| Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting JJC de Vries, JR Brown, N Couto, M Beer, P Le Mercier, I Sidorov, A Papa, ... Journal of Clinical Virology 138, 104812, 2021 | 67 | 2021 |
| Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples JJC de Vries, JR Brown, N Fischer, IA Sidorov, S Morfopoulou, J Huang, ... Journal of Clinical Virology 141, 104908, 2021 | 47 | 2021 |
| Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses I Hardmeier, N Aeberhard, W Qi, K Schoenbaechler, H Kraettli, JM Hatt, ... PLoS One 16 (6), e0252534, 2021 | 45 | 2021 |
| Viral Metagenomic Analysis of Aedes albopictus Mosquitos from Southern Switzerland J Kubacki, E Flacio, W Qi, V Guidi, M Tonolla, C Fraefel Viruses 12 (9), 929, 2020 | 45 | 2020 |
| Viral metagenomics in the clinical realm: lessons learned from a Swiss-wide ring trial T Junier, M Huber, S Schmutz, V Kufner, O Zagordi, S Neuenschwander, ... Genes 10 (9), 655, 2019 | 45 | 2019 |
| Active equine parvovirus‐hepatitis infection is most frequently detected in Austrian horses of advanced age M Badenhorst, P de Heus, A Auer, B Tegtmeyer, A Stang, K Dimmel, ... Equine veterinary journal 54 (2), 379-389, 2022 | 39 | 2022 |
| Implementation of next-generation sequencing for virus identification in veterinary diagnostic laboratories J Kubacki, C Fraefel, C Bachofen Journal of Veterinary Diagnostic Investigation 33 (2), 235-247, 2021 | 36 | 2021 |
| Complete genome sequences of two Swiss hepatitis E virus isolates from human stool and raw pork sausage J Kubacki, C Fraefel, M Jermini, P Giannini, G Martinetti, P Ripellino, ... Genome announcements 5 (35), 10.1128/genomea. 00888-17, 2017 | 27 | 2017 |
| Genome sequence of alongshan virus from ixodes ricinus ticks collected in Switzerland S Stegmüller, C Fraefel, J Kubacki Microbiology Resource Announcements 12 (3), e01287-22, 2023 | 17 | 2023 |
| Virus diversity, abundance, and evolution in three different bat colonies in Switzerland MA Wiederkehr, W Qi, K Schoenbaechler, C Fraefel, J Kubacki Viruses 14 (9), 1911, 2022 | 12 | 2022 |
| Differential viral genome diversity of healthy and RSS-affected broiler flocks J Kubacki, W Qi, C Fraefel Microorganisms 10 (6), 1092, 2022 | 11 | 2022 |
| An evaluation of hepatitis E virus molecular typing methods SA Baylis, C Adlhoch, L Childs Clinical Chemistry 68 (1), 181-191, 2022 | 10 | 2022 |
| Complete genome sequence of a Swiss hepatitis E virus isolate from the liver of a fattening pig V Wist, J Kubacki, J Lechmann, M Steck, C Fraefel, R Stephan, ... Genome announcements 6 (9), 10.1128/genomea. 00113-18, 2018 | 10 | 2018 |
| Exo-erythrocytic development of Plasmodium matutinum (lineage pLINN1) in a naturally infected roadkill fieldfare Turdus pilaris H Pendl, C Hernández-Lara, J Kubacki, N Borel, S Albini, G Valkiūnas Malaria journal 21 (1), 148, 2022 | 9 | 2022 |
| Genome sequence of equid Alphaherpesvirus 1 (EHV-1) from a nasal swab of a Swiss horse associated with a major EHV-1 outbreak following a show jumping event in Valencia, Spain J Kubacki, J Lechmann, C Fraefel, C Bachofen Microbiology Resource Announcements 10 (34), 10.1128/mra. 00732-21, 2021 | 9 | 2021 |
| RNA-seq analysis in equine papillomavirus type 2-positive carcinomas identifies affected pathways and potential cancer markers as well as viral gene expression and splicing events AS Ramsauer, J Kubacki, C Favrot, M Ackermann, C Fraefel, K Tobler Journal of General Virology 100 (6), 985-998, 2019 | 9 | 2019 |
| New subcluster of HEV genotype 3 strains linked to the first confirmed Swiss case of foodborne hepatitis E infection C Bachofen, J Kubacki, M Jermini, P Giannini, G Martinetti, P Ripellino, ... Case Reports Journal 1 (1), 003, 2017 | 9 | 2017 |
| Viral metagenomics in the clinical realm: lessons learned from a Swiss-wide ring trial. Genes (Basel) 10: 655 T Junier, M Huber, S Schmutz, V Kufner, O Zagordi, S Neuenschwander, ... | 8 | 2019 |
| Hazard potential of Swiss Ixodes ricinus ticks: Virome composition and presence of selected bacterial and protozoan pathogens S Stegmüller, W Qi, P Torgerson, C Fraefel, J Kubacki PLOS ONE 18 (11), e0290942, 2023 | 7 | 2023 |
| ESCV Network on Next-Generation Sequencing. Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis … JJC de Vries, JR Brown, N Couto, M Beer, P Le Mercier, I Sidorov, A Papa, ... J Clin Virol 138 (104812), 10.1016, 2021 | 6 | 2021 |
