Education

• M.Sc., Electrical Engineering and Information Technology, 2024
  • ETH Zürich, Zurich, Switzerland
• B.Sc., Computer Engineering, 2021
  • Bilkent University, Ankara, Turkey

Selected Publications

• Targetcall: Eliminating the wasted computation in basecalling via pre-basecalling filtering. Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, Onur Mutlu. Frontiers in Genetics, 2024.

• AirLift: a fast and comprehensive technique for remapping alignments between reference genomes. Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, and Onur Mutlu. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2024.

• MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. Nika Mansouri Ghiasi, Mohammad Sadrosadati, Harun Mustafa, Arvid Gollwitzer, Can Firtina, Julien Eudine, Haiyu Mao, Joël Lindegger, Meryem Banu Cavlak, Mohammed Alser, Jisung Park, Onur Mutlu. Proceedings of the 49th Annual International Symposium on Computer Architecture (ISCA), June 2024.

• RUBICON: a framework for designing efficient deep learning-based genomic basecallers. Gagandeep Singh, Mohammed Alser, Kristof Denolf, Can Firtina, Alireza Khodamoradi, Meryem Banu Cavlak, Henk Corporaal, Onur Mutlu. Genome Biology, 2024.

• Aphmm: Accelerating profile hidden markov models for fast and energy-efficient genome analysis. Can Firtina, Kamlesh Pillai, Gurpreet S Kalsi, Bharathwaj Suresh, Damla Senol Cali, Jeremie S Kim, Taha Shahroodi, Meryem Banu Cavlak, Joël Lindegger, Mohammed Alser, Juan Gómez Luna, Sreenivas Subramoney, Onur Mutlu. ACM Transactions on Architecture and Code Optimization, 2024.

• RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes. Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu. Bioinformatics, 2023.

• FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies. Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, and Onur Mutlu. Bioinformatics, btac554, 2022.

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