Splicing-specific Biomarkers and Drug Targets

Dr. Abdullah Kahraman's research focuses on omics-based biomarker and drug-target detection across cancer types. He and his lab at FHNW focus in particular on the detection of cancer-specific alternative splicing events driving oncogenesis, progression, and metastatic processes. For their investigations, they use data science and machine learning methods and integrate data from whole-genome, whole-exome, and targeted DNA sequencing; RNA sequencing; mass spectrometry-based proteomics and peptidomics; protein structures; and protein interaction networks. 

Abdullah works together with the CTP Lab as a permanent scientific guest.

Splicing-specific biomarkers

Overview of genomic, computational, clinical, and experimental approaches used to identify splicing-specific biomarkers and therapeutic targets (Image: Dr. Abdullah Karaman)

Key Papers

Heterogeneous and novel transcript expression in single cells of patient-derived clear cell renal cell carcinoma organoids
Karakulak, T., Zajac, N., Bolck, H. A., Bratus-Neuenschwander, A., Zhang, Q., Qi, W., ... & Kahraman, A. (2025). Genome Research, 35(4), 698-711.

MTPpilot: An Interactive Software for Visualization of Next-Generation Sequencing Results in Molecular Tumor Boards
Kahraman, A., Arnold, F. M., Hanimann, J., Nowak, M., Pauli, C., Britschgi, C., ... & Zoche, M. (2022). JCO Clinical Cancer Informatics, 6, e2200032.

Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network
Kahraman, A., Karakulak, T., Szklarczyk, D., & von Mering, C. (2020). Scientific reports, 10(1), 14453.

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