2026 Project: Early detection for early action: integrating multiple data sources for monitoring the SARS-CoV-2 epidemic in near real-time Machine learning-based short-term forecasting of COVID-19 hospital admissions using routine hospital patient data. 2026. Wohlfender, M. S., Bouman, J. A., Endrich, O., Ramette, A., Leichtle, A. B., Beldi, G., Althaus, C. L., & Riou, J. Epidemics: The Journal on Infectious Disease Dynamics. Link to article Project: Divided pandemic society and Public Health. Polarization in the Covid-19 pandemic response in Switzerland Polarization and health-related behaviors and outcomes during the COVID-19 pandemic: a systematic review. 2026. Ipekci, A.M., Filsinger, M., Buitrago-Garcia, D., Kobler Betancourt, C.I., Liwanag, H.J., Frahsa, A. and Low, N. SSM-Population Health. Link to article “Do you belong in my circle?” – a retrospective reflexive thematic analysis of the particularity and price of solidarity for socioculturally diverse communities in Switzerland during the COVID-19 pandemic. 2026. Ly, G.T., Kobler Betancourt, C.I., Hug, B.L. and Frahsa, A. SSM-Qualitative Research in Health. Link to article
2025 Project: Divided pandemic society and Public Health. Polarization in the Covid-19 pandemic response in Switzerland A scoping review of community participation in public health research and action during the COVID-19 pandemic: Exploring approaches on the continuum between utilitarianism and empowerment. 2025. Frahsa, A., Liwanag, H. J., Kobler Betancourt, C., Ipekci, A. M., Minder, B., & Schow, D. Social Science & Medicine. Link to article Project: Preparedness for surveillance in school rooms in pandemic and epidemic situations: multiple measure approach to estimate transmission and interventions for Covid-19 and seasonal influenza Absences, Symptoms and Respiratory Viruses in a Swiss School: Longitudinal Study With Serial Saliva Sampling. 2025. Banholzer N, Kronthaler D, Bittel P, Furrer L, Munday JD, Egger M, Hascher T, Jent P, Fenner L. Influenza Other Respir Viruses. Link to article Infection Control Measures in the Classroom During and in the Aftermath of the COVID-19 Pandemic: A Multidimensional Analysis of Secondary Student Well-Being and Emotions. 2025. Hascher T, Held T, Schnell J, Banholzer N, Zürcher K, Fenner L, Bittel P, Jent P. J Sch Health. Link to article The relative contribution of close-proximity contacts, shared classroom exposure and indoor air quality to respiratory virus transmission in schools. 2025. Banholzer, N., Munday, J. D., Jent, P., Bittel, P., Dall’Amico, L., Furrer, L., Bürki, C., Stadler, T., Egger, M., Hascher, T., Cattuto, C., & Fenner, L. Nature Communications. Link to article MCID core activity: BEready Cohort ‘Bern, get ready’, BEready, a household-based cohort study for pandemic preparedness research in Switzerland: pilot study. 2025. Hodel, E.M., Wegmüller, S., Lim, E.,, Grimm, K., Gasser, L, Di Domenico, L., Schuller, S., Wandeler, G., , Low, N., BMJ Open. Link to article Project: Role of sheep and rodent reservoirs for Wesselsbron, a neglected zoonotic flavivirus Mosquito-independent milk-associated transmission of zoonotic Wesselsbron virus in sheep. 2025. Zimoch, M., Grau-Roma, L., Liniger, M., Donzé, N., Godel, A., Escribano, D., Trüeb, B. S., Pramateftaki, P., Torres Puig, S., Cerón, J. J., Thiel, V., Jores, J., Summerfield, A., Ruggli, N., Benarafa, C., & García-Nicolás, O. PLoS Pathogens. Link to article Project: An integrative One Health network to monitor and characterize influenza A viruses circulating in the human and pig population Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus. 2025 Licheri, M., Mwanga, M., Licheri, M. F., Graaf-Rau, A., Sägesser, C., Bittel, P., Harder, T., Suter, F. M., Kelly, J. N., & Dijkman, R. Genome Medicine. Link to article Project: Deciphering the interplay between viral proteins and host cell mRNA metabolism Protocol for monitoring mRNA translation and degradation in human cell-free lysates. 2025. Schwaller, N., & Karousis, E. D. STAR Protocols. Link to article The impact of Coronavirus Nsp1 on host mRNA degradation is independent of its role in translation inhibition. 2025. Bäumlin, E., Andenmatten, D., Luginbühl, J., Lalou, A., Schwaller, N., Karousis, E. Cell Reports. Links: article, UniBE press release, MCID summary Efficient cell-free translation from diverse human cell types. 2025. Ziegelmüller, J., Kouvelas, N., Schwaller, N., Thambythurai, P., Hofer, A., Mühlemann, O., Karousis E.D. Journal of Biological Chemistry. Link to article. Project: Use of tailor-made bacteriophages for the treatment of infections caused by multi-drug resistant bacteria Beware of host immune responses towards bacteriophages potentially impacting phage therapy. 2025. Démoulins, T., Cherbuin, J. D. R., Yimthin, T., Eggerschwiler, L., Adnan, F., & Jores, J. Veterinary Research. Link to article. Complete genome sequences of three avian pathogenic Escherichia coli strains isolated from colibacillosis-affected poultry in Pakistan. 2025. Zhang, J., Cherbuin, J. D. R., Khan, M., Niaz, H., & Adnan, F. Microbiology Resource Announcements. Link to article. Complete genome sequences of the lytic bacteriophage PBM-3 and the avian pathogenic Escherichia coli strain PE144. 2025. Cherbuin, J. D. R., Zhang, J., Khan, M., Niaz, H. & Adnan. F. Microbiology Resource Announcements. Link to article Project: Confronting the rising epidemic of the zoonotic tick-borne encephalitis virus Three-dimensional mapping of tick-borne encephalitis virus distribution in the mouse brain using a newly engineered TurboGFP reporter virus. 2025. Berankova, M., Leoni, S., Holoubek, J., Haviernik, J., Salat, J., Grandgirard, D., Leib, S. L., & Ruzek, D. Emerging Microbes & Infections. Link to article Validated Methods for Inactivation of Tick-Borne Encephalitis Virus Compatible with Immune-Based and Enzymatic Downstream Analyses. 2025. Leoni, S., Leib, S. L., Summermatter, K., & Grandgirard, D. Viruses. Link to article Monkeypox virus spreads from cell-to-cell and leads to neuronal death in human neural organoids. 2025. Schultz-Pernice, I., Fahmi, A., Brito, F., Liniger, M., Chiu, Y., David, T., Oliveira Esteves, B.I., Golomingi, A., Zumkehr, B., Gerber, M., Jandrasits, D., Züst, R., Steiner, S., Wotzkow, C., Blank, F., Engler, O.B., Summerfield, A., Ruggli, N., Baud, D., Alves, M.P. Nature Communications. Links: article, UniBE press release, MCID summary. Project: Identification of monoclonal intenstinal antibodies against Klebsiella pneumoniae, an opportunistic pathogen Efficient Expression and Purification of Recombinant Mouse Dimeric IgA. 2025. Geisse, A., Zhang, T., Schreiber, J., Markova, K., Burkhalter, S., Wardemann, H., Macpherson, A. J., & Rollenske, T. H. European Journal of Immunology. Link: article Project: Covid-19: Science, Narratives and Policy Scientists in power plays: How substantive were scientists' narratives during the COVID‐19 pandemic? 2025. Ksinsik, J., Schlaufer, C. Policy Studies Journal. Links: article, MCID summary. Project: Ethical Considerations of the Relationship and Interactions between Science, Policy and the Media during the COVID-19 pandemic (ESPRIM) Bioethics at the intersection of politics, society, and healthcare: the significance of media debate analyses. 2025. Ellerich-Groppe, N., Zimmermann, B. BMC Medical Ethics. Link to article. Project: Co-infection of Hepatitis B virus (HBV) and malaria: from population level to immunological and cellular interaction Expanding the fluorescent toolkit: Blue fluorescent protein-expressing Plasmodium berghei for enhanced multiplex microscopy. 2025. Atchou, K., Caldelari, R., Roques, M., Schmuckli-Maurer, J., Beyeler, R., & Heussler, V. PLoS ONE. Link to article Project: menoBalance App: Use of AI methods to design a personalised chronic and infectious disease management medical device Comparing imputation approaches to handle systematically missing inputs in risk calculators.. 2025. Mühlemann, A., Stange, P. A., Faul, A. L., Lozza-Fiacco, S., Iskandar, R., Moraru, M., Theis, S., Stute, P., Spycher, B. D., & Ginsbourger, D. PLOS Digital Health. Link to article Project: Comparing the crisis resilience of national policy advisory systems during Covid-19 COVID-19 Vaccination Policy Compliance in Italy and Switzerland: The Mediating Effect of Trust in Scientists. 2025. Hornung, J. Political Studies. Link to article Policy advisory system quality under multilevel governance: the German COVID-19 experience. 2025. Hornung, J. and Trein, P. Policy and Society. Link to article Challenges to the legitamacy of scientific policy advice in three Swiss crises: can institutionalization shield against politicization? 2025. Schlaufer, C., Mavrot, C., Hornung, J. and Sager, F. Link to article Project: Early detection for early action: integrating multiple data sources for monitoring the SARS-CoV-2 epidemic in near real-time Individual and neighborhood based socioeconomic factors relevant for contact behaviour and epidemic control. 2025. Di Domenico, L., Reichmuth, M. L., & Althaus, C. L. Communications Medicine. Link to article Estimating Re and overdispersion in secondary cases from the size of identical sequence clusters of SARS-CoV-2. 2025. Hodcroft, E. B., Wohlfender, M. S., Neher, R. A., Riou, J., & Althaus, C. L. PLoS Computational Biology. Link to article Project: Liposomal nanotraps: non-antibiotic compounds for the treatment of enteropathogenic infections in humans and farm animals without contributing to antimicrobial resistance Liposomal Nanotraps Neutralize Listeria monocytogenes Toxins to Enhance Macrophage Viability and Antibacterial Capacity. 2025. Besançon, H., Polidori, M., Hostettler, A., Nizet, V., Oevermann, A., & Babiychuk, E. Infectious Microbes & Diseases. Link to article Project: Preparing the mainstream media for the next pandemic – understanding under which conditions conspiracy-related mainstream media content fosters conspiracy beliefs How do media contribute to the dissemination of conspiracy beliefs? A field study combining panel and web tracking at the outbreak of the COVID-19 pandemic. 2025. Adam, S., Rohrbach, T., Keller, F., Makhortykh, M., de León, E., Valli, C., Baghumyan, A., & Sydorova, M. Journal of Communication. Link to article
2024 Project: Deciphering the interplay between viral proteins and host cell mRNA metabolism Review: The art of hijacking: how Nsp1 impacts host gene expression during coronaviral infections. 2024. Karousis, E.D. Biochemical Society Transactions. Link to article Review: Coronavirus takeover of host cell translation and intracellular antiviral response: a molecular perspective. 2024. Karousis, E.D., Schubert, K., Ban, N. EMBO Journal. Link to article Project: Covid-19: Science, Narratives and Policy The devil-angel shift in times of crisis: How Swiss scientists used policy narratives during the COVID-19 pandemic. 2024. Ksinsik, J. European Policy Analysis. Link to article. Project: Ethical Considerations of the Relationship and Interactions between Science, Policy and the Media during the COVID-19 pandemic (ESPRIM) Swiss residents’ information behavior perceptions during the COVID-19 pandemic: A longitudinal qualitative study. 2024. Zimmermann, B. M. Social Science & Medicine. Link to article. Solidarity and reciprocity during the COVID-19 pandemic: a longitudinal qualitative interview study from Germany. 2024. Schönweitz, F. B., Zimmermann, B. M., Hangel, N., Fiske, A., McLennan, S., Sierawska, A., & Buyx, A. BMC Public Health. Link to article. Project: Interplay of infections and the microbiota on outcomes for host health Generation of a genetically double-attenuated Plasmodium berghei parasite that fully arrests growth during late liver stage development. 2024. Schmid, M., Beyeler, R., Caldelari, R., Rehmann, R., Heussler, V.T. and Roques, M. PLoS ONE. Link to article Project: Comparing the crisis resilience of national policy advisory systems during Covid-19 Taskforces: a cure for all ills? Policy advisory systems in times of polycrises. 2024. Mavrot, C., Schlaufer, C., Hornung, J., Sager, F., Hirschi, C. and Jaton, D. Policy Design and Practice. Link to article Media coverage of antimicrobial resistance in Germany and Switzerland: An interpretation through the multiple streams framework. 2024. Wyser, J., Puran, T., Hornung, J. and Fischer, M. Social Science and Medicine. Link to article Project: Early detection for early action: integrating multiple data sources for monitoring the SARS-CoV-2 epidemic in near real-time Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models. 2024. Bouman, J. A., Hauser, A. W., Grimm, S. L., Wohlfender, M. S., Bhatt, S., Semenova, E., Gelman, A., Althaus, C., & Riou, J. PLoS Computational Biology. Link to article Project: Preparedness for surveillance in school rooms in pandemic and epidemic situations: multiple measure approach to estimate transmission and interventions for Covid-19 and seasonal influenza Molecular detection of SARS-CoV-2 and other respiratory viruses in saliva and classroom air: a two winters tale. 2024. Banholzer N, Bittel P, Jent P, Furrer L, Zürcher K, Egger M, Hascher T, Fenner L. Clin Microbiol Infect. Link to article Airborne transmission risks of tuberculosis and COVID-19 in schools in South Africa, Switzerland, and Tanzania: Modeling of environmental data. 2024. Banholzer N, Schmutz R, Middelkoop K, Hella J, Egger M, Wood R, Fenner L PLOS Glob Public Health. Link to article Air Cleaners and Respiratory Infections in Schools: A Modeling Study Based on Epidemiologic, Environmental, and Molecular Data.2024. Banholzer N, Jent P, Bittel P, Zürcher K, Furrer L, Bertschinger S, Weingartner E, Ramette A, Egger M, Hascher T, Fenner L. Open Forum Infect Dis. Link to article Project: Divided pandemic society and Public Health. Polarization in the Covid-19 pandemic response in Switzerland Asymmetric affective polarization regarding COVID-19 vaccination in six European countries. 2024. Filsinger, M., & Freitag, M. Scientific Reports. Link to article Polarization and health-related behaviours and outcomes during the COVID-19 pandemic: a systematic review protocol. 2024. Ipekci A, Filsinger M, Buitrago-Garcia D, Betancourt, C, Frahsa A, Low N. F1000Research. Link to article Project: An integrative One Health network to monitor and characterize influenza A viruses circulating in the human and pig population A novel isothermal whole genome sequencing approach for Monkeypox Virus. 2024. Licheri, M., Licheri, M. F., Probst, L. M., Sägesser, C., Bittel, P., Suter-Riniker, F., & Dijkman, R. Scientific Reports. Link to article Multiplex PCR Approach for Rapid African Swine Fever Virus Genotyping. 2024. Licheri, M., Licheri, M. F., Mehinagic, K., Radulovic, E., Ruggli, N., & Dijkman, R. Viruses. Link to article
2023 Project: Deciphering the interplay between viral proteins and host cell mRNA metabolism Universal features of Nsp1-mediated translational shutdown by coronaviruses. 2023. Schubert, K., Karousis, E.D., Ban, I., Lapointe, C.P., Leibundgut, M., Bäumlin, E., Kummerant, E., Scaiola, A., Ziegelmüller, J., Puglisi, J.D., Mühlemann, O., Ban, N. Molecular Cell. Link to article. Project: Preparedness for surveillance in school rooms in pandemic and epidemic situations: multiple measure approach to estimate transmission and interventions for Covid-19 and seasonal influenza SARS-CoV-2 transmission with and without mask wearing or air cleaners in schools in Switzerland: A modeling study of epidemiological, environmental, and molecular data. 2023. Banholzer N, Zürcher K, Jent P, Bittel P, Furrer L, Egger M, Hascher T, Fenner L. PLoS Med. Link to article Project: Comparing the crisis resilience of national policy advisory systems during Covid-19 The non-use of evidence in the adoption of a sugar-sweetened beverage tax in OECD countries. 2023 Hornung, J., & Sager, F. European Journal of Public Health. Link to article
