Summary
I am a Senior Staff Scientist at the Bioinformatics & Omics Data Science platform of the Max-Delbrück-Center for Molecular Medicine. My current research is focused on the development of deep learning-based multi-modal data integration tools for precision oncology. My other roles in the platform include running research collaborations and supporting other researchers in the form of consultations, mentorships, workshops, and user-friendly software development for wet-lab researchers. My work in the last 15 years spanned various topics such as comparative genomics, protein sequence analysis in the context of molecular interactions and disease mechanisms, RNA bioinformatics, and omics data science with a focus on development of reproducible software for the bioinformatics community.
Profiles
Experience
Bioinformatics Scientist
Max-Delbrück-Center for Molecular Medicine
Berlin, Germany
Postdoctoral Fellow
European Molecular Biology Laboratory
Heidelberg, Germany
Education
PhD in Bioinformatics
European Molecular Biology Laboratory
Heidelberg, Germany
MSc in Bioinformatics
Simon Fraser University, BC Cancer Agency
Vancouver, Canada
BSc in Biological Sciences
Sabanci University
Istanbul, Turkey
News Articles
- Using deep learning for precision cancer therapy (mdc-berlin.de)
- New textbook for computational genomics (mdc-berlin.de)
- Searching the sewers for viruses (bionity.com)
- AI identifies cancer cells (bionity.com)
- Parallel Genome Editing in Microscopic Worms Maps Regulatory Genomic Elements to Physiology (genengnews.com)
- Stray proteins cause genetic disorders (sciencedaily.com)
- A genetic chaperone for healthy aging? (bionity.com)
Selected Publications
| Year | Paper | Journal |
|---|---|---|
| 2025 | Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond | Nature Communications |
| 2022 | Identifying tumor cells at the single-cell level using machine learning | Genome Biology |
| 2021 | Parallel genetics of regulatory sequences using scalable genome editing in vivo | Cell Reports |
| 2020 | Single-cell analyses of aging, inflammation and senescence | Aging Research Reviews |
| 2018 | PiGx: reproducible genomics analysis pipelines with GNU Guix | GigaScience |
| 2018 | Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs | Cell |
| 2017 | RCAS: an RNA centric annotation system for transcriptome-wide regions of interest | Nucleic Acids Research |