I am currently a Ph.D. student at Bilkent University.

Education

• Ph.D., Computer Engineering, Fall 2025 - present
  • Bilkent University, Ankara, Turkey
• M.Sc., Computer Engineering, Summer 2025
  • Bilkent University, Ankara, Turkey
  • Thesis: “Using Bloom filters to quickly and efficiently characterize genomic repeats and segmental duplications”.
• B.Sc., Computer Engineering, 2022
  • Konya Technical University, Konya, Turkey

Publications

• De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping. Zülal Bingöl , Berkan Şahin , Klea Zambaku , Ricardo Roman-Brenes , Konstantina Koliogeorgi , Can Firtina , Onur Mutlu , Can Alkan. Paper
• In-depth data movement characterization of DNA read mapping algorithms. Berkan Şahin , Ecem Ilgün , Klea Zambaku , Can Alkan. Paper
• Processing-in-memory for genomics workloads. William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi, Yann Falevoz, Yoshihiro Shibuya, Dominique Lavenier, Irem Boybat, Klea Zambaku , Berkan Şahin, Mohammad Sadrosadati, Onur Mutlu, Abu Sebastian, Rayan Chikhi, Can Alkan, BioPIM Consortium Paper
• MARS: Processing-in-memory acceleration of raw signal genome analysis inside the storage subsystem Melina Soysal, Konstantina Koliogeorgi, Can Firtina, Nika Mansouri Ghiasi, Rakesh Nadig, Haiyu Mao, Geraldo Francisco de Oliveira Junior, Yu Liang, Klea Zambaku , Mohammad Sadrosadati, Onur Mutlu Paper