Publications

• Google Scholar, ORCID, Web of science, Loop, Pubmed

Manuscripts accepted/in preparation, 2024

• B. Frey, et al., Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach. PLOS ONE. https://doi.org/10.1371/journal.pone.0300503
• Feng M. et al., Microbial genetic potential differs among cryospheric habitats of the Damma glacier. Submitted.
• ME Macha et al. Molecular characterization and epidemiology of multi-drug resistant Escherichia coli isolated from Patients with Urinary Tract Infections in Rural-Tanzania- Implications for Empirical Antibiotic Treatment Guidelines. Submitted.
• ME macha et al., High Magnitude of Fecal carriage of extended-spectrum Beta Lactamase producing Enterobacterales among patient’s urinary tract infections in rural Tanzania. Preliminary findings. Submitted.
• Flury J., et al., Six new reference genomes of Brassicaceae species from the Swiss Alps. In preparation.
• Zajac N. et al., Comparison of Single-cell Long-read and Short-read Transcriptome Sequencing of Patient-derived Organoid Cells of ccRCC: Quality Evaluation of the MAS-ISO-seq Approach. biorxiv. https://doi.org/10.1101/2024.03.14.584953
• Karakulak T. et al., Heterogeneous and Novel Transcript Expression in Single Cells of Patient-Derived ccRCC Organoids. biorxiv. . https://doi.org/10.1101/2024.03.15.585271
• Grubinger T. et al., Genomic variation contrasts with ecological and morphological divergence in two sister-taxa of wild tomatoes. In preparation.

Manuscripts accepted, 2023

• JM Silva et al., AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data. GigaScience. Accepted. doi:10.1093/gigascience/giad101/7471725
• Stegmüller S. et al. Hazard potential of Swiss Ixodes ricinus ticks: Virome composition and presence of selected bacterial and protozoan pathogens. PLOS ONE. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0290942.
• A Bösch et al. Resistance development in Escherichia coli to delafloxacin at pHs 6.0 and 7.3 compared to ciprofloxacin. Antimicrob Agents Chemother. 2023 Oct 26:e0162522. doi: 10.1128/aac.01625-22.
• Feng M. et al. Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential. Environmental Microbiology. http://doi.org/10.1111/1462-2920.16497
• E Felley-Bosco et al., The pattern of RNA editing changes in pleural mesothelioma upon epithelial-mesenchymal transition. Int. J. Mol. Sci. 2023, 24(3), 2874; https://doi.org/10.3390/ijms24032874
• L Frachon et al. Putative signals of generalist plant species adaptation to local pollinator communities and abiotic factors. Mol Biol Evol. 2023 Feb 16:msad036. doi: 10.1093/molbev/msad036. Epub ahead of print. PMID: 36795638.
• C Sannino et al., Distinct taxonomic and functional profiles of High Arctic and alpine permafrost-affected soil microbiomes. Environmental Microbiome 18, 54 (2023). https://doi.org/10.1186/s40793-023-00509-6

Manuscripts accepted in 2022

• W Qi et al. The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features. Gigacience. https://doi.org/10.1093/gigascience/giac028
• B. Frey et al. Shotgun metagenomics of deep forest soil layers show evidence of altered microbial genetic potential for biogeochemical cycling. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2022.828977
• Y Lim et al. Mutations in DNA polymerase δ subunit 1 mediate CMD2-type resistance to Cassava Mosaic Geminiviruses. Nature Communications. https://doi.org/10.1038/s41467-022-31414-0
• J Kubacki et al. Differential viral genome diversity of healthy and RSS-affected broiler flocks. Microorganisms. https://doi.org/10.3390/microorganisms10061092
• M Wiederkehr et al. Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland. Viruses. https://doi.org/10.3390/v14091911
• B. Frey et al. Long-term mercury contamination does not affect the microbial gene potential for C and N cycling in soils but enhances detoxification gene abundance. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2022.1034138
• A Hariharan et al. Heterogeneity of RNA editing in mesothelioma and how RNA editing enzyme ADAR2 affects mesothelioma cell growth, response to chemotherapy and tumor microenvironment. Molecular Oncology. https://doi.org/10.1002/1878-0261.13322
• J Rüthi et al. Shotgun metagenomics of the plastisphere microbiome reveals altered microbial genetic potential for plastic degradation and biogeochemical cycling in alpine soils. Journal of Hazardous Materials. https://doi.org/10.1016/j.jhazmat.2022.129941
• S Sun et al. Viral mimicry response is associated with clinical outcome in pleural mesothelioma. JTO Clinical and Research Reports. https://doi.org/10.1016/j.jtocrr.2022.100430
• Z Zhong et al. Haplotype resolved DNA methylome of African cassava genome. Plant Biotechnology. https://doi.org/10.1111/pbi.13955

Professional services

• Peer review for scientific journals including BMC Bioinformatics, Scientific Data, F1000Research, Viruses, Microorganisms, Microbial Ecology
• Review editor Frontiers

Teaching

• BIO 694 Genetic variation analysis course
• BIO 680 DNA Next Generation Sequencing – from theory to practice
• BIO 638 Next Generation Sequencing applied to Metagenomics
• FGCZ Bioinformatics Trainning
• Genetic Variant Analysis, 2020. FGCZ, C-CAMP, Swissnex India
• Virtual Lab for Precision Medicine (2019, 2020)
• Genome medicine (2016-2019)