GCB Annual Report 2025

Page 1/60 Annual Report GCB 2025Annual Report GCB 2025Faculty of MedicineFaculty of ScienceFaculties of Veterinary Medicine (Vetsuisse Faculty)Figure 1*. Fluttering valve design: Vortex development and breakdown over time visualized byisosurfaces of the λ2 criterion [18] colored in streamwise velocity component.K.-M. Bornemann** and D. Obrist, Transition to turbulence past bioprosthetic aortic valves,Physical Review Fluids, 10, 110504 (2025)*This paper is associated with a video that won a 2024 American Physical Society's Division of Fluid Dynamics (DFD) Gallery of Fluid Motion Award for work presented at the DFD Gallery of Fluid Motion. The original video is available online at the Gallery of Fluid Motion, https://doi.org/10.1103/APS.DFD.2024.GFM.V2560348.**Best Thesis Award winner, 2025, see page 46

Page 2/60 Annual Report GCB 2025Table of ContentsAnnual Report GCB 2025 11. Introduction 31.1 Letter from the President 32. Vision & Mission 42.1 GCB Offices, Mittelstrasse 43, 3012 Bern 53. Organization 63.1 Organization Chart 63.2 PhD & Expert Committee Organization 63.3 Mentor Guidelines 83.4 Training 93.5 PhD Program Structure 103.6 PhD, DDS & DVM Curriculum 103.7 MD,PhD Program & Curriculum 113.8 PhD Specializations 124. Courses & Seminars 164.1 Individual Study Program 164.2 Lectures, Tutorials, Book Clubs, Practicals 164.3 Transferable Skills Lectures, Courses, and Workshops 164.4 GCB Seminars, Summer School, and Retreats 174.5 International Summer School 2025, Institute of Pharmacology, University of Bern 194.6 Tumor Biology Annual Retreat 2025 205. GCB Academic Events 215.1 Annual Symposium 215.2 Graduations 255.3 Student Awards & Recognitions 486. Facts and Figures 546.1 Highlights | 2025 546.2 Highlights | Graduates2025 556.3 Five-Year Figures (2021-2025) 577. Digital Presence 587.1 Communication and Social Media 588. Acknowledgments 59

Page 3/60 Annual Report GCB 20251. Introduction1.1 Letter from the PresidentDear Colleagues, Partners and Friends,This year brought not only academic achievements but also meaningful collaborations across disciplines. Our students published groundbreaking research, secured competitive grants, and claimed numerous prizes through their work. We also continued to develop and expand professional development programs, ensuring our graduates are prepared for diverse career paths in academia, industry, and beyond.The year 2025 was particularly special, as the graduate school celebrated its 20th year anniversary. In recognition of that milestone, we held a special anniversary event during the annual Graduate School for Cellular and Biomedical Sciences (GCB) Symposium in June. We were inspired by the science and novel ideas shared with more than 400 registered participants, the majority of whom were PhD students, alongside supervisors, mentors, and representatives of the seven GCB PhD specializations. The day began with opening remarks from PD Dr. Monica Schaller, GCB Coordinator, followed by a welcome address from GCB President Prof. Sebastian Leidel, who reflected on past achievements and offered an optimistic outlook for the future. The opening session was further enriched by congratulatory words from Prof. Claudio Bassetti (Dean of the Faculty of Medicine), Prof. Jean-Louis Reymond (Dean of the Faculty of Sciences), and Prof. Gertraud Schüpbach (Dean of the Vetsuisse Faculty). Their recognition of the GCB’s accomplishments highlighted the significance of this milestone and set the tone for a day of imagination and celebration.None of these accomplishments would be possible without the dedication of our three jointly administering faculties (Medicine, Phil. Nat., Vetsuisse), staff, alumni, and partners. We are particularly grateful to the dedication and leadership provided by the PhD Steering Committee. All your commitment to mentorship, innovation, and excellence continues to shape the future of research and education at the GCB.As we look ahead, we remain committed to advancing knowledge, nurturing talent, and addressing the pressing challenges of our time. Together, we will continue to make our graduate school a place where curiosity thrives, and ideas transform the world.It’s been an exciting year. Now, I invite you to look more closely at the highlights, progress, and moments that made this year special in the pages that follow.With gratitude and optimism,Prof. Dr. med. Guido BeldiPresident, GCB PhD Committee

Page 4/60 Annual Report GCB 20252. Vision & MissionVision and Mission StatementThe GCB provides comprehensive, internationally competitive training in theory and practice of experimental research as well as in-depth specialist knowledge of the individually selected research area. It directs students towardsindependent scientific work and enables them to assumescientific responsibility.The GCB PhD program promotes doctoral programexcellence. The graduate school promotes high quality, teachingand training programs combined with rigorous, experimental, translational biomedical research. At the same time, it ensureshigh standards of integrity and encourages the students to work independently and responsibly while acquiring profound knowledge in selected research areas.• Deliver Excellence. Offer an excellent comprehensivegraduate course curriculum that educates students in broadand multidisciplinary areas including the most current biomedical research developments. The graduate schoolprovides opportunities for students to individually tailor their course curriculum to specific needs.• Quality and Integrity. Develop and maintain high quality graduate programs to impart knowledge, foster innovation, and drive creativity while ensuring excellence and integrityin training and research, using state-of-the-art methods in molecular life sciences, biomedical sciences, andbiomedical engineering.• Preparedness. Prepare graduates for professional careersand post-doctoral studies by steady presence and strongsupport from the graduate school across all touchpoints in the student life (including academic and professional), such as mentoring resources for professional career development and self-care that enhances experiences,mental and psychological health, and exposing thestudent to the social network, culture, and broader practicenorms and requirements associated with their selecteddiscipline.• Support and Develop. Provide programs that encourage students coming from other cultures to produce welltrained, skilled, and innovative graduates who are positioned to be successful leaders who will thencontribute productively whether here in Switzerland,intheir country of origin and on an international level, andwhether in academia, industry, government or nonprofit organizations.• Raise the recognition and visibility of the GCB to attractquality students, build networks and connections, and toserve as a conduit to agencies and organizations relevant toall students; prospective, current, or recently graduated.MISSIONVISION

Page 5/60 Annual Report GCB 20252.1 GCB Offices, Mittelstrasse 43, 3012 Bern

Page 6/60 Annual Report GCB 20253. Organization3.1 Organization Chart3.2 PhD & Expert Committee OrganizationThe Graduate School for Cellular and Biomedical Sciences (GCB) of the University of Bern, jointly administered by the Faculties of Medicine, Science and Vetsuisse, offers structured, experimental research training programs leading to the following degree titles: • PhD in Cell Biology• PhD in Biochemistry and Molecular Biology• PhD in Biomedical Sciences• PhD in Immunology• PhD in Neurosciences• PhD in Biomedical Engineering• PhD in Computational Biology • MD,PhD (Doctor of Medicine and Philosophy) • DVM,PhD (Doctor of Veterinary Medicine and Philosophy)• DDS,PhD (Doctor of Dentistry and Philosophy)The PhD program provides comprehensive, internationally competitive training in the theory and practice of experimental research as well as in-depth specialist knowledge of students' individually selected research areas. It directs students towards independent scientific work, enabling them to assume scientific responsibility.

Page 7/60 Annual Report GCB 2025Research training is available in the areas of biochemistry and molecular biology, biomedical engineering, biomedical sciences, cell biology, immunology, neuroscience, and epidemiology. GCB applicants possess a master’s degree or equivalent in life sciences or related areas; engineering, physics, or computer science; medicine, dentistry, or veterinary medicine.The GCB is supervised by the PhD Committee (executive committee), comprised of members of the Faculty of Medicine, the Faculty of Science, and the Vetsuisse Faculty Bern, as well as the Program Coordinator. Each faculty member acts as President, alternating every two years. GCB Expert CommitteesFive expert committees with competencies in• biological systems• biomedical engineering• biomedical sciences• cell biology• molecular biology and biochemistryare responsible for the admittance, guidance, and evaluation of the PhD candidates. Each research project is assigned to one of the GCB Expert Committees, with one of its members acting as mentor to the PhD candidate. The supervisor, mentor and student plan the individual training program of the PhD together. The GCB Organization Chart on the previous page lists the expert committee membership in 2025. 3.2.1 2025 Expert Committee Membership ChangesBiological SystemsBiomedical EngineeringBiomedical Sciences Cell Biology Molecular Biology & BiochemistryJoinedPascal Escher Benjamin IneichenAntje Knopf Martina RothenbühlerStefan WederGuido Beldi, Chair Biomedical Sciences, named President GCB PhD Committee, 2025 – 2027.

Page 8/60 Annual Report GCB 20253.3 Mentor GuidelinesGood supervision is central to the successful progress of the doctorate and integration into the scientific community. Advice and support must not only be provided by the persons who are responsible as doctoral supervisors. Good supervision also includes a network, which is offered within the framework of the graduate school, by experienced colleagues and by mentoring. Mentors are experienced GCB PhD supervisors from one of the jointly administering Faculties of Medicine, Science and Vetsuisse. General duties and responsibilities of the mentor:• The mentor is the link between the GCB and each student’s thesis committee and must therefore always be a member of one of the GCB expert committees. The mentor ensures that the GCB rules are observed. Thus, s/he must be acquainted with the most important rules of the GCB regulations, in particular the points which relate to course requirements (minimal ECTS) and examination regulations.• Each expert committee member should be prepared to serve as mentor for several PhD students.• Interview meetings of the GCB expert committees are conducted three times a year to evaluate prospective PhD candidates, often more than one session per application date. The mentor attends the meetings whenever possible.• Following the interview, each PhD student is assigned an individual mentor.• The mentor does not require specific expertise in the research project but monitors the progress of the work in relation to the submitted research plan and intervenes if problems arise.• The mentor is the primary contact for the PhD student and the supervisor if any conflicts arise between them.Five main responsibilities comprise the GCB mentor role throughout a PhD project:1. leads the mentor meeting 2. evaluates the annual progress reports 3. chairs the mid-term evaluation4. chairs the thesis defense 5. mediates if required in case of conflict

Page 9/60 Annual Report GCB 20253.4 TrainingThe GCB offers structured training in experimental research in the fields of biochemistry, cell and molecular biology, immunology, biomedical sciences, epidemiology, neuroscience, and biomedical engineering, leading to a PhD, MD,PhD, DDS,PhD or DVM,PhD degree. The thesis projects are carried out at laboratories of the three participating faculties (Faculty of Medicine, Faculty of Science, and Vetsuisse Faculties, Bern, and Zurich) or at affiliated institutions. In 2025, these included:• Agroscope, Veterinary Physiology, Vetsuisse Faculty• AO Research Institute, Davos• Bern University of Applied Sciences• Biberach University of Applied Sciences• Biotechnology Institute Thurgau (BITg)• Centre for Fish and Wildlife Health (FIWI)• Center for Translational Medicine and Biomedical Entrepreneurship sitem• Centre for Infectious Disease Research in Zambia • CK-Care AG Davos• Institute for Research in Biomedicine (IRB), Bellinzona• EMPA• Haute Ecole Arc Ingénierie• HSLU Institute of Medical Engineering• Interfaculty Bioinformatics Unit/Laboratory Spiez• IVI Mittelhäusern• IRB- Institute of Research in Biomedicine• Kantonsspital Aarau• Kantonsspital St. Gallen• Laboratory for Artificial Intelligence and Translational Theranostics (AITT)• Lucerne University of Applied Sciences and Arts, Institute of Electrical Engineering • Makerere University• RMS Foundation• Schweizer Paraplegiker Zentrum, Radiologie• Swiss Institute of Equine Medicine, Bern• Veterinary Public Health Institute (VPH), Liebefeld• Zahn Medizinische Kliniken - Department of Periodontology

Page 10/60 Annual Report GCB 20253.5 PhD Program StructureEach PhD candidate is supervised by a thesis committee consisting of supervisor, co-advisor, and member of the appropriate GCB expert committee, the mentor. The roles are specified as follows:Supervisor. Hires the student and is responsible for the research project, adequate supervision, the laboratory infrastructure, and the salary of the candidate.Co-advisor. Should not be affiliated with the same institute as the supervisor but should be an expert in the research area of the thesis project. Meets with the candidate at least twice annually to discuss and assess progress of the thesis work, as well as to advise and support the candidate.Mentor. Decides on the individual, tailor-made training program together with the candidate and the supervisor, considering the candidate’s previous education and relevance to the planned research work.External Co-referee. Toward the end of the PhD studies, an additional expert is added to the team, to promote independent evaluation of the thesis and oral defense. No common publication with the supervisor and/or PhD candidate for the last 5 years is a stringent qualification criterion.3.6 PhD, DDS & DVM CurriculumI Earn a minimum 6.0 ECTS of scientifically oriented courses, of which at least 3.0 ECTS must be lecture courses or book clubs which include a graded examination. Exams must be passed after a maximum of two attempts, as regulated by the Promotion Regulations, Art. 92 and Art. 191).II Participate in Scientific Integrity lecture.Annual Progress Reports.III Pass a mid-term evaluation during the 2nd year – students present their work in a scientific seminar in the presence of their PhD thesis committee, to demonstrate in-depth knowledge of their research field.IV Attend and participate in the annual GCB Symposium starting with the 2nd year of PhD studies.V After three, maximum four years, submit written thesis and successfully defend the thesis orally.

Page 11/60 Annual Report GCB 20253.7 MD,PhD Program & CurriculumThe MD-PhD Program thus consists of basic training (comprising 25ECTS) and the additional mandatory course work (6 ECTS) in subjects which are suitable for preparing them for their specific research project (cell biology, biochemistry, molecular biology, immunology, neurobiology, tumor biology, etc.), and for the PhD thesis. Comprehensive guidelines are available on the GCB website.I Earn a minimum 25 ECTS, some of which may be obtained through previous laboratory work (MD thesis or other, maximum 10 ECTS). Generally, the ECTS can be obtained by participating in approved, project-related, and interdisciplinary courses, workshops, seminars, and lectures. Course work for 6 ECTS (3 ECTS of which come from a course with a graded examination) tailored to the research project in addition to the basic 25 ECTS is mandatory (total 31 ECTS).II At least 3.0 ECTS must be earned from lecture courses or book clubs which include a graded examination. Exams must be passed after a maximum of two attempts, as regulated by the Promotion regulations, Art. 92 and Art. 191).III Participate in the course Scientific Integrity course. Annual Progress Reports.IV Pass a mid-term evaluation during the 2nd year – students present their work in a scientific seminar in the presence of their PhD thesis committee, to demonstrate in-depth knowledge of their research field.V Attend and participate in the annual GCB Symposium beginning with the 2nd year of PhD studies.VI After three, maximum four years, submit written thesis and successfully defend the thesis orally. A fundamental requirement includes in-depth education in natural science subjects. This basic training consisting of course work of 25 ECTS may be carried out either in parallel to the medical studies during the third to sixth year (Track I), or during the research work for the PhD thesis (Track II). Track I students receive personal mentoring by experienced researchers.

Page 12/60 Annual Report GCB 20253.7.1 MD-PhD FellowshipsThe Swiss Academy of Medical Sciences (SAMS) announced in 2023 the fellowship program would end in 2024. In 2025, SAMS established new partnerships with foundations and faculties to support their program. The program will continue in 2026, with a call for applications just started, deadline for submission is May 15, 2026 on their website. David Studer Emanuel, from the Insel Hospital, University Hospital Bern, was granted CHF 148’321. His grant is funded by Monique Dornonville de la Cour Foundation.3.8 PhD SpecializationsWithin the framework of the GCB PhD Program, seven PhD specialization programs are offered. Participants acquire ECTS in the specialization which will be listed as a separate achievement on the diploma supplement, thus complementing their PhD degree.Specialization Distribution 2025

Page 13/60 Annual Report GCB 20253.8.1 Cell MigrationThe PhD Program Cell Migration started as an SNF-supported ProDoc program on October 1st, 2011. It has brought together a growing group of highly innovative and successful Swiss research groups in the field of cell migration in morphogenesis, immunosurveillance, inflammation and cancer. The participating institutions and their principal investigators bring together complementary scientific expertise and methodological skillsets in the field of cell migration that permit for embedding a cutting-edge Swiss training program on Cell Migration for highly qualified and motivated PhD and MD-PhD students in the fields of biology, biochemistry, (molecular) human and veterinary medicine, immunology, pharmaceutical sciences, chemistry, physics, bioinformatics and mathematics with a focus on life sciences.More information on the Cell Migration Website.3.8.2 Cutting Edge Microscopy (CEM)The main aim of the CEM program is to provide an interdisciplinary training program to PhD students to become first-class experts in biological imaging. Here, the unique and interdisciplinary framework established by the Microscopy Imaging Center (MIC) provides the necessary infrastructure and expert knowledge. The profile of the PhDs at the end of their training is that of a life science researcher with a deep insight into advanced microscopy and image analysis and with the necessary know-how to develop automated image analysis protocols. By providing this complementary training in different disciplines, the Cutting-EdgeMicroscopy PhD program educates young researchers with the ability to bring innovative approaches to academia and industry, closing an exciting knowledge gap amongst the life science experts in advanced microscopy.More information on the CEM website.3.8.3 Stem Cells and Regenerative Medicine (SCRM)SCRM launched in August 2018, is jointly offered by the GCB and the Platform for Stem Cells in Regenerative Medicine (SCRM). The program aims at fostering a new and innovative multidisciplinary approach to unravel the communication network of cells within the tissue and throughout the body during tissue regeneration.More information on the SCRM website.

Page 14/60 Annual Report GCB 20253.8.4 Tumor BiologyThe Tumor Biology curriculum is embedded in the Graduate School for Cellular and Biomedical Sciences of the University of Bern (GCB) and benefits from the existing Berner Cancer Research Cluster (BCRC) network. PhD students registered to the program will benefit from: basic knowledge in molecular and cell biology, as well as advanced cancer research methods and concepts from the 20 cancer research groups currently collaborating in BCRC activities. These cancer research groups are part of 8 different Departments and Institutes at the University of Bern (DBMR, Institute of Pharmacology, Medical Oncology, Institute of Tissue Medicine and Pathology, Institute of Anatomy, Vetsuisse, TKI, and the Department of Nuclear Medicine).From 2024 on, the BCRC is named “Cancer Research Network Bern (CRNB)” and organizationally embedded into the University Cancer Center Inselspital (UCI). More information can be found on the GCB PhD Specializations website page.3.8.5 Cardiovascular Research PhD ProgramThe Cardiovascular Research PhD Program will offer PhD or MD-PhD students the opportunity to receive indepth cardiovascular education and to complement their PhD degree with additional coursework in Cardiovascular Research. As cardiovascular diseases are the leading cause of death globally, a greater understanding of cardiovascular physiology and pathophysiology is of utmost importance. Consequently, several teams of the University of Bern and of the Inselspital, Bern University Hospital are actively involved in research concerning the function and development of the heart, arteries, and veins, as well as the mechanisms involved, in healthy and diseased states. This research ranges from fundamental science to pre-clinical and clinical studies and relies on a multitude of different experimental models. To promote cardiovascular research teams in Bern as leaders in cardiovascular (patho)physiology and in the development of approaches to reduce disease burden, the Cardiovascular Research Cluster (CVRC) Bern was established in 2015 for all UniBE and Inselspital members with an interest in cardiovascular research. One of the CVRC’s aims is to enrich the training environment of junior researchers. Another goal of the CVRC is to promote interactions and collaborations among clinical and fundamental cardiovascular research, whichwill be addressed with the development of this dynamic PhD Specialization option by incorporating students from the MD,PhD program. Cardiovascular PhD Program.

Page 15/60 Annual Report GCB 20253.8.6 Neuroscience PhD ProgramThe Neuroscience PhD specialization program supports training for GCB doctoral students in neuroscience during their doctorate. It includes a basic training in neurophysiology, with an optional neuro-anatomy course, and provides an up-to-date teaching in current areas of neuroscience research and techniques through the BENEFRI Neuroscience Workshop and the BENEFRI Hands-on Workshop, respectively. The BENEFRI Neuroscience program is integrated into the course offered by both the Graduate Schools for Health Science (GHS) and Graduate School for Cellular and Biomedical Sciences (GCB) including the BENEFRI program between the University of Bern and the University of Fribourg. The theoretical and practical teaching are organized in the Universities of Bern and Fribourg and include external international-standing lecturers from Swiss or European academic institutions. GCB students who apply will be granted admission at the request of the doctoral student by the Program Committee of the Specialized Neuroscience Program consisting of two representatives from the Universities of Bern and Fribourg without any additional evaluation or selection of the doctoral students or their projects. The program is open to students with background in Neuroscience including Neurology, Psychiatry, Physiology, Anatomy, Biology, Neuropsychology.More information can be found on the BENEFRI website at the University of Bern.3.8.7 Precision MedicinePrecision Medicine is a new paradigm. It incorporates individual characteristics in the treatment of patients, such as genetic predisposition, environmental factors, and lifestyle – therapies will be “tailored” to individuals to allow measurable health improvements and to avoid adverse effects. The PhD Specialization in Precision Medicine was launched in 2024. It is a cutting-edge training program on the subject, organized in a close collaboration between the Graduate School for Cellular and Biomedical Sciences (GCB) and the Bern Center for Precision Medicine (BCPM). For more information, check out the Bern Center for Precision Medicine website.

Page 16/60 Annual Report GCB 20254. Courses & Seminars4.1 Individual Study ProgramThe individual education and training program assigned to each PhD candidate considers the student's previous training and relevance to their research work. PhD candidates may attend courses at the University of Bern or external courses and summer schools offered by other recognized institutions. External courses for the PhD students are subject to their mentor's agreement. GCB teaching events are administered using the University of Bern Core Teaching System (CTS/KSL). Approved courses that have been tracked since 2020 included 540 Lectures, Tutorials, and Book Clubs. Of those, 319 (59%) were offered by the University of Bern institutes, 41 (8%) took place at ETH Zürich (Eidgenössische Technische Hochschule Zürich), 14 (3%) at EPFL (École Polytechnique Fédéral de Lausanne), 13 (2%) Swiss Bioinformatics Institute (SIB), 14(3%) University of Zurich, and the remaining courses were from other institutes. These courses* are sponsored by the GCB.4.2 Lectures, Tutorials, Book Clubs, PracticalsPopular Lectures, Tutorials, and Book Clubs• Immunology Tutorial* (9-10 senior scientists)• Cell Biology* («Happy Cell») Tutorial, (9-10 senior scientists)• Principles in Transgenic Mouse Technology(C. Benarafa, U. Deutsch, & P. Krebs)• Stem Cells & Regenerative Medicine (V. Enzmann and others)• Antibiotic-Resistant Bacteria and One Health: From the Plate to the Bedside (A. Endimiani and others)• Topics in Tumor Biology (D. Stroka, M. P. Tschan)• Lecture Course: International PhD Program in Immunology, Cell Biology and Biochemistry(S. Monticelli, IRB Bellinzona)• Vascular Cell Biology* (Britta Engelhardt)• Cell Migration* (Britta Engelhardt)• Introduction to R (D. Stroka, D. SanchezTaltavull)• DNA Sequencing and Variant Analysis: Basics of Sanger and Next Generation group laboratory (V. Jagannathan, T. Leeb)• Concepts and measures of Animal Welfare, M. Toscano, H. Würbel• Book Clubs, Journal Clubs and Seminars(Institute of Social and Preventive Medicine ISPM)4.3 Transferable Skills Lectures, Courses, and Workshops• Scientific Integrity (T. Ochsenreiter)• Scientific Communications for PhD Students, (S. Longnus)• Presenting with Confidence*, (D. Levine, C. Winfield)• Effective Grant-Writing for Young Scientists, (M. Toscano, J. Bailoo)• Communicating Science - Scientific Writing Course, Inselspital

Page 17/60 Annual Report GCB 20254.4 GCB Seminars, Summer School, and Retreats4.4.1 PhD Specialization in Cardiovascular Research: Swiss-wide Cardiovascular Student Retreat 2025Photo 1Cardiovascular Research Retreat, group photoThe second edition of the Swiss-wide Cardiovascular Student Retreat once again was a successful meeting. It continues to expand to additional Swiss universities and doctoral programs, and our aim remains unchanged: to bring together early career investigators in the field of cardiovascular research to foster exchanges and symbioses. 38 students from 7 Swiss universities gathered on November 14/15, 2025, to take part in the Swiss-wide Cardiovascular Student Retreat in Murten/ Morat, canton of Fribourg. PhD and MD-PhD students presented their research in the form of flash and poster presentations. The meeting was complemented by two keynote lectures given by Prof. Burkhard Ludewig, head of the Medical Research Center at the Cantonal Hospital St. Gallen, and head of the Translational Cardioimmunology Unit at the University Hospital Zurich, and by Prof. Camilla Schinner, Assistant Professor at Hannover Medical School (MHH), Assistant Professor at the University of Bern and at the University Medical Center Hamburg-Eppendorf (UKE).The best student presentations were chosen by the students (audience prize). Congratulations to the winners: 1st Prize – Marina Vannucci (Department of Physiology, University of Bern), 2nd Prize – Michael Winhelbauer (Department of Health Sciences and Technology D-HEST, University of Zurich). Likewise, the best posters received an audience award. Congratulations to the winners: 1st Prize – Lisa Teoldi (Department of Biomedical Sciences, University of Lausanne), 2nd Prize – Adrita Chanda (Department for Biomedical Research, University of Bern).We would like to express our sincere gratitude to all organizing universities / doctoral programs, the University of Bern (PhD Specialization Program in Cardiovascular Research), University of Lausanne (Cardiovascular and Metabolism PhD Program of the Faculty of Biology and Medicine (FBM) and the University Hospital (CHUV)), Università della Svizzera italiana (Cardiovascular / Human Cardiovascular Sciences PhD Program), and University of Zurich (Center for Translational and Experimental Cardiology (CTEC)). Special thanks go to the host of this year’s meeting: the University of Lausanne, for making this successful event a reality.In addition, we would like to express our gratitude to our sponsors for their generous support: FUJIFILM VisualSonics, Olink, as well as the University of Bern, for their financial support of the PhD Program in Cardiovascular Research in Bern (Förderprogramm “Doktoratsprogramme/Graduate Schools Universität Bern 2021-2026”). Finally – a big thank-you to all participating students who made this retreat an engaging and inspirational event!

Page 18/60 Annual Report GCB 20254.4.2 12th SCRM PhD Student RetreatPhoto 2 SCRM Student Retreat group photoAs per tradition, the beautiful location of Gurten Park in Bern hosted our 12th annual PhD students retreat onthe 9th of September 2025. We were very happy to have Prof. Dr. Andrea Lunardi, head of the ArmeniseHarvard Laboratory of Cancer Biology and Genetics at the University of Trento (Italy), as our academicmentor, and Sandra Kugelmeier, Co-founder and Member of the BoD of Kugelmeiers Ltd. and OnconiX AG, as our industry mentor. Exceptionally for this year we hosted Dr. Markus Mühlemann, Co-founder ofOnconiX AG and senior scientist at Kugelmeiers Ltd., as a second industry mentor.This year’s event again drew strong participation, with 21 attendees in total, 11 of whom shared their work in presentations. Each talk gave rise to engaging discussions that encouraged contributions from everyone and fostered a constructive exchange of ideas. Beyond the formal sessions, the coffee breaks, lunch, and the closing Apéro offered further opportunities for conversation and networking in a more informal setting, both among students and with mentors and members of the SCRM committee. We are pleased with how the event unfolded and look forward to continuing this tradition in the coming years.We would like to express our sincere gratitude to our mentors for their valuable contributions during theretreat. This year, our two industry mentors, Sandra Kugelmeier and Dr. Markus Mühlemann, shared personal insights into their professional journeys, offering both practical perspectives on founding and growing a startup as well as broader reflections on working in the private sector. Their openness and advice sparked many thoughtful conversations with the students. Our academic mentor, Prof. Dr. Andrea Lunardi, concluded the meeting with a memorable talk, recounting his own path to becoming a professor and the challenges and opportunities he encountered along the way. We also warmly thank Prof. Eliane Müller, Prof. Volker Enzman, Prof. Benjamin Gantenbein and Prof. Andreina Schöberlein, whose participation in the keynote session and the Apéro enriched the discussions and provided valuable guidance.We are very grateful to the Fund for the Promotion of Early Career Researchers, the Stem Cell Research and Regenerative Medicine Platform and to the GCB for their financial support, which made our retreat possible.Just as important, we would like to thank all the students who took part with such enthusiasm and openness. Their active involvement, both during the presentations and in the informal moments, created the engaging and supportive atmosphere that made the event so enjoyable.We are excited to welcome new participants to our next retreat on the 8th of September 2026 and hope many students will join us again.The Organizing Committee 2025Andrea Brunello, Jaap-Jan Roukens, Leon Schlagenhof and Sara Dori

Page 19/60 Annual Report GCB 20254.5 International Summer School 2025, Institute of Pharmacology, University of BernPhoto 3 International Summer School 2025, Group photoThe International Summer School 2025 took place from Wednesday, 20 August to Friday, 22 August, in the beautiful setting of Bönigen, directly on the shores of Lake Brienz. The three-day event gathered an international group of researchers working in pharmacology and related scientific areas.The program featured keynote lectures from four invited speakers, alongside presentations by thirteen young researchers and twelve scientific posters. These sessions sparked insightful discussions and fostered valuable exchanges—both during the formal program and in informal settings.Participants, especially students and early-career researchers, had the opportunity to receive feedback on their work and to gain perspective on how experienced scientists approach project design and development. One of the key aims of the summer school is to support long-term scientific collaboration between participating institutions and researchers.The International Summer School is an accredited course within the Graduate School for Cellular and Biomedical Sciences at the University of Bern, awarding 1.0 ECTS.As in previous years, the 2025 edition proved to be a great success, offering a dynamic and engaging environment for high-level scientific exchange on current advances in pharmacology and its interfacing disciplines.

Page 20/60 Annual Report GCB 20254.6 Tumor Biology Annual Retreat 2025Photo 4 Tumor Biology retreat participantsPhoto 5 Tumor Biology retreat participantsPhoto 6 L to R: Prof. Carsten Riether, PD Dr. Thomas Marti, PD Dr. Michaela Medová, Prof. Deborah Stroka, Prof. Mario Tschan, Prof. Aurel PerrenAt the annual network meeting on 5 June 2025, around 120 researchers from the Cancer Research Network Bern (CRNB) gathered on the Gurten for the annual scientific exchange. The scientific program provided a comprehensive overview of basic, translational and clinical cancer research by 12 oral and 38 poster presentations from PhD- and MD/PhD-students as well as postdocs. This broad range from basic to clinical research was also highlighted by the following three invited keynote speakers: Prof. Dr. phil. nat. Sylviane Muller, Director of the Strasbourg Institute for Drug Development and Discovery (IMS), gave an interesting insight into the challenges and excitement of basic scientific questions and its transformation into applied targets in immune diseases. Prof. Dr. med. & Dr. phil. nat. Sacha Rothschild, Medical Director Tumor Center & Chief Physician Oncology & Hemotology at the Cantonal Hospital Baden (KSB), who took the audience from the diagnosis to the therapy of lung cancer as a role model for contemporary oncology. Dr. phil. nat. Fréderic Saltel, Director Bordeaux Institute of Oncology (BRIC), Université de Bordeaux and Coordinator of the “ENLIGHT Cancer Network” introduced the collaborative research exchange by the ten European ENLIGHT-universities that form an alliance for students, teachers and researchers. The various research projects were actively discussed and ideas were exchanged, while further intensifying and expanding the network. Two researchers received awards for the best talk and the best poster. The awards were presented by Prof. Deborah Stroka, member of the Steering Committee of the Cancer Research Network Bern.Another highlight was the contribution by Ms. Riccarda Melchior. In her presentation ‘Charity Concert for Cancer Research in Memory of Simone Rido’, she explained how relatives and friends of persons affected by cancer can take initiative and support research groups by privately collecting donations for cancer research. The event demonstrates the strong commitment of the University Hospital Inselspital and the University of Bern to basic, translational and clinical cancer research in order to serve patients with state-of-the-art diagnostics and therapies. Research drives progress by enabling people to share their findings, learn from one another and collaboratively develop new solutions. Especially in complex areas such as cancer research, collaborations between experts from different disciplines are crucial to make progress.This is precisely where the Cancer Research Network Bern (CRNB) provides support. On the one hand, national and international funding organizations are increasingly supporting longer-term projects with larger, interdisciplinary teams. On the other, collaborations often accelerate research results to be translated into clinical routine, which ultimately benefits patients.The year 2025 marked a new milestone. The CRNB Annual Retreat 2025 was held for the first time formally under the auspices of the University Comprehensive Cancer Centre Inselspital (UCI), which was officially designated as Comprehensive Cancer Centre – a Centre of Excellence in oncology – in November 2024.Text: Dr. phil. nat. Nicole von Allmen, Chief Operating Officer Cancer Research Network Bern (CRNB)Photos: Janosch Abel, photographer Inselspital

Page 21/60 Annual Report GCB 20255. GCB Academic Events5.1 Annual SymposiumPhoto 7 GCB Annual Symposium 2025, Poster Session, PhD Committee member and mentor, Prof. Dr. Dominik Obrist discussing with PhD students.As part of the doctoral training, the GCB organizes an annual academic research symposium for its PhD candidates and their thesis committees. From the second year of study onwards, doctoral candidates are offered the opportunity to present their research projects in the form of brief lectures (posters - many of them combined with an additional Poster Flash presentation). The presentations highlight the wide range of research projects, as well as demonstrating the candidates’ high level of competence and in-depth knowledge in the fields of cellular and biomedical sciences, and biomedical engineering. The talks are thematically grouped according to the five competency areas (GCB expert committees) to which the research projects belong. The symposium also offers opportunities for GCB candidates, as well as for their supervisors and mentors to engage in mutually rewarding and highly stimulating discussions. It is for this reason, mandatory participation is required from the second program year, providing each student with at least two chances to present their research in this setting. Additionally, the symposium facilitates opportunities for active networking among peers and senior researchers. The GCB Symposium 2025 was again held in person on June 26, at the Uni von Roll. Presentations included: 40 talks, 138 blitz talks with posters, and 91 posters without talks. The PhD Specialization poster booth expanded to include in addition to the Cutting-Edge Microscopy, Stem Cells and Regenerative Medicine, and Cell Migration programs, Cardiovascular, Neuroscience, and Precision Medicine. The Microscopy Imaging Center also attended with a poster. Again in 2025, the PhD Committee generously awarded three best thesis prizes for the 2024 theses.

Page 22/60 Annual Report GCB 20255.1.1 Special Session – Anniversary Event2025 was a special year for the Graduate School of Cellular and Biomedical Sciences (GCB) as we celebratedits 20th anniversary. The GCB officially opened on September 1, 2005. Since then, over 1,400 doctoral students from three faculties (Medicine, Science, and Veterinary Medicine) working in various fields of cellular and biomedical sciences have obtained an interfaculty doctorate. The GCB PhD program provides comprehensive, internationally competitive training in theory and practice of experimental research, directingthe students towards independent scientific work and enabling them to assume scientific responsibility. The program is structured around the PhD student at the center, supported by a committee consisting of asupervisor, a co-advisor, and a mentor. In the first GCB annual report published in 2007, then GCB president Prof. Daniel Schümperli stated “the expected final size of the GCB will be about 400 students.” By the end of 2024, the GCB boasted 549 registered students, clearly exceeding the 2007 predictions. The graduate school continues to grow, adding an average of 150 new students each year while approximately 120 students graduate annually. While 17 mentors supported the initial 45 students in 2005, this number has grown to 122 for 549 students. To mark the 20-year milestone, we organized a special program that took place during this year’s annual research symposium on June 26, 2025. We enjoyed sharing science and novel ideas with well over 400 registered participants, the majority being PhD students, together with supervisors, mentors and representatives of the seven GCB PhD specializations. PD Dr. Monica Schaller, GCB Coordinator kicked off the day with opening remarks. GCB president Prof. Sebastian Leidel followed with a welcome address, a brief look back and optimistic view of the GCB´s future. The opening session was completed with Prof. Claudio Bassetti (Dean of the Faculty of Medicine), Prof. Jean-Louis Reymond (Dean of the Faculty of Sciences) and Prof. Gertraud Schüpbach (Dean of the Vetsuisse Faculty) each sharing congratulatory words and recognition of the GCB achievements to commemorate our 20th anniversary.The symposium program continued with 10 parallel scientific sessions distributed amongst each of the fiveGCB expert committees where PhD students shared their projects with their peers. The keynote lecture waspresented by Prof. Dr. Alex Schier, Director of the Biozentrum, University of Basel, who led us on a fantastic journey through different studies in developmental biology.The day included a round table session, \"Fostering the Next Generation of PhDs”, moderated by Prof. Torsten Ochsenreiter (Institute of Cell Biology, University of Bern). The participants included Prof. Alexander Eggel(Department of BioMedical Research, University of Bern), Prof. Michaela Medová (Department for BioMedical Research, University of Bern), Dr. Simone Rufener (State Secretariat for Education, Research and Innovation (SBFI)) and Dr. Giuseppe Angelo Zito (Advanced Imaging Research (AIR), group Swiss Paraplegic Research), all of them former PhD students that have followed different career paths.The session began with comments from Prof. Dr. em. Ernst Peterhans, former President of the GCB, and PD Dr. Marlene Wolf, first coordinator of the GCB. They shared GCB history and their experiences, as well as giving advice for the future. The roundtable conversation addressed critical questions: What should you focus on during your PhDstudies? What did you learn during your PhD studies that you can apply to the next step in your career? How did the GCB help you during your PhD studies? The participants all emphasized that a PhD program should focus not only on conducting strong research. They also agreed that developing analytical thinking, critical reasoning, and strong writing skills is equally important, as these are highly transferable skills that can be applied to a wide range of career paths.One key take-home message from Prof. Peterhans stands out: “As you prepare to take the next step in your career as a postdoc, look for a group leader who does innovative research in a top international institution. This will not only expose you to a vibrant scientific atmosphere and stimulate your own creativity. Often, such scientific contacts evolve to lasting friendships that enrich your life in other ways.” At the GCB, the present is deeply rooted in a flexible, yet solid framework established 20 years ago. Today, the GCB proudly supportsover 500 PhD students. We are excited about the future and confident that with the GCB’s structure and dynamic community, it will be bright and promising. We thank all GCB mentors and supervisors, past and

Page 23/60 Annual Report GCB 2025present. None of what the GCB has or will achieve would be possible without their dedication. Above all, we are grateful for and acknowledge the perseverance of our PhD students. We look forward to continuing our mission of supporting young scientists and fostering excellence in cellular and biomedical research -advancing science one PhD at a time.5.1.2 GCB in uniAKTUELLMonica Schaller, coordinator of the GCB program, Karoline-Marie Bornemann and Lucilla Giammarino, two of the three winners of the best thesis award 2024, were interviewed for uniAKTEULL.20 Jahre GCB - Promoting young talent in biomedicine: read the full article (in German) here.

Page 24/60 Annual Report GCB 20255.1.3 Keynote AddressPhoto 8 Prof. Dr. Alex SchierProfessor Dr. Alex SchierDepartment of Biosystems Science and Engineering, ETH Zurich, Basel, SwitzerlandAlex Schier has been Professor and Director of the Biozentrum at the University of Basel, Switzerland since 2018. He started his lab in 1996 at the Skirball Institute of the New York University School of Medicine and joined Harvard University in 2005, where he was the Leo Erikson Life Sciences Professor and Chair of the Department of Molecular and Cellular Biology. Schier is a pioneer in developmental biology. He defined the first morphogen-inhibitor pair for Turing-like pattern formation, discovered the microRNA-induced degradation of maternal mRNAs and dissected the role and regulation of Nodal signaling. He and his collaborators developed creative technologies to establish zebrafish as a model system, including the establishment of large-scale genetic screens and the development of behavioral profiling and whole-brain imaging to analyze drugs and mutants. Schier and his collaborators pioneered methods for understanding development at global scales. Through genomic barcode editing technology, single-cell sequencing and spatial transcriptomics they reconstructed the lineage relationships, spatial location, gene expression and differentiation trajectories of thousands of cells. Schier has been recognized by NIH MERIT and PIONEER awards, an ERC Advanced Grant, and election to EMBO,Academia Europaea, the American Association for the Advancement of Science, and the US National Academy of Sciences. His research was featured as Science Breakthrough of the Year 2018.Schier’s impact is also evidenced by the success of his many collaborators and his trainees. 20 of 24 graduate students in the Schier lab went on to postdoctoral research positions, and 33 of 40 postdocs started their own labs at leading institutions, including Yale, Princeton, Caltech, and University of Cambridge.Abstract Title: Global views of developmentAbstract: The interplay between transcription factors and chromatin accessibility regulates spatiotemporal gene expression and cell type diversification. However, comprehensive atlases and gene regulatory networks underlying these processes have remained elusive. I will present our recent efforts in single-cell multiomics and spatial transcriptomics to address this challenge. We generated a single-cell multiomics atlas of RNA expression and chromatin accessibility during zebrafish embryogenesis and developed DeepDanio, a deep learning model to dissect cis-regulatory interactions. In parallel, we developed a whole-embryo imaging platform to quantify the expression of hundreds of genes at subcellular resolution. Integration with the singlecell multiomics data generated an atlas detailing the expression of ~25,000 genes and the accessibility of ~300,00 chromatin regions, as well as the online browser MERFISHEYES. I will discuss how exploration of the atlas and the gene regulatory network identified instant differentiation as a novel mode of cell differentiation and how changes in gene expression generate sharp boundaries during gastrulation.

Page 25/60 Annual Report GCB 20255.2 GraduationsCongratulations to the 135 graduates in 2025.5.2.1 Thesis Defense PhotosPhoto 9 Vanessa Vallesi thesis defense, September Photo 10 Vanessa Vallesi thesis team1, 2025Photos 11, 13, 14 Melanie Scalise, thesis defense January 9, 2026

Page 26/60 Annual Report GCB 2025Photo 15 Asli Adak, thesis defense December 10, 2025Photo 16 Aurelia Bucciarelli, thesis defense March 19, 2025Photo 17 Christina Wapp, thesis defense March 18, 2025Photo 18 Fei Wu, thesis defense March 28, 2025

Page 27/60 Annual Report GCB 2025Photo 19 Elias Baumann, thesis defense July 17, 2025Photo 20 Huixiang Ge, thesis defense May 28, 2025Photo 21Karin Farah Schmid, thesis defense October 22, 2025

Page 28/60 Annual Report GCB 2025Photo 22 Lena Carolina Bruhin, thesis defense November 24, 2025Photo 23 Lorenzo Ferrari, thesis defense March 24, 2025Photo 24 Mauro Bruno Gwerder, thesis defense September 15, 2025Photo 25 Micaela Borsa, thesis defense March 18, 2025

Page 29/60 Annual Report GCB 2025Photo 26 Milica Bulatović, thesis defense September 5, 2025 Photo 27 Pedro Pereira Amado, thesis defenseOctober 29, 2025Photo 28 Pelin Kasap, thesis defense April 28, 2025Photo 29 Rina Mehmeti, thesis defense June 20, 2025

Page 30/60 Annual Report GCB 20255.2.2 Medical Faculty Diploma Award Ceremony March 2026 (2025 Graduates)Photo 30 (top) PD Dr Monica Schaller, GCB Coordinator, Medical Faculty Graduation Ceremony, March 7, 2026Photo 31 (bottom) Professor Dr. med Claudio Bassetti, Dean, Medical Faculty Graduation Ceremony, March 7, 2026

Page 31/60 Annual Report GCB 2025Photo 32 GCB PhD graduates, Medical Faculty Graduation Ceremony, March 7, 2026Photo 33 GCB PhD graduates, Medical Faculty Graduation Ceremony, March 7, 2026

Page 32/60 Annual Report GCB 2025Photo 34 GCB PhD graduates, Medical Faculty Graduation Ceremony, March 7, 2026Photo 35 GCB PhD graduates, Medical Faculty Graduation Ceremony, March 7, 2026

Page 33/60 Annual Report GCB 20255.2.3 GraduatesAAsli Adak, PhD in Cell Biology (December 10)Institute of Anatomy (Prof. Dr. Nadia Isabel Mercader Huber)“Investigating the Influence of Zebrafish Heart Regeneration-Associated Secreted Factors on Human iPSCDerived Cardiomyocytes and Fibroblasts”Nicolò Alerni, PhD in Biomedical Sciences (January 15)Department of Physiology (Prof. Dr. Katja Elisabeth Odening, )“Electro-mechanical and mechano-electrical interactions in Long QT, Short QT and Wild-Type rabbits”Bettina Katharina Amberg, PhD in Biomedical Sciences (December 19)Institute of Animal Pathology, Department of Infectious Diseases and Pathobiology (DIP) (Prof. Dr. Sven Rottenberg)“Leveraging Spatial Transcriptomics for Preclinical Drug Development”Raphael Raschid Andonie, PhD in Biomedical Engineering (July 3)ARTOG (Prof. Dr. Stefan Andreas Weder)“Cochlear Implant Telemetry for Objective Cochlear Health Monitoring”Nadine Anslinger, PhD in Immunology (November 26)BITg (Prof. Dr. Daniel Legler)“Exploring Model Systems to Investigate Dendritic Cell Immune Functions”Isabel Arenas Hoyos, MD PhD (Doctor of Medicine and Philosophy) (January 13)DBMR (Prof. Dr. Radu Olariu, Dr. Nicoletta Sorvillo)“Vascularized composite allotransplantation: A model for understanding graft rejection”Ainhoa Asensio Aldave, PhD in Biomedical Sciences (November 27)DBMR, Visceral and Transplantation Surgery (Prof. Dr. Deborah M. Keogh-Stroka)“Oxidative Stress in Metabolic Liver Disease and PCSK9-Deficient Livers: A Focus on DNA Damage and Hepatocyte Proliferation”Ruben Mordehaï Assaraf, PhD in Biomedical Sciences (October 28)DCBP (PD Dr. Carlos Ros Bascunana)“Deciphering Capsid Shielding by Host Protease Inhibitors in Parvovirus B19 Infection”Bianca Manuela Atchou, PhD in Cell Biology (August 11)Institute of Cell Biology (Prof. Dr. Torsten Ochsenreiter)“Mitochondrial Genome Replication and Transcription in Trypanosoma brucei”

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Page 35/60 Annual Report GCB 2025Kodzo Atchou, PhD in Biomedical Sciences (November 28)Institute of Cell Biology (IZB) (Prof. Dr. Volker Heussler)“Host Cell Vesicle Trafficking and Parasite Microtubule Dynamics During the Plasmodium Liver Stage”BElias Baumann, PhD in Biomedical Sciences (July 17)Institute of Pathology (Prof. Dr. Inti Zlobec)“Cellular Cartography: Nuclei Segmentation for Biomarker Discovery in Colorectal Cancer”Sven Patric Baumann, PhD in Biochemistry and Molecular Biology (June 16)DBMR (Prof. em. Dr. Matthias Hediger)“Structural elements of the ZIP8 (SLC39A8) metal ion/bicarbonate cotransporter and its role in health and disease”Julia Isabella Bayer, PhD in Immunology (March 27)Visceral and Transplantation Surgery (PD Dr. Joel Zindel, Prof. Dr. Deborah M. Keogh-Stroka)“Role of Macrophage-Mesothelial Cell Crosstalk in Pathological Scarring within the Peritoneal Cavity”Patricia Katiana Beer, DVM PhD (Doctor of Veterinary Medicine and Philosophy) (February 6)Clinic for Small Animal Surgery/ Department for Small Animals (PD Dr. med. vet. Mirja Christine Nolff)“Targeted near-infrared Fluorescence imaging for intraoperative soft tissue sarcoma visualization: crossspecies target analysis and in vivo imaging in dogs”Fabienne Esther Birrer, PhD in Biomedical Sciences (January 20)DBMR (Prof. Dr. Deborah M. Keogh-Stroka)“Characterization of the Mc4rKO mouse model to investigate the immune landscape in MASH livers”Francesco Bonollo, PhD in Biomedical Sciences (Arpil 23)DBMR (Prof. Dr. Marianna Kruithof-de Julio, Dr. Sofia Karkampouna)“Cancer-associated fibroblasts in tumor microenvironment dynamics during prostate cancer progression”Micaela Borsa, PhD in Neuroscience (March 18)Zentrum für Experimentelle Neurologie (ZEN), Department of Neurology, Inselspial University Hospital Bern(Prof. Dr. Antoine Roger Adamantidis)“Synergy of Cortical Dynamics and Synaptic Tuning in REM Sleep for Emotional Memory Encoding”Lena Carolina Bruhin, PhD in Biomedical Engineering (November 24)ARTORG (Prof. Dr. Tobias Nef)“Solutions for Healthcare Challenges in Aging Populations: Leveraging Sensor-Based Monitoring to Extract Activity Patterns”Aurelia Lucilla Bucciarelli, PhD in Biomedical Engineering (March 19)ARTORG (Prof. Dr. Dominik Obrist)“Dynamics of Red Blood Cell Partitioning and Flow in In Vitro Microvascular Networks: The Roles of Lingering Red Blood Cells and Pericyte Activation”Milica Bulatović, PhD in Biomedical Engineering (September 5)ARTORG (Prof. Dr. Stefan Weber)“Thermal Ablation Tailored to Distinct Tumor Shapes”

Page 36/60 Annual Report GCB 2025CFrancesco Stefano Carzaniga, PhD in Neuroscience (February 14)Department of Neurology, Inselspital, Sleep-Wake-Epilepsy-Center, NeuroTec, University Bern (Prof. Dr. Kaspar Anton Schindler)“Vector-Symbolic Architectures and Generative AI for Multivariate Time-Series Analysis: Advancing Seizure Detection and Understanding of Human Electroencephalography”Filippo Manlio Cattalani Tognola, PhD in Biochemistry and Molecular Biology (February 28)Institute of Animal Pathology (Prof. Dr. Horst Posthaus)“Unveiling the molecular and structural mechanism of action of Clostridium perfringen Necrotizing enteritis toxin F (NetF)”Shuimu Chen, MD PhD (Doctor of Medicine and Philosophy) (July 29)DBMR (Prof. Dr. Benjamin Gantenbein)“A Mechanistic Study of Different Intervertebral Disc Phenotypes and Their Effects on Spinal Fusion”Wanli Cheng, MD PhD (Doctor of Medicine and Philosophy) (March 27)DBMR (Prof. Dr. Marianna Kruithof-de Julio, Dr. Sofia Karkampouna)“Novel Therapeutic Strategies Exploiting Mechanisms and Vulnerabilities in Castration-Resistant Prostate Cancer”Camille Danielle Catherine Clamagirand, PhD in Immunology (November 4)BITg (Prof. Dr. Jérémie Rossy)“Dentritic cells shape the immune synapse architecture to direct T cell responses”Alexia Aurélia Danielle Maryvonne Clavier, PhD in Biomedical Sciences (December 1)Department of Cardiac Surgery (Prof. Dr. Sarah Henning Longnus)“Cardiac graft quality with donation after circulatory death: Proteomics and sex difference investigations”Katherine Briana Crump, PhD in Biomedical Engineering (May 28)DBMR (Prof. Dr. Benjamin Gantenbein)“Mechanobiology and pro-inflammatory cytokines in the intervertebral disc: An in vitro, ex vivo, and in silicoinvestigation”DSusan De Groof, PhD in Biomedical Sciences (August 18)Inselspital (PD Dr.phil. Loretta Lina Müller)“Bacterial Lysate-Induced Modulation of Nasal Epithelial and NK Cell Responses to Rhinovirus.”Nadia Djabeur, PhD in Biochemistry and Molecular Biology (October 1)IBMM (Prof. Dr. Dimitrios José Fotiadis )“Structural insights into selected bacterial and viral proteins”Paulo Eduardo do Vale Sampaio e Souza, PhD in Biomedical Engineering (November 7)ARTOG (Prof. Dr. Raphael Sznitman)“Mueller matrix polarimetry for fresh pancreatic tissue characterization”

Page 37/60 Annual Report GCB 2025EYasmine Eddoubaji, PhD in Biomedical Sciences (December 18)IFIK (Prof. Dr. Andrea Endimiani)“Using Zophobas morio larvae to design a new in vivo model of intestinal colonization due to multidrugresistant Enterobacterales”Bryce Ridley Evans, PhD in Immunology (January 22)DBMR, Angiology (Prof. Dr. Yvonne Döring)“ChemR23 prevents phenotypic switching of vascular smooth muscle cells into macrophage like foam cells in atherosclerosis”FLorenzo Ferrari, PhD in Biomedical Engineering (March 24)ARTOG (Prof. Dr. Dominik Obrist)“Experimental Flow Field Assessment of Surgical Valve Prostheses with Tomographic Particle Image Velocimetry: Impact of Model, Size and Cardiac Output”Timothée Louis Fettrelet, PhD in Immunology (February 21)Institute of Pharmacology (Prof. em. Dr. Hans-Uwe Simon)“Molecular regulation of eosinophil differentiation and functions: the emerging role of long non-coding RNAs”Ana Leni Frei, PhD in Biomedical Engineering (March 25)Pathology (Prof. Dr. Inti Zlobec)“Geometric deep learning and graph-based analysis to study the effect of neoadjuvant chemoradiotherapy in rectal cancer”Matteo Frigelli, PhD in Biomedical Engineering (March 3)ARTOG (Dr. Sabine Kling, Prof. Dr. Philippe Büchler)“Localized Corneal Stiffening for Refractive Correction: Experiments and Computational Analysis”Daniel Fuchs, DVM PhD (Doctor of Veterinary Medicine and Philosophy) (October 31)Vetsuisse Faculty University of Zurich, Institute of Veterinary Pharmacology and Toxicology (Prof. Dr. med. vet. Enni Markkanen)“Cross-species characterization of malignant soft-tissue sarcomas to identify targets for near-infrared fluorescence-guided surgery and pharmacotherapy”Patricia Sonja Fuchs, PhD in Biomedical Sciences (September 1)Federal Department of Economic Affairs, Education and Research, Agroscope (Prof. Dr. Rupert Max Bruckmaier)“Investigations of a virtual fencing system focusing on technical and chronobiological aspects to ensure animal welfare of cattle”GJasmin Galli, DVM PhD (Doctor of Veterinary Medicine and Philosophy) (November 28)Institute of Veterinary Anatomy (PD Dr. Karl Rüdiger Klisch, Prof. Dr. Mariusz P. Kowalewski)“Placental extracellular vesicles: Comparative aspects in different placentation types”Stefano Gallo, PhD in Biochemistry and Molecular Biology (April 4)DCBP (Prof. Dr. Norbert Polacek)

Page 38/60 Annual Report GCB 2025“Regulation of angiogenesis and cancer cell proliferation by human vault RNA1-2”Huixiang Ge, PhD in Biomedical Sciences (May 28)DBMR (PD Dr.phil.nat. Thomas Marti, PD Dr.med. Patrick Dorn)“Targeting Metabolic Vulnerabilities in Lung Cancer: LDHB and GLDC Regulate the Role of Glutathione in Metastasis and Ferroptosis”Oliver Johannes Gerken, PhD in Cell Biology (October 10)BITg (Prof. Dr. Daniel Legler)“Atypical Chemokine Receptors in Scavenging Homing Chemokines and Beyond”Vincent Gloe, PhD in Immunology (September 10)BITg (Jérémie Rossy)“Role of co-stimulatory molecules expressed by dendritic cells in formation of immunological synapse”Benjamin Andreas Grädel, PhD in Cell Biology (November 5)Institute of Cell Biology (Prof. Dr. Olivier Pertz)“Quantifying Spatiotemporal Signalling Dynamics Across Scales”Arno Joeffroy Granier, PhD in Neuroscience (November 25)Department of Physiology (Prof. Dr. Walter Senn)“Understanding computation in canonical circuits of cortical cell types”Silja Anna Griss, DVM PhD (Doctor of Veterinary Medicine and Philosophy) (August 12)Veterinary Public Health Institute (Prof. Dr. Gertraud Irene Schüpbach)“Paratuberculosis in Swiss Dairy Cattle: Disease Impact, Economic Consequences and Potential Control Strategies”Mauro Bruno Gwerder, PhD in Computational Biology (September 15)Institute of Pathology (Prof. Dr. Inti Zlobec)“Unsupervised Assessment of Tumor Buds and their Micro-Environment using Multiplexed Immunofluorescence and Image Analysis Approaches in Colorectal Cancer”HPaul Haider, PhD in Neuroscience (November 13)Department of Physiology (Dr. Mihai Alexandru Petrovici)“Deep, local learning in dynamical networks outside of equilibrium”Kai Pascal Alexander Hänggeli, PhD in Cell Biology (January 22)Institute of Parasitology (Prof. Dr. Andrew Hemphill)“Characterisation and validation of putative targets for intervention in Toxoplasma gondii and Neospora caninum infection”Elio Luca Herzog, PhD in Biomedical Sciences (March 28)University Clinic for Ophtalmology (Dr.phil. Denise Corinne Zysset, Prof. Dr. Martin Sebastian Zinkernagel)“Linking the Ocular Surface Microbiome to the Local Mucosal Immune System in Mice”Giselle Hevia Hernandez, PhD in Immunology (June 19)Institute of Pharmacology (Prof. Dr. Stephan von Gunten)“Exploring immunoglobulin-mediated mechanisms in immune regulation”

Page 39/60 Annual Report GCB 2025Lucien Simon Hinderling, PhD in Cell Biology (June 24)Institute of Cell Biology (Prof. Dr. Olivier Pertz)“Using real-time feedback control microscopy to study cellular processes across scales”Alexander Michael Hofer, PhD in Biochemistry and Molecular Biology (August 29)DCBP (Prof. Dr. Oliver Mühlemann)“Studying Progranulin’s Role in Disease – From Neurodegeneration to Cancer”Jiaxi Hu, MD PhD (Doctor of Medicine and Philosophy) (August 19)Department of Nuclear Medicine (Prof. Dr. Kuangyu Shi)“A Systems-Medicine Investigation for the Optimization of the PSMA-Directed Radiopharmaceutical Therapy”Lazar Ivanovic, PhD in Biochemistry and Molecular Biology (April 29)IBMM (Prof. Dr. Wanda Kukulski)“Molecular and architectural organization of tricalbin-mediated ER-PM contact sites in budding yeast”JDamian Jandrasits, PhD in Biomedical Sciences (October 29)Institute of virology and immunology and Laboratoy Spiez (Prof. Dr. Volker Earl Thiel, Dr. Roland Züst)“Antivirals, Host Factors and Vaccines: Crimean-Congo hemorrhagic fever and Monkeypox virus - two emerging viral threats”Clirim Jetishi, PhD in Cell Biology (September 12)Institute of Cell biology (Prof. Dr. Torsten Ochsenreiter)“From the Basal Bodies to the Mitochondrial Genome: The Tubular Segregation Machinery in Trypanosoma brucei”Romano Josi, PhD in Immunology (March 24)RI- Immunologie - Inselspital (Prof. Dr. Martin Bachmann, Prof. Dr. Mona Omar Mahmoud Mohsen)“Virus-Like Particles as Platforms for Cancer Vaccines and Immunotherapeutic Strategies”KAmith Jagannath Kamath, PhD in Biomedical Engineering (September 19)ARTOG (Prof. Dr. Mauricio Reyes)“Fast and Reliable AI-based Dosimetric Contour Quality Assurance for Radiotherapy”Pelin Kasap, PhD in Biomedical Sciences (April 28)Theodor Kocher Institute (Prof. Dr. Britta Engelhardt)“Towards Building an Isogenic Human Neurovascular Unit-on-a-Chip to Study the Blood-Brain Barrier in Health and Disease”Oleksiy-Zakhar Khoma, PhD in Biomedical Engineering (August 22)Institute of Anatomy (PD Dr. Ruslan Hlushchuk, Dr. David Haberthür)“Micro(angio)CT in preclinical peri-implant research”Mohammadamin Khosrozadeh, PhD in Neuroscience (January 30)Institute of Anatomy (Prof. Dr. Benoît Zuber)“Morphological Principle of Synaptic Transmission Regulation Using Cryo-Electron Tomography and DataDriven Models”

Page 40/60 Annual Report GCB 2025Gabija Krutkyte, MD PhD (Doctor of Medicine and Philosophy) (June 16)University Clinic for Diabetology, Endocrinology, Nutritional Medicine and Metabolism (UDEM) (Prof. Dr. Lia Claudia Bally)“Optimising Perioperative Care Using Metabolic Phenotyping”Nicholas Fabian Küng, PhD in Biochemistry and Molecular Biology (August 28)University Institute of Clinical Chemistry (Prof. Dr. Ursula Amstutz)“From Donor-Derived to Tissue-of-Origin: A Multifaceted Exploration of Cell-Free DNA in Transplantation”LReto Mario Lang, PhD in Biochemistry and Molecular Biology (November 11)IVI (Prof. Dr. Volker Earl Thiel)“Investigating the role of stress granules during virus infections”Jana Leuenberger, PhD in Neuroscience (September 30)Institute of Anatomy (Prof. Dr. Benoît Zuber)“Integrative Analysis of Synaptic Structure and Function in PC12, SH-SY5Y, and iPSC-Derived Motor Neurons: A Multimodal Evaluation of Model Characteristics”Jiaqi Li, PhD in Biomedical Sciences (April 4)DBMR (PD Dr. Benjamin Misselwitz, Prof. Dr. Bahtiyar Yilmaz)“Oxidative stress resilience of gut microbial strains under healthy and inflammatory conditions”Shuang Li, MD PhD (Doctor of Medicine and Philosophy) (October 28)DBMR (Prof. Dr. Marianna Kruithof-de Julio, Federico La Manna)“Molecular investigation of prostate cancer residual disease in a model of bone microenvironment”Xiaodong Li, PhD in Cell Biology (October 30)Institute of Cell biology (Prof. Dr. Mariusz Nowacki)“DNA N6-methyladenine function in Paramecium tetraurelia”Yuebing Li, MD PhD (Doctor of Medicine and Philosophy) (January 22)University Hospital for Ophthalmology (Prof. Dr. Volker Enzmann, PD Dr.med. Souska Sophie Zandi)“Rho-kinase involvement in ocluar fibrosis”Lea Lingg, PhD in Biomedical Sciences (February 14)Institute of Animal Pathology (Prof. Dr. Sven Rottenberg)“Refining Precision Oncology: Understanding Mechanisms of Therapy Response in BRCA1;p53- Deficient Mammary Tumors”Kirill Lotonin, PhD in Immunology (September 15)Institute of Virology and Immunology (Prof. Dr. Artur Summerfield)“Adaptive immune responses against African swine fever”

Page 41/60 Annual Report GCB 2025MMagreth Erick Macha, PhD in Biomedical Sciences (August 21)Kantonsspital St. Gallen (PD Dr. Baharak Babouee Flury)“Distribution and Resistance Mechanisms of Uropathogenic Escherichia coli in patients with symptoms of Urinary Tract Infections and concurrent Gut Colonization by Resistant Enterobacterales in rural Tanzania”Marine Massy, PhD in Biomedical Sciences (July 3)Department of Neurology (Prof. Dr. Robert Wilhelm Walther Hoepner)“Investigating the Sex Effect on Efficacy and Withdrawal of Sphingosine 1-Phosphate Receptor Modulators”Rina Mehmeti, MD PhD (Doctor of Medicine and Philosophy) (June 20)Institute of Pathology (Prof. Dr. Mario Paul Tschan, Prof. Dr. Inti Zlobec)“From Chromatin Modification to Cellular Motility: Epigenetically Repressed CDX2 Promotes Colorectal Cancer Cell Migration and Tumor Budding”Julia Moser, PhD in Biomedical Sciences (June 27)Veterinary Public Health Institute, Vetsuisse Faculty Bern (Prof. Dr. Gertraud Irene Schüpbach)“Veal Calf Barn Housing Climate: Ammonia and Forced Ventilation Measurements”NSaranda Nimani, MD PhD (Doctor of Medicine and Philosophy) (January 29)Department of Physiology - UNIBE (Prof. Dr. Katja Elisabeth Odening)“QT syndromes: arrhythmogenic mechanisms and novel therapeutic approaches”OAndreas Werner Öhm, DVM PhD (Doctor of Veterinary Medicine and Philosophy) (July 4)Institute of Parasitology, Vetsuisse Faculty of Zürich (PD Dr. Manuela Schnyder, Prof. Dr. Salomé Leibundgut-Landmann)“Host-parasite interactions in canid angiostrongylosis: from antigenic characterisation to cellular models”Quentin-Florian Pierre Oliveres, PhD in Cell Biology (December 17)Institute of Plant Sciences (Prof. Dr. Doris Rentsch)“Post-translational modifications for amino acid transporters in Trypanosoma brucei”PIrida Papapostolou, PhD in Biochemistry and Molecular Biology (December 17)University of Bern (Prof. Dr. Christine Peinelt)“Investigation of nAChR and TRPM4 in cancer hallmark functions in 2D and 3D cancer models”Dixy Parakkattel, PhD in Biomedical Sciences (June 2)Inselspital (Prof. Dr. med. Johannes Heverhagen)“From blood to brain: A novel route for gadolinium-based contrast agent entry into the brain”Alessandro Pardini, PhD in Immunology (September 19)Department of Rheumatology and Immunology (Prof. Dr. Martin Bachmann, Prof. Dr. Monique Vogel)“Preclinical Development of Virus-Like Particle-Based Influenza Vaccines”

Page 42/60 Annual Report GCB 2025Valentina Pecoraro, PhD in Biochemistry and Molecular Biology (December 17)DCBP (Prof. Dr. Norbert Polacek)“Characterization of hY3 as a ribosome-associated non-coding RNA and its functional role in translation regulation and the integrated stress response”Pedro Pereira Amado, PhD in Biomedical Engineering (October 29)University of Bern, ARTORG Center for Biomedical Engineering Research (PD Dr. Francesco Clavica)“Investigating the interplay between urine flow, crystal deposition and bacteria to improve the performance of ureteral stents”Laura Peters, PhD in Immunology (October 3)BITg (Prof. Dr. Jérémie Rossy)“Mechanobiology of the immunological Synapse betweeen T Cells and Dendritic Cells”Mariafrancesca Petrucci, DVM PhD (Doctor of Veterinary Medicine and Philosophy) (January 9)DBMR, Experimental Surgery facility (ESF), University of Bern (Dr. Daniela Casoni, Prof. Dr. Robert Rieben)“Unravelling pain in minipigs undergoing experimentally induced myocardial infarction.Can it also mirror ischaemic pain in humans?”Simone Roberto Rolando Pisano, DVM PhD (Doctor of Veterinary Medicine and Philosophy) (June 27)FIWI (Prof. Dr. Heike Schmidt-Posthaus)“Eco - epidemiology of crayfish plague in Switzerland”Margherita Polidori, PhD in Neuroscience (June 3)Wiederkäuerklinik, Vetsuisse Fakultät Universität Bern (Prof. Dr. Anna Oevermann)“Host pathogen interactions in Listeria monocytogenes-infected microglia and monocyte-derived macrophages”Sigma Pradhan, PhD in Biochemistry and Molecular Biology (March 28)Institute of Cell Biology (Prof. Dr. Benjamin Daniel Towbin)“Diet-induced intergenerational control of growth and proteome composition in C. elegans”Lukas Martin Probst, PhD in Biochemistry and Molecular Biology (January 21)IFIK (PD Dr. Ronald Dijkman)“Characterization of the Interaction of Influenza D Virus with the Host Innate Immune System”QLuis Fernando Quiñones Olvera, PhD in Neuroscience (December 18)IBMM (Prof. Dr. Jürg Gertsch)“Dissecting ACSL4 and MAGL Isoforms: Structural and Functional Insights into Membrane Lipid Remodeling and Endocannabinoid Signaling”RSiavash Rahimi, MD PhD (Doctor of Medicine and Philosophy) (December 9)DBMR (Prof. Dr. Eliane Jasmine Müller)“The Role of Cell Adhesion in Tissue Self-organization and Regeneration: a Systems Biology Approach to Pemphigus vulgaris”Chiara Rodella, PhD in Computational Biology (August 20)

Page 43/60 Annual Report GCB 2025IBMM (Prof. Dr. Thomas Max Lemmin)“Large Language Model Methods for Protein Engineering and Antibody Discovery”Virginia Roland Victor, PhD in Cell Biology (June 13)DBMR (Prof. Dr. Marco Osterwalder)“Functional architecture of cardiac TF regulatory landscapes in control of mammalian heart development”Alessia Rosina, PhD in Biochemistry and Molecular Biology (July 7)DCBP (Prof. Dr. Norbert Polacek)“Fine-tuning the ribosome: the role of rRNA expansion segments and rancRNAs in Saccharomyces cerevisiae translation regulation”Dominik Alexander Rothen, PhD in Immunology (January 24)RI-Immunologie Inselspital (Prof. Dr. Martin Bachmann)“Multi‐Target Vaccine Against Flaviviruses Based on Virus‐Like Particles”Adrian Cyrill Ruckli, PhD in Biomedical Engineering (January 24)Department of Orthopaedic Surgery and Traumatology, University of Bern (PD Dr. Kate Alicia Gerber)“Uncertainty-based error localisation and correction for deep learning anatomy segmentation for treatment planning in orthopaedics”SYasaman Safarkhanlo, PhD in Biomedical Engineering (August 25)Department of Cardiology Inselspital (Prof. Dr. Christoph Gräni, Prof. Dr. Jessica Bastiaansen)“Noninvasive Assessment of Cardiac Function, Structure, and Hemodynamics in Patients with Mitral Valve Regurgitation using Cardiac Magnetic Resonance Imaging”Neda Salimi Afjani, PhD in Immunology (June 18)DBMR (Prof. Dr. Yvonne Döring, Prof. Dr. Robert Rieben)“Investigating Xenograft Compatibility: Testing Genetically Modified Porcine Endothelial Cells in a Novel InVitro Flow Model and Evaluating Unconventional Anti Rejection Drugs.”Fanny Kristina Sandberg, MD PhD (Doctor of Medicine and Philosophy) (October 17)Inselspital, Department of Clinical Chemistry (Prof. Dr. Ursula Amstutz)“Advancing Liquid Biopsies in Transplantation Beyond Fractional Donor-Derived Cell-Free DNA in Plasma”Osman Berk Satir, PhD in Biomedical Engineering (January 07)ARTORG (Prof. Dr. Philippe Büchler)“Deep learning for automatic characterization of shoulder bone and muscle morphology and degeneration from CT images”Melanie Cristine Scalise, PhD in Biomedical Sciences (December 29)DBMR (Prof. Dr. Maria Luisa Balmer)“In search of obesogenic bacteria and their metabolites using gnotobiotic mice”

Page 44/60 Annual Report GCB 2025Alexandria Marie Schauer, PhD in Biomedical Sciences (February 18)Institute of Bee Health (Prof. Dr. Peter Neumann)“Arthropod-virus interactions from the tissue to the landscape level”Leonhard Maximilian Schink, PhD in Immunology (November 25)Institute of Biotechnology Thurgau BITg (Prof. Dr. Daniel Legler)“From Trail to Trail: Investigating the Impact of CCR7 C-terminal Truncation Mutations on Receptor Signaling Dynamics and Immune Cell Migration”Karin Farah Schmid, PhD in Biomedical Sciences (October 22)ARTOG Center, Organs-on-Chip Technologies (Prof. Dr. Olivier Thierry Guenat)“Towards a vascularized metastatic tumor-on-chip”Christine Schneider, MD PhD (Doctor of Medicine and Philosophy) (April 02)Department of Pediatric Hematology and Oncology (Prof. Dr. Jochen Karl Rössler)“Prospective multicentre cohort study of early pulmonary dysfunction inchildhood cancer patients”Guy-Alain Georges Schnidrig, PhD in Biomedical Sciences (May 14)Vetsuisse Unibe (Prof. Dr. Gertraud Irene Schüpbach)“Anomaly detection in the veterinary antibiotic prescription surveillance system (IS ABV)”Tiana Carina Schwab, PhD in Biomedical Sciences (June 10)Institute of Social and Preventative Medicine (ISPM) (Prof. Dr. Lukas Fenner, Prof. em. Dr. Matthias Egger)“Sequencing Approaches for Improved Tuberculosis and Infectious Disease Diagnostics in Sub-Saharan Africa”Leonor Serrano Lopes, MD PhD (Doctor of Medicine and Philosophy) (June 16)ARTORG (Prof. Dr. Kuangyu Shi)“Artificial Intelligence in Neurodegenerative Diseases: Advancing Diagnosis and Prognosis”Akanksha Arunkumar Shanbhag, PhD in Biochemistry and Molecular Biology (August 26)DCR-VPN, Vetsuisse Faculty (Prof. Dr. Philippe Plattet)“Potent cross-neutralising single-domain antibodies to fight morbilliviral infections”Mathieu Simon, PhD in Biomedical Engineering (January 20)ARTOG (Prof. Dr. Philippe Zysset)“Multi-Scale Bone Morphology-Mechanical Property Relations in Ageing and Disease”Michael Andreas Single, PhD in Biomedical Engineering (February 05)ARTORG (Prof. Dr. Tobias Nef, Dr. Stephan Moreno Gerber)“Digital Biomarkers to Characterize Motor Functions of People with a Neurodegenerative Disease”Xiaoqing Song, DDS PhD (Doctor of Dentistry and Philosophy) (June 2)School of Dental Medicine, Department of Periodontology, Laboratory of Oral Cell Biology (PD Dr. Mariya Bozhidarova Asparuhova, Prof. Dr. Anton Sculean)“Human palatal connective tissue grafts: molecular profiles and cell-cell interactions”Sebastian Peter Spiegel, PhD in Neuroscience (February 26)Department of Neuroimmunology (Prof. Dr. Andrew Hao-Kuang Chan, Prof. Dr. Vincent Pernet)“Mechanisms underlying nose-to-brain transport of therapeutic antibody in the context of autoimmune diseases”

Page 45/60 Annual Report GCB 2025Ruth Theresia Steinberg, MD PhD (Doctor of Medicine and Philosophy) (March 18)Division of Paediatric Respiratory Medicine and Allergology, Department of Paediatrics, Inselspital (Prof. Dr. med.,Dr. phil. Philipp Latzin)“Impact of the airway microbiome on clinical outcomes in children with cystic fibrosis and healthy controls and the possible influence of environmental factors, such as the COVID-19 pandemic.”Philip Stettler, PhD in Biochemistry and Molecular Biology (August 21)DCBP (Prof. Dr. André Schneider)“Functional Architecture of the Tripartite Attachment Complex of Trypanosoma brucei”Saurav Subedi, PhD in Biomedical Sciences (July 11)Urology Group, Cancer Therapy Resistance (Prof. Dr. Marianna Kruithof-de Julio, Federico La Manna)“Metabolic Drivers of Cancer Progression”TVahoura Tahsini, PhD in Biomedical Engineering (May 26)ARTOG (Dr. Sabine Kling, Prof. Dr. Philippe Büchler)“Material characterization of lens, cornea and sclera in healthy eyes with age”Darien Toledo Santamaria, PhD in Immunology (September 18)Institute of Pharmacology, University of Bern (Prof. Dr. Stephan von Gunten)“Unravelling the role of sialic acids and their implications in melanoma progression: from clinical evidence to exosomes”Federico Turco, PhD in Biomedical Engineering (March 7)Institute of Diagnostic and Inverventional Neuroradiology (Prof. Dr. Johannes Slotboom)“Development of High-Performance MRSI Analysis and Processing Tool Based on Artificial Intelligence.”Péter Demeter Túrós, PhD in Computational Biology (May 28)Institute of Animal Pathology (Prof. Dr. Volker Earl Thiel, Prof. Dr. Sven Rottenberg)“Decoding Spatially Resolved Biology: Machine Learning Methods to Uncover Tissue Complexity”UVAndrea Gaspare Valenti, PhD in Biochemistry and Molecular Biology (December 2)Institute of Animal Pathology (PD Dr. Philipp Alexander Olias, Prof. Dr. Sven Rottenberg)“Identifying essential host factors for Toxoplasma gondii infection”Vanessa Vallesi, PhD in Neuroscience (September 1)Schweizer Paraplegiker Zentrum, Radiologie (Prof. Dr. Johannes Slotboom)“Multimodal MRI of motor impairment and inhibition: Functional connectivity and neurometabolic profiles in spinal cord injury and functional paralysis”

Page 46/60 Annual Report GCB 2025Antoine Dominique Vautrin, PhD in Biomedical Engineering (June 27)AO Research Institute Davos (PD Dr. Peter Varga)“Numerical modeling of dental implant biomechanics towards design optimization and planning”Anne-Cathrine Sarah Vogt, PhD in Immunology (March 31)RI- Immunologie - Inselspital (Prof. Dr. Martin Bachmann)“Immunotherapy Targeting Amyloid-Related Diseases”WChristina Wapp, PhD in Biomedical Engineering (March 18)ARTORG (Prof. Dr. Philippe Zysset)“The Development of a Personalised Fragility Hip Fracture Risk Calculator”Jim Weber, DVM PhD (Doctor of Veterinary Medicine and Philosophy) (December 17)Clinic for Ruminants, Vetsuisse- Faculty, University of Bern (Prof. Dr. Adrian Steiner)“Development and implementation of a novel bovine digital dermatitis control program in Switzerland”Tobias Adrian Weber, PhD in Biomedical Engineering (June 19)ARTORG (Prof. Dr. Olivier Thierry Guenat)“Development of a Breathing Lung-on-Chip: An Advanced In Vitro Model for Drug Testing”Fei Hugo Wu, PhD in Biomedical Engineering (March 28)ARTOG (Prof. Dr. Raphael Sznitman)“Alleviating the Issue of Annotation Scarcity in Semantic Segmentation using Active Learning”XJun Xu, MD PhD (Doctor of Medicine and Philosophy) (February 24)Institute of Pathology (Prof. Dr. Mario Paul Tschan)“Function and post-translational regulation of the oncogenic splice variant DMTF1β”YYudong Yan, PhD in Neuroscience (January 24)Zentrum fur Experimentelle Neurologie (ZEN), Department of Neurology, Inselspital University Hospital Bern (Prof. Dr. Antoine Roger Adamantidis)“Stability of Hypothalamic Neural Population Activity Across Sleep-Wake States”Anaïs Elodie Yerly, PhD in Immunology (August 28)Universitätsklinik für Angiologie (Prof. Dr. Yvonne Döring)“Loss of B cell-ACKR3 reduces atherosclerosis by attenuation of plasma cells and pro-inflammatory antibodies”ZJingyi Zhang, MD PhD (Doctor of Medicine and Philosophy) (December 11)DBMR, Institute of Pharmacology (Prof. Dr. Ren-Wang Peng)“Ferroptosis Evasion via Cancer–Immune Cell Crosstalk as a Barrier to KRAS Inhibitor Therapies”

Page 47/60 Annual Report GCB 2025Matteo Zoia, PhD in Cell Biology (May 5)DBMR (Prof. Dr. Marco Osterwalder)“Deciphering the cis-regulatory architecture of the Shox2 transcriptional regulator essential for embryonic development”Valentina Zollet, PhD in Biomedical Sciences (June 20)DBMR (Prof. Dr. Robert Rieben)“Extracellular traps and hypercitrullination in ischemia reperfusion injury, cancer and xenotransplantation”

Page 48/60 Annual Report GCB 20255.3 Student Awards & Recognitions5.3.1 Best 2024 Theses, Awarded at GCB Symposium 2025Karoline-Marie BornemannARTORG Center for Biomedical Engineering ResearchMedical FacultySupervisors: Dominik ObristCo-Advisor: Peter SchmidMentor: Bernd JungInstability mechanisms leading to laminar-turbulent transition past bioprosthetic aortic valvesAbstractBioprosthetic heart valves (BHV) create turbulent flow during the systolic phase of the cardiac cycle. This turbulent flow is suspected to negatively influence BHV durability and performance. Although a comprehensive analysis of laminar-turbulent transition mechanisms is crucial for the identification of the onset of turbulent flow, complex flow phenomena such as shear layers, an unsteady aortic jet, recirculation regions and vortex shedding complicate the isolation of specific instability mechanisms. This thesis therefore applies a variety of methods such as numerical fluid-structure interaction (FSI) simulations as well as local and global stability analysis to identify the origin of laminar-turbulent transition past BHV. Fluttering and non-fluttering valves are analyzed placed in parameterized aortic roots of different dimensions to apply the results to a wide range of valve designs and patient anatomies.For a 2D case, a starting vortex (SV) formed during the initial opening of the leaflets is advected downstream. Its impingement with the aortic wall creates a secondary, counter-rotating vortex which moves towards the leaflet shear layer. As it reaches the shear layer, we observe a shear layer instability of potentially absolute character as it travels upstream and triggers leaflet oscillations which occurs earlier for a narrower aorta. A 1D framework comprising modified Orr-Sommerfeld equations with FSI extension term suggests both KelvinHelmholtz as well as FSI instabilities in a physiological Reynolds number range.Increasing the complexity to capture 3D instabilities, three 3D configurations assessing the impact of leaflet fluttering and aortic root dimension on vortex breakdown are created. For a fluttering valve, a three-lobed SV is formed followed by streamwise vortex pairs above each valve post. Synchronized with the leaflet fluttering frequency, secondary vortices are shed periodically. The interaction of all three vortex types seems to lead to the breakdown to smaller-scale vortices which again occurs quicker for a narrower aorta. A non-fluttering valve, however, alters vortex formation fundamentally and creates a six-lobed SV which breaks down faster.Next, global stability analysis is performed for both fluttering and non-fluttering valve. Base flows representing different time instances during systolic acceleration are generated. While unstable modes span across a wide range of frequencies and increase in growth rate over time for the non-fluttering valve, both frequency and growth rates increase over time for the fluttering valve with unstable modes located above the valve posts. Later during systolic acceleration, eigenmodes of both valves form a distinct arch, suggesting an additional low-frequency mode.An additional translational study is performed investigating the relation between THVT and larger aortic roots observed in patient data. Lagrangian particle tracing and platelet activation are compared in a larger aortic root of THVT patients with and without neo-sinus and a control group. Larger aortic roots are found to increase platelet activation levels, especially in the neo-sinus, and reduce sinus washout efficiency, indicating a higher risk for thrombus formation.This thesis evaluated instability mechanisms leading to laminar-turbulent transition mechanisms providing various conclusions which can be beneficial in both future valve design and choice of valve size. Rather than a universal solution valid for every patient, the optimal combination of valve geometry, valve kinematics and the individual patient anatomy must be considered simultaneously to provide the most favourable outcome for the patient.

Page 49/60 Annual Report GCB 2025Lucilla GiammarinoInstitute for PhysiologyMedical FacultySupervisor: Katja OdeningCo-Advisor: Niels VoigtMentor: Anna Oevermann and Thomas LutzTailoring personalized medicine approaches in cardiac electrical diseases: unraveling sex differences in atrial electrical properties and assessing gene therapy efficacy in LQT1 channelopathyAbstractAdvances in cardiac electrophysiology have made significant strides in the treatment of cardiac electrical diseases. However, a drastic improvement in outcomes and patient’s quality of life may result from the use of personalized and more specific approaches. Firstly in this thesis, we attempt to unravel sex-specific mechanisms underlying sex-differences in atrial fibrillation (AF). AF is a rhythm disorder characterized by irregular atrial activation. Pronounced sexdifferences are known in the AF incidence, underlying mechanisms, and response to treatment. Particularly at younger age, men carry a higher risk for AF development than women. A plausible explanation could be the role of sex hormones in atrial electrophysiology. By performing ex vivo and in vivo experiments, our results reveal not only that sex impacts atrial electrical features, but also suggest that sex hormones play a pivotal role in mediating sex-differences in atrial electrophysiology that might impact the propensity to develop AF. A deeper understanding of the interplay between sex, sex hormones, and atrial electrophysiology could improve atrial arrhythmias management and facilitate the development of sex-specific therapies. Secondly, this thesis explores the efficacy of a tailored therapy for the treatment of a congenital channelopathy, long QT syndrome type 1 (LQT1) caused by pathogenic variants in the KCNQ1 gene. Current therapies are symptom-directed and do not address the underlying molecular cause. Hence, this study investigates the efficacy of a AAV9-mediated KCNQ1 suppression-replacement (SupRep) gene therapy in a transgenic LQT1 rabbit model. Herein our findings demonstrate that KCNQ1-SupRep gene therapy rescues the pathologically prolonged QT index and cellular action potential duration in transgenic LQT1 rabbits both at baseline and under β-adrenergic stimulation.

Page 50/60 Annual Report GCB 2025Lukas RimleDepartment of Chemistry, Biochemistry and Pharmaceutical SciencesFaculty of ScienceSupervisor: Christoph von BallmoosCo-Advisor: Jean-Marc NuofferMentor: Torsten OchsenreiterInvestigations into the mode of action of Leucinostatin A and its derivatives on mitochondria and mitochondrial ATP synthaseAbstract: Living organisms rely on the continuous uptake of energy to develop and grow, but also to respond to environmental stimuli. Various sources provide energy in different forms (e.g. light, nutrients), which have to be converted into a molecular energy currency that can be metabolically used by living organisms. The most abundant cellular energy currency is adenosine triphosphate (ATP), a molecule that is predominantly synthesized at energy-conserving membranes embedded with a variety of respiratory enzyme complexes. In a cascade of enzymatic reactions, energy-rich metabolites are sequentially oxidized concomitant to proton translocation across the membrane, which results in the establishment of an electrochemical proton gradient (proton motive force, pmf) that empowers ATP production by the ubiquitous ATP synthase.The coordinated interplay between those respiratory complexes eventually leading to ATP synthesis can be studied in vitro by reconstitution of individually purified components into membrane-mimetic systems (e.g. liposomes). This bottom-up synthetic biology approach using liposomes allows to investigate respiratorydriven processes in a compartmentalized setup with a defined lipid and protein composition. While such systems show simplicity and well-delineated conditions, membrane protein reconstitution may be accompanied by random insertion of the target membrane protein into the synthetic vesicle, a process that is difficult to control and modulate but has consequences on the experimental setup (e.g. substrate accessibility).In a first project of this work, we provide methodology to determine the orientation of membrane proteins in liposomes independent of their activity. The novel approach is based on fluorescently labelled membrane proteins that are quenched with membrane-impermeable Tris(2-carboxyethyl)phosphine (TCEP). Upon liposome solubilization, TCEP gains access to initially inside-oriented membrane proteins, thus allowing TCEP to quench the previously protected fluorophores. By comparing the different quench intensities before and after liposome solubilization, the assay allows rapid estimation of the orientation distribution of membrane proteins in artificial lipid vesicles.Using this approach, we observed a lipid-dependent topological organization of the E. coli cytochrome bo3 ubiquinol oxidase (bo3 oxidase) in liposomes, with a preferred inside-out orientation (inside pumping) in presence of positively charged membrane lipids. The bo3 oxidase has been frequently used in our group as an important building block for various bottom-up synthetic biology systems, in which this enzyme operates as a proton pump to establish an electrochemical proton gradient. Uniformly oriented bo3 oxidase is thus expected to increase pmf and consequently ATP synthesis. Based on the electrostatic surface charge distribution of bo3 oxidase, we propose a charge-mediated reconstitution process into liposomes. While positively charged lipids are beneficial for bo3 oxidase orientation and thus pmf strength, previous work in our group revealed an incompatibility of highly-positively charged liposomes with ATP synthesis. Here, we circumvent this dilemma (positively charged lipids beneficial for bo3 oxidase orientation, but incompatible with ATP synthesis) by employing an engineering trick using ionizable DODAP lipids that provide a temporarily positively charged membrane at pH 6.5 for bo3 oxidase and ATP synthase reconstitution. After successful co-reconstitution of both enzymes, fusion with negatively charged lipids renders overall neutral proteoliposomes and subsequent adjustment to physiological pH results in negatively charged vesicles. This engineering trick promotes bo3 oxidase inside-out orientation in liposomes while also enabling NADH-driven ATP synthesis empowered by the peripheral membrane protein NDH-2. This NADH-consuming enzyme strongly depends on the presence of negatively charged lipids for efficient activity, i.e. reduction of membrane-soluble ubiquinone and thus bo3 oxidase activation and follow-up ATP synthesis. Using this strategy, we observed maximal ATP production when transiently positively charged proteoliposomes were fused with liposomes consisting of cardiolipin and phosphatidylserine. Strikingly, we report a three-fold increased ATP synthesis rate over the currently most efficient system with DOPC vesicles and DTT/Q1 as electron source and mediator, respectively.