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Rasmus Magnusson

Postdoc

I develop and implement large-scale systems biology models to analyze human high-throughput intracellular data. In collaboration with clinical teams, I apply these models to gain insights into disease-related processes.

Summary

My research focuses on understanding high-throughput biological data using computational methods, including machine learning, statistical modeling, and systems biology. I aim both to support medical and biological teams as a computational resource, and to develop new tools that reveal disease-driven intracellular changes. A particular interest of mine is projecting insights from well-characterized healthy systems, where data are typically abundant, onto human diseases where material is often limited.

My research path began in 2014, when I was introduced to mechanistic modeling and systems biology as a student visiting IMT. After completing my MSc, this interest led me to pursue a PhD in bioinformatics at the Department of Physics, Chemistry and Biology, where I focused on predicting high-confidence gene regulatory networks from RNA-seq data. Following my thesis defense, I continued as a postdoctoral researcher at the University of Skövde in collaboration with pharmaceutical companies. There, I also initiated my first project as a senior research leader, where I led the development of variational autoencoders, which are artificial neural networks designed to extract disease-specific groups of interconnected genes.

Now back at IMT, my work emphasizes continued method development and the application of computational approaches to real-world biomedical data. My long-term goal is to establish a hub that supports the interpretation of diverse high-throughput datasets across the life sciences.

Publications

2024

Hendrik Arnold de Weerd, Dimitri Guala, Mika Gustafsson, Jane Synnergren, Jesper Tegne, Zelmina Lubovac-Pilav, Rasmus Magnusson (2024) Latent space arithmetic on data embeddings from healthy multi-tissue human RNA-seq decodes disease modules PATTERNS, Vol. 5, Article 101093 (Article in journal) Continue to DOI

2022

Rasmus Magnusson, Olof Rundquist, Min Jung Kim, Sandra Hellberg, Chan Hyun Na, Mikael Benson, David Gomez-Cabrero, Ingrid Kockum, Jesper N. Tegner, Fredrik Piehl, Maja Jagodic, Johan Mellergård, Claudio Altafini, Jan Ernerudh, Maria Jenmalm, Colm Nestor, Min-Sik Kim, Mika Gustafsson (2022) RNA-sequencing and mass-spectrometry proteomic time-series analysis of T-cell differentiation identified multiple splice variants models that predicted validated protein biomarkers in inflammatory diseases Frontiers in Molecular Biosciences, Vol. 9, Article 916128 (Article in journal) Continue to DOI
Rasmus Magnusson, Jesper N. Tegner, Mika Gustafsson (2022) Deep neural network prediction of genome-wide transcriptome signatures - beyond the Black-box npj Systems Biology and Applications, Vol. 8, Article 9 (Article in journal) Continue to DOI

2021

Tilda Herrgårdh, Vince I Madai, John D. Kelleher, Rasmus Magnusson, Mika Gustafsson, Lili Milani, Peter Gennemark, Gunnar Cedersund (2021) Hybrid modelling for stroke care: Review and suggestions of new approaches for risk assessment and simulation of scenarios NeuroImage: Clinical, Vol. 31, Article 102694 (Article, review/survey) Continue to DOI
Sandra Hellberg, Johanna Raffetseder, Olof Rundquist, Rasmus Magnusson, Georgia Papapavlou, Maria Jenmalm, Jan Ernerudh, Mika Gustafsson (2021) Progesterone Dampens Immune Responses in In Vitro Activated CD4(+) T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy Frontiers in Immunology, Vol. 12, Article 672168 (Article in journal) Continue to DOI

Organisation