Author

Jasper Menger

University of FreiburgORCID 0009-0000-9521-2281Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Approach:contrastive learning· 1 Approach:deep learning· 1 Research Focus:dimensionality reduction· 1 Organism:human· 1 Assay:scRNA-seq· 1

Frequent Co-Authors

Harald BinderiD· 2 shared Maren HackenbergiD· 2 shared Sonia Maria KrissmeriD· 2 shared Clemens KreutziD· 1 shared Johan RolliniD· 1 shared Tanja VogeliD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

6 top collaborators · 13 mutual co-author links

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2 shared papersBioinformatics

Harald BinderORCID

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2 papers

Recent·Most cited

BioinformaticsBioinformaticsPeer-reviewedMay 22, 2026

mmContext: an open framework for multimodal contrastive learning of omics and text data

Jasper Menger, Sonia Maria Krissmer, Clemens Kreutz…·Maren Hackenberg

The paper introduces mmContext, a framework for multimodal contrastive learning of omics and text data, and demonstrates its utility in RNA-Seq and text integration tasks.

DOI 10.1093/bioinformatics/btag338

bulk RNA-seqcontrastive learning

𝕏 PostBluesky

BioinformaticsbioRxivPreprintAug 23, 2025

Adding layers of information to scRNA-seq data using pre-trained language models

Sonia Maria Krissmer, Jasper Menger, Johan Rollin…·Maren Hackenberg

The paper fine-tunes biomedical language models to integrate text-based knowledge with scRNA-seq data, enhancing cell identity preservation and adding functional and disease-related context.

1 citation

humanscRNA-seq

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