Viktoria Brunner

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

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

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

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

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. 

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

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