Author: Jürgen Pahle

Ole Lennart Decker finished his Bachelor’s thesis titled “Gene Ontology Term Prediction from Protein Sequences: A Comparison of Transformer and xLSTM Architectures”.

Dario Andrea Prifti finished his Bachelor’s thesis on “Analyzing Training Dynamics and Generalization of Reinforcement Learning Agents in Simulated Bacterial Chemotaxis across Novel Maze Environments”.

Both students worked on their projects during the summer term 25 and employed AI methods, i.e. large language models (LLMs) and reinforcement learning (RL), for tackling biological research questions. Ole and Dario both submitted their theses on 1. August 2025.

Jürgen Pahle and Sven Sahle (BioQuant Centre, Heidelberg University) organised a COPASI tutorial at the International Conference on Systems Biology (ICSB2024), 30. November – 5. December 2024, at the Indian Institute of Technology (IIT Bombay), Mumbai, India.

This conference was the first one in the ICSB conference series taking place in India.

During the tutorial on 1. December 2024 (Victor Menezes Convention Centre (VMCC), IIT Bombay, Mumbai) we introduced the participants to the basic functionality and some more advanced features of our software COPASI for the modelling, simulation and analysis of biochemical systems. In particular, we covered parameter estimation in COPASI and the use of our companion software CoRC. The COPASI R Connector (CoRC) provides a high-level API for COPASI’s simulation and analysis backend that can be used comfortably from the R programming environment or in R Markdown or Shiny documents.

Szilárd Varga defended his Master’s thesis titled “Dynamic Insights into the CD8⁺ T Cell Response to Yellow Fever Infection: A Multiscale Approach Using Metabolic Data” on 1. July 2024. Congratulations, Szilárd!

This work was done in collaboration with Prof. Dr. Frederik Graw (FAU Erlangen).

Lena Lenkeit defended her Master’s thesis titled “Design, development, and experimental verification of a framework for fully-differentiable, gradient-based optimal control of biological systems” on 23. October 2023.

This work was done in collaboration with Dr. Dr. Stefan Kallenberger who is also based at the BioQuant.

Emma Kray finished her Bachelor’s thesis titled “A model-based investigation of immune system composition upon vaccinations against influenza” in August.

Pascal Lukas defended his Master’s thesis on “Analyzing and modeling the spatio-temporal dynamics of the interferon response to Dengue virus infection” on 29. September 2023.

Both projects were done in collaboration with the group of Prof. Dr. Frederik Graw at the FAU Erlangen.

The 30th International Dynamics & Evolution of Human Viruses conference is taking place from April 19 to 22, 2023 at the German Cancer Research Center (DKFZ) and the Marriott in Heidelberg.

This meeting series was designed to promote discussion between specialists in quantitative and computational approaches in two areas in the field of virology where these are particularly important:

1. Modeling of viral and cellular dynamics 
2. Viral evolution and population genetics

We co-organised this meeting together with Frederik Graw, Emma Hodcroft, Denise Kühnert, Richard Neher. Organising institutions are the BioQuant / Heidelberg University and the School of Medicine at UC San Diego.

We provided travel grants for exceptional young researchers from abroad.

You can find more information at the conference webpage.

Johanna Daas successfully defended her Master’s thesis titled “Model workflows with the COPASI R Connector (CoRC)” on 10th June 2022.

Congratulations, Johanna!

PS It should be mentioned that Johanna had already published an article as first author in Mathematical Biosciences during her Master’s project:
J.CJ. Daas, J.D Förster and J. Pahle (2022)
Dynamic Publication Media with the COPASI R Connector (CoRC).
Mathematical Biosciences, doi:10.1016/j.mbs.2022.108822 (open access)

Pablo Naranjo successfully defended his Master’s thesis titled “Understanding the relationship between antigenic distance and susceptibility to influenza virus infection” on 19. May 2022.

Congratulations, Pablo!

Mathematical Biosciences accepted our new manuscript, titled “Dynamic Publication Media with the COPASI R Connector (CoRC)” for publication in their special issue “Dynamic Publication Media in Mathematical Biology”.

Dynamic publication media are becoming a popular tool for authors to effectively compose and publish their work. In this article we show how dynamic publication media and the COPASI R Connector (CoRC) can be combined in a natural and synergistic way to communicate (biochemical) models.

For further information please have a look at:
J.CJ. Daas, J.D Förster and J. Pahle (2022)
Dynamic Publication Media with the COPASI R Connector (CoRC).
Mathematical Biosciences, doi:10.1016/j.mbs.2022.108822 (open access)

Tim Ingenbrand defended his Master’s thesis (in Physics) titled “Chemotaxis and Memory in Escherichia Coli” successfully on 29th October 2021.

Congratulations, Tim!