Timo Lassmann

GeneInsight synthesizes gene set annotations using topic modeling and language models to provide interpretable summaries that reveal biologically significant insights overlooked by traditional enrichment analyses.

Interaction-finder automates the discovery of biological entity associations from literature, producing a ranked list with quoted provenance, and outperforms existing methods in recall.

UORCA automates large-scale reanalysis of public transcriptomic data to identify biological patterns and generate hypotheses for drug design.

This study investigates age-dependent tumor-immune interactions in pediatric cancer using mouse models and patient samples, finding that pediatric tumors have distinct immune profiles and poor response to immunotherapy, which can be improved by modulating the tumor microenvironment.

CDR-g detects subtle condition-specific gene coexpression changes in single-cell data, identifying novel biological pathways and subpopulations not found by conventional differential expression analysis.

The paper compares single-cell and single-nucleus RNA-seq workflows in adult mouse kidneys to identify protocol-specific biases in cell type recovery and transcriptional profiles.

C1 CAGE detects transcription start sites and enhancer activity in lung cancer cells, revealing subpopulations with distinct responses to TGF-β and enhancer RNA dynamics.

The paper identifies shared expression patterns of genetic variants across tissues and cell types, enabling fine mapping of disease-associated variants and revealing key cell types involved in disease pathogenesis.

The paper enhances the FANTOM5 expression atlas by associating gene-orphan promoter regions with their transcripts using CAGEscan.

The paper generates a single-cell RNA-seq dataset of HeLa cells labeled with Fucci reporters and provides an open workflow for data processing and quality control.

The paper identifies YY1's role in X-linked gene escape from inactivation by analyzing promoter activity and allelic binding in human datasets.