Viktoria Brunner
Main research interests: Using mathematical and computational tools to tackle biological challenges, currently applied to antibiotic susceptibility prediction in infectious diseases. Aspiring to understand how various different biological systems are wired and aiming to apply the generated knowledge to improve disease treatment, predict drug responses or design synthetic entities with well-defined properties.
Research Experience
PhD Project: 09/2022 - present
Improving antimicrobial susceptibility prediction in M. tuberculosis and E. coli using structural and sequencing data; Philip Fowler (University of Oxford, NDM)
Aim to improve predictions by including information beyond the presence of resistance mutations, such as presence of compensatory mutations, minor resistant populations and structural connectivity in proteins affected by resistance. Integrating structural and sequencing data through various machine learning approaches, including graph neural networks
PhD Rotation Project: 04/2022 - 08/2022
Investigation of the human nudix family protein NUDT22; Kilian Huber (University of Oxford, NDM)
Validated the co-localization of NUDT22 with OGT through proximity labeling and refuted interaction with free RNA
PhD Rotation Project: 01/2022 - 04/2022
Compensatory mutations in the RNA polymerase of M. tuberculosis increase fitness above wild-type levels; Philip Fowler (University of Oxford, NDM)
Confirmed 81 previously known and novel compensatory mutations in the RNA polymerase by statistical association testing. Proved their positive effect on fitness by employing available growth data and showed that the fitness increase can exceed wild-type levels
Master Thesis Project: 03/2021 - 09/2021
P. putida and P. aeruginosa evolved distinct strategies for dealing with the universal trade-off between growth and lag in fluctuating environments; Uwe Sauer (ETH Zürich)
Assessed lag time lengths after carbon source switching in P. putida and modelled central carbon metabolism in a MATLAB-based framework to explain different adaptive strategies in bacteria
Semester Project: 10/2020 - 02/2021
MCMC sampling in the context of mixture nested effects models; Nico Beerenwinkel (ETH Zürich)
Analysed single cell data from CRISPR experiments to decipher the underlying mixture of differentially wired gene networks using MCMC sampling
Semester Project: 02/2020 - 07/2020
Characterization of ER-phagy regulators using CRISPR-transcriptional activation; Jacob Corn (ETH Zürich)
Validated hits of a CRISPRa screen in order to identify novel ER-phagy receptors by use of CRISPR-transcriptional activation and cDNA expression in HDT116 cells
Teaching Experience
University of Oxford
Tutor for Quantitative Biochemistry 10/2023 - present
Tutor for Introduction to programming (graduate course) 10/2022 - 11/2024
ETH Zürich
Molecular genetics and cell biology for Medicine and Health Science 09/2019 - 01/2020
Lab preparations for basic biology courses 01/2019 - 06/2019
Biochemistry for Medicine 01/2019 - 06/2019
Genetics, Genomics, Bioinformatics 09/2018 - 12/2018
Statistics for Biology 02/2018 - 06/2018
Education
PhD in Interdisciplinary Bioscience 2021 - present
University of Oxford, UK
MSc in Systems Biology 2019 - 2021
ETH Zürich, Switzerland
BSc in Biology 2016 - 2019
ETH Zürich, Switzerland
High School 2007 - 2015
Droste-Hülshoff-Gymnasium, Freiburg im Breisgau, Germany
Scholarships, Awards and Grants
Highly commended impact award for lay blog post, 100 GBP 06/2024
DTC Oxford
Old members travel grant, 500 GBP 04/2024
University College, Oxford
Oxford-Radcliffe Graduate Scholarship, 62 500 GBP 09/2021 - present
University of Oxford
Excellence Scholarship & Opportunity Programme (ESOP), 36 000 CHF 09/2019 - 09/2021
ETH Zürich
Publications
Brunner, V. & Fowler, P. (February, 2024). Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of M. tuberculosis. Microbial genomics.
Brunner, V. & Fowler, P. (November, 2022). Compensatory mutations in M. tuberculosis increase fitness above wild type levels. Poster prize at the 2022 Multidisciplinary Approaches to AMR conference, Oxford, UK.
Schink, S. J., Christodoulou, D., Mukherjee, A., Athaide, E., Brunner, V., Fuhrer, T., Bradshaw, G. A., Sauer, U., & Basan, M. (December, 2021). Glycolysis/ gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing. Mol. Syst. Biol.
Language and Computer Skills
Computer Skills
Bash, SQL, Git (version control), Nextflow
Python (genomic data analysis with pandas, application of machine learning algorithms with scipy)
R (statistical analysis, population dynamic modelling, algorithms for network inference)
MATLAB (metabolic network modelling)
Java (object-oriented programming, design of simple algorithms)
Language Skills
German - native speaker
English - near native/ fluent (Cambridge Certificate of Profiency, grade A)
French - basic
Spanish - basic
Internships and Extracurricular Activities
Summer schools
Roche PMDA chapter: Predicting protein turnover, Basel, Switzerland 08/2024
ESCMID summer school, Sevilla, Spain 07/2023
Volunteer Experience 03/2020 - 06/2020
Covid-19 case data quality control for the Statistical Office Canton Zürich
Student Representative
Administrative Secretary, Middle Common Room at University College, Oxford 03/2023 - present
Event Organization Officer of VeBiS, the biology student association of ETH Zürich 03/2018 - 09/2019