Profile Picture

About

I am a pharmacologist turned research software engineer, and I am particularly interested in disentangling causal relationships in molecular biology with the help of modern artificial intelligence approaches. I pursue this goal as a Principal Investigator at the Institute of Computational Biology at Helmholtz Centre Munich since 2025, and in affiliation with the Open Targets group at the European Bioinformatics Institute (EMBL-EBI) since 2024. I also serve as the head of computational biology at the German Centre for Diabetes Research.

Effectively dealing with the avalanche of biomedical measurements of today—without throwing away large parts of the data—requires smart digital infrastructure. To approach this challenge, I am actively developing a unified framework for biomedical knowledge representation, BioCypher, with the aim of automating harmonisation of biomedical representations for a multitude of research tasks.

Building on this infrastructure, I am developing methods for integrating Large Language Models into the biomedical research workflow, with the aim of increasing accessibility of biomedical knowledge and methods. The BioChatter project is a framework for connecting Large Language Models and auxiliary technologies to the biomedical world. Application examples for the framework’s functionalities can be found at https://chat.biocypher.org and the vignette section of our website.

I have received funding from the DFG and Open Targets to develop a new generation of biomedical knowledge mangement systems and a surrounding community, starting in 2024.

Affiliations

Institute of Computational Biology, Helmholtz Centre, Munich, Germany (ROR: https://ror.org/00cfam450)
German Centre for Diabetes Research, Munich, Germany (ROR: https://ror.org/04qq88z54)
Open Targets, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, United Kingdom (ROR: https://ror.org/000bp7q73 & https://ror.org/02catss52)

Short bio in third person

Dr. Sebastian Lobentanzer is a seasoned biomedical researcher and research software engineer with extensive expertise in systems pharmacology. Having completed a PhD in pharmacology and toxicology, he is particularly interested in disentangling causal relationships in molecular biology. He has pursued this focus as a postdoctoral researcher in the lab of Julio Saez-Rodriguez at Heidelberg University Hospital from 2021 to 2025 and, since 2024, in affiliation with the Open Targets group at the European Bioinformatics Institute (EMBL-EBI). Since 2025, he is a Principal Investigator at Helmholtz Munich and leads the Computational Biology Unit at the German Centre for Diabetes Research (https://slolab.ai).

Sebastian’s research bridges the gap between biomedical science and information technology. During his PhD training in pharmacology, he combined his biomedical expertise with computational approaches, using tools like Java, R, and graph database systems. His postdoctoral work emphasises open-source Python frameworks with a particular focus on biomedical applications. An advocate for open science and reproducibility, he is known for developing innovative frameworks that focus on user-friendliness and community engagement (https://biocypher.org).

Sebastian leads the development of BioCypher, an ecosystem for automating biomedical knowledge management. Building on this infrastructure, he develops methods to integrate Large Language Models into biomedical workflows, enhancing the accessibility of biomedical knowledge and methods. These developments have the ultimate goal of furthering our understanding of artificial intelligence methods as we apply them to biological questions; in one word: AI-readiness.