berthoud, Hélène; Guggenbuhl, Barbara; Eugster, Elisabeth; Bruggmann, Rémy (2018). Conversion of Methionine to Cysteine in Lactobacillus paracasei Depends on the Highly Mobile cysK-ctl-cysE Gene Cluster. Frontiers in Microbiology, 9(2415) Frontiers 10.3389/fmicb.2018.02415
Wüthrich, Daniel; Wenzel, Claudia; Bavan, Tharmatha; Bruggmann, Rémy; Berthoud, Hélène; Irmler, Stefan (2018). Transcriptional Regulation of Cysteine and Methionine Metabolism in Lactobacillus paracasei FAM18149. Frontiers in Microbiology, 9(1261) Frontiers 10.3389/fmicb.2018.01261
Boujon, Céline; Koch, Michel Christoph; Wüthrich, Daniel; Werder, Simea; Jakupovic, Dennis; Bruggmann, Rémy; Seuberlich, Torsten (2017). Indication of Cross-Species Transmission of Astrovirus Associated with Encephalitis in Sheep and Cattle. Emerging infectious diseases, 23(9), pp. 1604-1608. U.S. National Center for Infectious Diseases 10.3201/eid2309.170168
Truchet, Laura Rosyne Hedwig; Walland, Julia Gianna Marlene; Wüthrich, Daniel; Boujon, Céline; Posthaus, Horst; Bruggmann, Rémy; Schüpbach, Gertraud; Oevermann, Anna; Seuberlich, Torsten (2017). Neuropathological survey reveals underestimation of the prevalence of neuroinfectious diseases in cattle in Switzerland. Veterinary microbiology, 208, pp. 137-145. Elsevier 10.1016/j.vetmic.2017.07.027
Endimiani, Andrea; Allemann, Aurélie; Wüthrich, Daniel; Lupo, Agnese; Hilty, Markus (2017). First report of the macrolide efflux genetic assembly (MEGA) element in Haemophilus parainfluenzae. International journal of antimicrobial agents, 49(2), pp. 265-266. Elsevier 10.1016/j.ijantimicag.2016.11.006
Wüthrich, Daniel; Berthoud, Hélène; Wechsler, Daniel; Eugster, Elisabeth; Irmler, Stefan; Bruggmann, Rémy (2017). The Histidine Decarboxylase Gene Cluster of Lactobacillus parabuchneri Was Gained by Horizontal Gene Transfer and Is Mobile within the Species. Frontiers in Microbiology, 8(218) Frontiers 10.3389/fmicb.2017.00218
Awasthi, Nivedita; Drögemüller, Cord; Jagannathan, Vidhya; Keller, Irene; Wüthrich, Daniel; Bruggmann, Rémy; Beck, Julia; Schütz, Ekkehard; Brenig, Bertram; Demmel, Steffi; Moser, Simon; Signer-Hasler, Heidi; Pieńkowska-Schelling, Aldona; Schelling, Claude; Sande Melon, Marcos; Rongen, Ronald; Rieder, Stefan; Kelsh, Robert N.; Mercader Huber, Nadia and Leeb, Tosso (2017). A structural variant in the 5’-flanking region of the TWIST2 gene affects melanocyte development in belted cattle. PLoS ONE, 12(6), e0180170. Public Library of Science 10.1371/journal.pone.0180170
Moser, Aline; Wüthrich, Daniel; Bruggmann, Rémy; Eugster-Meier, Elisabeth; Meile, Leo; Irmler, Stefan (2017). Amplicon Sequencing of the slpH Locus Permits Culture-Independent Strain Typing of Lactobacillus helveticus in Dairy Products. Frontiers in Microbiology, 8(1380) Frontiers 10.3389/fmicb.2017.01380
Seuberlich, Torsten; Wüthrich, Daniel; Selimovic-Hamza, Senija; Drögemüller, Cord; Oevermann, Anna; Bruggmann, Remy; Bouzalas, Ilias (2017). Identification of a second encephalitis-associated astrovirus in cattle. Emerging Microbes & Infections, 6(1), p. 1. Nature Publishing Group 10.1038/emi.2017.56
Storari, Michelangelo; Kulli, Sandra; Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle (2016). Genomic approach to studying nutritional requirements of Clostridium tyrobutyricum and other Clostridia causing late blowing defects. Food microbiology, 59, pp. 213-223. Elsevier 10.1016/j.fm.2016.05.013
Seuberlich, Torsten; Wüthrich, Daniel; Selimovic-Hamza, Senija; Drögemüller, Cord; Oevermann, Anna; Bruggmann, Rémy; Bouzalas, Ilias (2016). Identification of a second encephalitis-associated astrovirus in cattle. Emerging Microbes & Infections, 5(8), e71. Nature Publishing Group 10.1038/emi.2016.5
Wüthrich, Daniel; Boujon, Céline; Truchet, Laura Rosyne Hedwig; Selimovic-Hamza, Senija; Oevermann, Anna; Bouzalas, Ilias; Bruggmann, Rémy; Seuberlich, Torsten (2016). Exploring the virome of cattle with non-suppurative encephalitis of unknown etiology by metagenomics. Virology, 493, pp. 22-30. Academic Press 10.1016/j.virol.2016.03.009
Bouzalas, Ilias; Wüthrich, Daniel; Selimovic-Hamza, Senija; Drögemüller, Cord; Bruggmann, Rémy; Seuberlich, Torsten (2016). Full-genome based molecular characterization of encephalitis-associated bovine astroviruses. Infection, genetics and evolution, 44, pp. 162-168. Elsevier 10.1016/j.meegid.2016.06.052
Storari, Michelangelo; Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle (2015). Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese. Genome Announcements, 3(2) American Society for Microbiology 10.1128/genomeA.00078-15
Hilty, Markus; Wüthrich, Daniel; Salter, Susannah J; Engel, Hans Jürg; Campbell, Samuel; Sá-Leão, Raquel; de Lencastre, Hermínia; Hermans, Peter; Sadowy, Ewa; Turner, Paul; Chewapreecha, Claire; Diggle, Mathew; Pluschke, Gerd; McGee, Lesley; Eser, Ozgen Köseoğlu; Low, Donald E; Smith-Vaughan, Heidi; Endimiani, Andrea; Küffer, Marianne; Dupasquier, Mélanie; ... (2014). Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages. Genome biology and evolution, 6(12), pp. 3281-3294. Oxford University Press 10.1093/gbe/evu263
Bouzalas, Ilias G; Wüthrich, Daniel; Walland, Julia Gianna Marlene; Drögemüller, Cord; Zurbriggen, Andreas; Vandevelde, Marc; Oevermann, Anna; Bruggmann, Rémy; Seuberlich, Torsten (2014). Neurotropic astrovirus in cattle with nonsuppurative encephalitis in Europe. Journal of clinical microbiology, 52(9), pp. 3318-3324. American Society for Microbiology 10.1128/JCM.01195-14
Schaffner, Thierry Oliver; Hinds, Jason; Gould, Katherine A; Wüthrich, Daniel; Bruggmann, Rémy; Küffer, Marianne; Mühlemann, Kathrin; Hilty, Markus; Hathaway, Lucy Jane (2014). A point mutation in cpsE renders Streptococcus pneumoniae nonencapsulated and enhances its growth, adherence and competence. BMC microbiology, 14(210), p. 210. BioMed Central 10.1186/s12866-014-0210-x
Gunasekera, Kapila; Wüthrich, Daniel; Braga-Lagache, Sophie; Heller, Manfred; Ochsenreiter, Torsten (2012). Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry. BMC Genomics, 13, p. 556. London: BioMed Central 10.1186/1471-2164-13-556
