DO NOT PUT grapes in the microwave..

    — Z. Bingöl

Education

• Ph.D. Student, Computer Engineering, Fall 2020 - Summer 2026
  • Bilkent University, Ankara, Turkey
• M.Sc., Computer Engineering, Summer 2020
  • Bilkent University, Ankara, Turkey
  • Thesis: “GateKeeper-GPU: Accelerated Pre-Alignment Filtering in Short Read Mapping”.
• B.Sc., Computer Engineering, 2017
  • Bilkent University, Ankara, 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. Full Paper: Briefings in Bioinformatics 2026.

• PG2: algorithms and a web-based tool for effective layout and visual analysis of pangenome graphs. Görkem Kadir Solun, Ugur Dogrusoz, Zülal Bingöl, Can Alkan. Full Paper: BMC Bioinformatics 2026.

• LCPan: efficient variation graph construction using locally consistent parsing. Akmuhammet Ashyralyyev, Zülal Bingöl, Begüm Filiz Öz, Kaiyuan Zhu, Salem Malikic, Uzi Vishkin, S. Cenk Sahinalp, Can Alkan. Full Paper: Genome Biology 2026 / arXiv preprint

• GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan. Full Paper: IEEE-TC 2024 / arXiv preprint / Extended Abstract: HiCOMB 2021

• SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping. Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger, Zülal Bingöl, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie S. Kim, Nika Mansouri Ghiasi, Gagandeep Singh, Juan Gomez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu. In Proceedings of the 49th International Symposium on Computer Architecture (ISCA) (June 2022) Paper

• GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu. In Proceedings of the 53rd International Symposium on Microarchitecture (MICRO) (October 2020). Paper

• Accelerating Genome Analysis: A Primer on an Ongoing Journey. Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu. IEEE Micro (September 2020) Paper