Education

• M.Sc., Computer Engineering, 2017
  • Bilkent University, Ankara, Turkey
  • Thesis: “Assessment and correction of errors in DNA sequencing technologies”.
• B.Sc., Computer Engineering, 2015
  • Bilkent University, Ankara, Turkey

After Alkan Lab

Can Firtina is a Ph.D. student in the SAFARI Research Group at ETH Zurich, advised by Prof. Onur Mutlu.

His current research interests broadly span bioinformatics and computer architecture topics, including accurately and quickly identifying sequence similarities, hardware/software co-design for accelerating bioinformatics applications and genomic data analysis, correcting sequencing errors, and developing computational tools for gene editing. He is generally interested in developing new algorithms and architectures for bioinformatics applications to enable fast and accurate genome analysis.

Publications

• 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 Kim, Taha Shahroodi, Meryem Banu Cavlak, Joel Lindegger, Mohammed Alser, Juan Gómez Luna, Sreenivas Subramoney, and Onur Mutlu. arXiv, 2207.09765, 2022.

• 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.

• From Molecules to Genomic Variations: Accelerating Genome Analysis via Intelligent Algorithms and Architectures. Mohammed Alser, Joel Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gomez-Luna, and Onur Mutlu. Computational and Structural Biotechnology Journal (CSBJ), 2022.

• Demeter: A Fast and Energy-Efficient Food Profiler using Hyperdimensional Computing in Memory. Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser, Stephan Wong, Onur Mutlu, and Said Hamdioui. IEEE Access, Aug 1; 10:82493-82510 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.

• Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities. Mohammed Alser, Sharon Waymost, Ram Ayyala, Brendan Lawlor, Richard J. Abdill, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, Andre M. Ribeiro-dos-Santos, Can Firtina, Nour Almadhoun Alserr, Varuni Sarwal, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do, Kim, Malak S. Abedalthagafi, Onur Mutlu, and Serghei Mangul. arXiv, 2203.16261, 2022.

• GenStore: A High-Performance in-Storage Processing System for Genome Sequence Analysis. Nika Mansouri Ghiasi, Jisung Park, Harun Mustafa, Jeremie Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, and Onur Mutlu. Proceedings of the 27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), Lausanne, Switzerland, March 2022.

• BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches. Can Firtina, Jisung Park, Mohammed Alser, Jeremie S. Kim, Damla Senol Cali, Taha Shahroodi, Nika Mansouri Ghiasi, Gagandeep Singh, Konstantinos Kanellopoulos, Can Alkan, and Onur Mutlu,. arXiv, 2112.08687, 2021.

• Modeling Economic Activities and Random Catastrophic Failures of Financial Networks via Gibbs Random Fields. Levent Onural, Mustafa Çelebi Pınar, and Can Firtina. Computational Economics, Jul 9; 58:203–232, 2021.

• 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. bioRxiv, 2021.02.16.431517, 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 Gómez-Luna, Amirali Boroumand, Anant Norion, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu. Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2021.

• Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A Ercument Cicek, Can Alkan, and Onur Mutlu. Bioinformatics, Jun 15; 36(12):3669-3679, 2021.

• Hercules: a profile HMM-based hybrid error correction algorithm for long reads. Can Firtina, Ziv Bar-Joseph, Can Alkan, and A. Ercument Cicek. Nucleic Acids Research (NAR), Nov 30; 46(21):e125, 2018.

• GLANET: genomic loci annotation and enrichment tool. Burçak Otlu, Can Firtina, Sündüz Keleş, and Oznur Tastan. Bioinformatics, Sep 15; 33(18):2818–2828, 2017.

• On genomic repeats and reproducibility. Can Firtina and Can Alkan,. Bioinformatics, Mar 11; 32(15):2243–2247, 2016.