I am a computational biologist who enjoys exploring cell signalling through data-driven mathematical modeling. Recently graduated from the joint Master’s programme in Molecular Techniques in Life Science, I am a PhD candidate in Evangelia Petsalaki’s research group (Whole Cell Signalling) at the European Bioinformatics Institute and the University of Cambridge as part of the EMBL International PhD Programme.

During my studies in Heidelberg and Stockholm, I specialized in systems biology by attending several classes dealing with programming languages, mathematical modeling/computational pathway simulations, and statistical methods, which provided me insight into data science and the complexity of dynamic processes in living cells. I am especially interested in understanding the dynamic interplay of systems components and how information is specifically processed and linked to cell-fate decisions despite presence of (biochemical) noise.

As an active member of the preLights community, I select and highlight interesting preprints and interact with their authors. Launched in 2018, preLights is a community supported by The Company of Biologists, which provides a platform for highlighting and discussing new preprints across the biological sciences. My preLight-posts can be found here.

Scientific Programming Languages

Python (advanced), R (advanced), C++ (intermediate), Julia (beginner), Matlab (beginner)

Cell Modelling and Simulation Tools

COPASI (advanced), COBRApy (intermediate), VCell (intermediate), NFsim (intermediate), PhysiBoSS/MaBoSS/PhysiCell (intermediate), Kappa (beginner)

Other Frameworks

Containerisation (Singularity & Docker), workflow management systems (Nextflow & SnakeMake), scripting (Shell/Bash, LaTex), version control systems (GitHub & GitLab), high performance computing (Codon & SLURM)

Skills

Mathematical Mechanistic Modeling (Rule-based, ODE-based, logical | Whole-Cell, Genome-Scale, Detailed | Metabolic, Signalling, Population), Machine Learning, Genetic Algorithms, Network Analysis, Data Analysis, Statistical Modeling and Algorithms, Sequence Analysis, Seeding Algorithms

Languages

German (C2), English (C2), Swedish (B2), French (A2), Spanish (A2)

News

2024

• 🗣️ November: Presented “SELPHI2: Data-driven extraction of human kinase-substrate relationships from omics datasets” at SymBLS.
• 🌱 November: Workshop Report out in Science Editor highlighting how publishers and early-career researchers are working together and guiding initiatives.
• 🌱 September: Preprint out in bioRxiv introducing a machine learning-based model to derive a probabilistic kinase-substrate network from omics datasets and an associated webserver.
• ♦️ February: Invited by the Company of Biologist to attend the 9th Researcher to Reader Conference in London, UK as PreLight representative and represent early career researchers in the Workshop: Publishers and ECRs Working Together.

2023

• 🗣️ December: I was interviewed by Reinier Prosée, the Community Manager of preLights, where we discussed my journey into science, the role of preprints, and my current research interests. You can read the full interview here.
• 🌱 May: Paper out in Genome Research showing that entropy predicts fuzzy-seed sensitivity.
• 🗣️ April: Presented “Entropy predicts sensitivity of pseudo-random seeds” at RECOMB
• ♦️ March: Awarded a travel fellowship from PerMedCoE to attend the PerMedCoE summer school: from pathway modelling tools to cell-level simulations in Seva, Spain
• ♦️ March: Awarded a travel fellowship from RECOMB to present my work at RECOMB in Istanbul, Turkey
• ♦️ January: Awarded a travel fellowship from Churchill College, Cambrige University, UK to present my work at RECOMB in Istanbul, Turkey

2022

• 🌱 October: Preprint out showing that entropy predicts fuzzy-seed sensitivity
• 🌱 October: Paper out in PLOS Computational Biology on stochastic dynamics of type-I interferon responses.
• 🎓 June: Graduated with a joint M.Sc. in Molecular Techniques in Life Science from Karolinska Institute, KTH Royal Institute of Technology and Stockholm University, Sweden
• ♦️ February: Admission to the EMBL International PhD programme (acceptance rate ~ 2%)

2021

• 🗣 September: Featured talk on the “quantitative interplay of chromatin organization and gene co-expression at the single-cell level” at EpiChrom
• ♦️ March: Awarded with the SciLifeLab summer internship fellowship to “predict nuclear 3D organization from single-cell gene expression” in the Pelechano Lab (Karolinska Institute)

2020 and before

• 🎓 June 2020: Graduated with a B.Sc. in Biological Science from Heidelberg University, Germany
• ♦️ January 2020: Awarded with a graduate fellowship by the German Academic Scholarship Foundation
• ♦️ January 2018: Awarded with a undergraduate fellowship by the German Academic Scholarship Foundation
• ♦️ June 2017: Karl-von-Frisch-Award for outstanding high school graduate achievements in the subject of biology.