Events

Helena will talk about Joint profiling of cell morphology and gene expression in neuronal disease models

Abstract

Differentiation of induced pluripotent stem cells (iPSC) towards neuronal lineages has enabled diverse cellular models of human neurodevelopment and related disorders. While mutations in genes encoding for epigenetic regulators are an established cause for neurodevelopmental disorders (NDD), their exact molecular mechanisms remain unknown and there is a need for systematic phenotyping of in vitro neurons at scale. We have used Cell Painting, a high-content imaging assay, jointly with transcriptomic profiling in single cells to characterize the biological heterogeneity in developing cortical neurons. We observed that image-based morphological phenotypes enhanced our ability to quantify the biological processes that determine neuronal differentiation outcomes over time and allowed us to identify disease-relevant phenotypes.

About the speaker

Helena Kilpinen is  a tenure-track associate professor in human genetics and genomic medicine at Helsinki Institute of Life Science (HiLIFE) at the University of Helsinki (UH) in Finland and the Faculty of Medicine, and a group leader at FIMM and the Neuroscience Center. Her lab investigates the cellular genetics and the cellular basis of developmental and other brain-related disorders using human induced pluripotent stem cells (iPSC) as models, and combine computational and experimental methods. 

Contact: Laura Godfrey (+49 221 478 51455, laura.godfrey@iccb-­cologne.org), Stefanie Fleer (+49 221 478 15104, stefanie.fleer@iccb­-cologne.org)

Join our third iteration of our workshop to take your Git, Conda and Docker skills to the next level!

While this workshop is suitable for beginners and advanced users alike, explicit focus is placed on advanced usage of aforementioned tools to make your research more efficient and reproducible. Each of the three blocks will be presented in a dedicated, interactive session. Finally, participants will use the learned skills in a practical hands-on project.

Ideally, you are already familiar with basic shell usage (commands like ls, grep, rm, etc. no longer scare you) and basic git commands (add, commit, push, pull, etc.). You know what a Dockerfile is, you may have even heard of docker-compose and have pulled and ran a docker image before.
You do not tick all the boxes? Do not be discouraged! Most importantly, you should bring curiosity, the willingness to learn and to ask questions.

We will cover the following topics:
- Software development in largerscale projects using Git
- Package management with CondaWe will cover the following topics:
- Application management with Docker including continuous integration (CI), setting up and using runners

Prerequisites:
- Basic Linux command line knowledge (e.g. commands as ls, grep, cd, etc.)
- Working installations of Git, Conda and Docker Desktop as well as your favorite IDE
- Basic knowledge of python as well as common libraries (pandas, numpy, matplotlib)

Participants from our second workshop in February are very welcome!

If you are interested please register until 02nd of November 2025.

register

Maxime will talk about Unfolding the somatic genome evolution of human cancers from fertilisation to resection

Abstract

Genomes in our cells start to evolve from the initial genomes of our parents and accumulate somatic mutations. Most of these are silent or will not lead to malignant growth. We study how different classes of somatic changes, including single nucleotide substitutions and copy-number  changes, accumulate over time on the parental genomes.

About the speaker

Maxime Tarabichi is Associate Professor IRIBHM Jacques E. Dumont, Université Libre de Bruxelles in Belgium. His lab investigates the somatic and cancer genome evolution of different tissues, including in the context of sarcomas and thyroid cancers.

Contact: Laura Godfrey (+49 221 478 51455, laura.godfrey@iccb-­cologne.org), Stefanie Fleer (+49 221 478 15104, stefanie.fleer@iccb­-cologne.org)

Niko will talk about Modeling tumor progression from single-cell sequencing data 

Abstract

Cancer progression is an evolutionary process characterized by the accumulation of genetic alterations and responsible for tumor growth, clinical progression, and drug resistance development. He will discuss (1) how to reconstruct the evolutionary history of a tumor from single-cell sequencing data and present probabilistic models and efficient inference algorithms for mutation calling and learning tumor phylogenies from mutation and copy number data, and (2) how tumor phylogenies enable integrating single-cell DNA and RNA data obtained from tumor biopsies, finding common patterns of tumor evolution among patients, and inferring the underlying cellular fitness landscape of cancer evolution.

About the speaker

Niko Beerenwinkel is Full Professor of Computational Biology at the Department of Biosystems Science and Engineering of ETH Zurich in Basel. His research is at the interface of mathematics, statistics, and computer science with biology and medicine. It includes statistical, evolutionary, and network modeling of molecular profiling data. He has developed several computational methods for supporting molecular diagnostics in oncology and virology, including for the analysis of tumor singlecell genomics data and of deep sequencing data obtained from virus populations.

Contact: Laura Godfrey (+49 221 478 51455, laura.godfrey@iccb-­cologne.org), Stefanie Fleer (+49 221 478 15104, stefanie.fleer@iccb­-cologne.org)

Johannes will talk about Generic Solutions for Specific Problems in Genomics: Snakemake, Datavzrd, and Varlociraptor in 2025

Abstract
At the example of the successful open source projects Snakemake, Datavzrd, and Varlociraptor, I outline the development of continuously maintained, tested, and improved software solutions that arose from the necessity to solve at first sight rather specific and narrowly scoped bioinformatics problems. I describe the generalization steps and demonstrate how this approach enhanced their sustainability, leading to their current feature sets and ongoing advancements.

About the speaker
Johannes Köster is professor for Bioinformatics and Computational Oncology at the Institute for AI in Medicine (IKIM), University Medicine Essen, University of Duisburg-­Essen with a focus on algorithm engineering and data analysis. Johannes studied computer science at the University of Dortmund. Johannes' research is focused on reproducibility in three ways. First, he is the author of the popular workflow management system Snakemake and the founder of the Bioconda project for sustainably distributing bioinformatics software as easily installable packages. Second, Johannes is the author of the Rust-­Bio library, enabling the use of the Rust programming language for bioinformatics by providing standard bioinformatics algorithms and data structures. Third, Johannes is working in the field of Bayesian statistics (e.g., for variant calling and single cell transcriptomics) in order to provide algorithms for analysis of high­throughput data while capturing and quantifying all known sources of uncertainty, thereby providing more reproducible predictions.

Contact: Laura Godfrey (+49 221 478 51455, laura.godfrey@iccb-­cologne.org), Stefanie Fleer (+49 221 478 15104, stefanie.fleer@iccb­-cologne.org)