I am a Ph. D. Candidate at Bilkent University.

Education

• Ph.D. Student, Computer Engineering, Fall 2020 - present
  • 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

• 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

• GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping. Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, Can Alkan. (arXiv preprint arXiv:2103.14978 (2021) Paper: arXiv preprint / Extended Abstract: HiCOMB 2021

• 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