Education

• PhD, Electrical and Computer Engineering (D-ITET), 2018–2024
  • ETH Zurich, Zurich, Switzerland
  • Advisor: Prof. Onur Mutlu
  • Thesis: “Enabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and Techniques”
  • Slides: ppt, pdf, video
  • Thesis committee: Prof. Heng Li, Prof. Benjamin Langmead, Prof. Reetuparna Das, Dr. Hasindu Gamaarachchi
• MSc, Computer Engineering, 2015–2018
  • Bilkent University, Ankara, Turkey
  • Advisor: Prof. Can Alkan
  • Thesis: “Assessment and Correction of Errors in DNA Sequencing Technologies”
• BSc, Computer Engineering, 2011–2015
  • Bilkent University, Ankara, Turkey

After Alkan Lab

After graduating from Alkan Lab, Can Firtina started as a PhD student at ETH Zurich in 2018.

Can Firtina is currently an Assistant Professor in the Department of Computer Science at the University of Maryland, College Park (UMD). He leads the STORM Research Group at UMD. His research focuses on algorithms and computing systems for bioinformatics.

His interests span bioinformatics, artificial intelligence, and computer architecture. He works on a broad range of problems to address key challenges in computer science and computational biology. He designs methods and builds systems that use emerging computing paradigms and memory technologies to enable fast, accurate, energy-efficient, and real-time analysis of biological data. He is also interested in developing solutions for applications such as genome editing. He received the ETH Doctoral Medal Prize in 2025, the highest prize awarded for doctoral dissertations at ETH Zurich. His research has been published in major bioinformatics and computer architecture venues.

Previously, he was a Senior Researcher and Lecturer at ETH Zurich, where he taught courses on accelerating genome analysis with hardware–algorithm co-design. His lecture videos and materials are available on YouTube. He received his PhD from ETH Zurich under the supervision of Prof. Onur Mutlu in the SAFARI Research Group.

Publications

• Furkan Eris, Ulysse McConnell, Can Firtina, and Onur Mutlu.
  “RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques”
  Proceedings of the 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2025), Philadelphia, PA, USA, October 2025.
  Paper online pdf
  Conference Talk pptx pdf

• Melina Soysal, Konstantina Koliogeorgi, Can Firtina, Nika Mansouri Ghiasi, Rakesh Nadig, Haiyu Mao, Geraldo Francisco Oliveira Junior, Yu Liang, Klea Zambaku, Mohammad Sadrosadati, and Onur Mutlu.
  “MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem”
  Proceedings of the 39th International Conference on Supercomputing (ICS 2025), Salt Lake City, Utah, USA, June 2025.
  Paper online pdf
  Conference Talk video pptx pdf

• Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi, Mohammad Sadrosadati, Mohammed Alser, and Onur Mutlu.
  “RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment”
  IEEE Access, December 2024.
  Paper online pdf code

• Can Firtina, Maximilian Mordig, Harun Mustafa, Sayan Goswami, Nika Mansouri Ghiasi, Stefano Mercogliano, Furkan Eris, Joel Lindegger, Andre Kahles, and Onur Mutlu.
  “Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism”
  arXiv, October 2024.
  Paper online pdf code
  ISMB 2024 Talk video pptx pdf
  CSHL 2024 Talk video pptx pdf
  Social Media Thread Twitter (X) LinkedIn

• Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joel Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, and Onur Mutlu.
  “TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering”
  Frontiers in Genetics, September 2024.
  Paper online pdf code

• Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, and Onur Mutlu.
  “AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes”
  IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), August 2024.
  Paper online pdf code
  APBC 2023 Talk video pptx pdf

• Can Firtina, Melina Soysal, Joël Lindegger, and Onur Mutlu.
  “RawHash2: Mapping Raw Nanopore Signals Using Hash-Based Seeding and Adaptive Quantization”
  Bioinformatics, July 2024.
  Paper online pdf code

• Nika Mansouri Ghiasi, Mohammad Sadrosadati, Harun Mustafa, Arvid Gollwitzer, Can Firtina, Julien Eudine, Haiyu Mao, Joël Lindegger, Meryem Banu Cavlak, Mohammed Alser, Jisung Park, and Onur Mutlu.
  “MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing”
  Proceedings of the 51st Annual International Symposium on Computer Architecture (ISCA 2024), Buenos Aires, Argentina, July 2024.
  Paper online pdf code
  Conference Talk pptx pdf

• Mohammed Alser, Brendan Lawlor, Richard J. Abdill, Sharon Waymost, Ram Ayyala, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, André M. Ribeiro-dos-Santos, Nour Almadhoun, Varuni Sarwal, Can Firtina, Tomasz Osinski, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do Kim, Malak S. Abedalthagafi, Onur Mutlu, and Serghei Mangul.
  “Packaging and containerization of computational methods”
  Nature Protocols, April 2024.
  Paper online pdf

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

• 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, and Onur Mutlu.
  “ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis”
  ACM Transactions on Architecture and Code Optimization (TACO), February 2024.
  Paper online pdf code
  HiPEAC 2024 Talk video pptx pdf

• Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joel Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, and Said Hamdioui.
  “Swordfish: A Framework for Evaluating Deep Neural Network-Based Basecalling Using Computation-In-Memory with Non-Ideal Memristors”
  Proceedings of MICRO 2023, Toronto, ON, Canada, November 2023.
  Paper online pdf
  Conference Talk pptx pdf

• Konstantinos Kanellopoulos, Rahul Bera, Kosta Stojiljkovic, F. Nisa Bostanci, Can Firtina, Rachata Ausavarungnirun, Rakesh Kumar, Nastaran Hajinazar, Mohammad Sadrosadati, Nandita Vijaykumar, and Onur Mutlu.
  “Utopia: Fast and Efficient Address Translation via Hybrid Restrictive and Flexible Virtual-to-Physical Address Mappings”
  Proceedings of MICRO 2023, Toronto, ON, Canada, November 2023.
  Paper online pdf code

• Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joel Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, and Onur Mutlu.
  “MetaTrinity: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation”
  arXiv, November 2023.
  Paper online pdf code

• Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joel Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, and Onur Mutlu.
  “SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences”
  arXiv, October 2023.
  Paper online pdf code

• Onur Mutlu and Can Firtina.
  “Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design”
  Proceedings of DAC 2023, San Francisco, CA, USA, July 2023.
  Paper online pdf

• Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, and Onur Mutlu.
  “RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes”
  Proceedings of ISMB 2023 and ECCB 2023, Lyon, France, July 2023.
  Paper online pdf code
  Conference Talk video pptx pdf
  Preprint online pdf
  Social Media Thread Twitter (X)

• 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.
  “BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis”
  NAR Genomics and Bioinformatics (NARGAB), March 2023.
  Paper online pdf code
  Preprint online pdf
  RECOMB 2023 Talk video pptx pdf
  Social Media Thread Twitter (X) Twitter (X)

• Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, and Onur Mutlu.
  “GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping”
  Proceedings of MICRO 2022, Chicago, IL, USA, October 2022.
  Paper online pdf
  Conference Talk pptx pdf

• Jeremie S Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, and Onur Mutlu.
  “FastRemap: a tool for quickly remapping reads between genome assemblies”
  Bioinformatics, September 2022.
  Paper online pdf code

• Mohammed Alser, Joel Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gomez-Luna, and Onur Mutlu.
  “From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures”
  Computational and Structural Biotechnology Journal (CSBJ), August 2022.
  Paper online pdf code

• Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser, Stephan Wong, Onur Mutlu, and Said Hamdioui.
  “Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory”
  IEEE Access, August 2022.
  Paper online pdf

• 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.
  “SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping”
  Proceedings of ISCA 2022, New York City, NY, USA, June 2022.
  Paper online pdf code
  Conference Talk video pptx pdf

• 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.
  “GenStore: A High-Performance in-Storage Processing System for Genome Sequence Analysis”
  Proceedings of ASPLOS 2022, Lusanne, Switzerland, February 2022.
  Paper online pdf code
  Conference Talk video pptx pdf

• Levent Onural, Mustafa Çelebi Pınar, and Can Firtina.
  “Modeling Economic Activities and Random Catastrophic Failures of Financial Networks via Gibbs Random Fields”
  Computational Economics, August 2021.
  Paper online pdf

• 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.
  “GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis”
  Proceedings of MICRO 2020, Virtual, October 2020.
  Paper online pdf code
  Conference Talk video pptx pdf

• Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A Ercument Cicek, Can Alkan, and Onur Mutlu.
  “Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm”
  Bioinformatics, June 2020.
  Paper online pdf code

• Can Firtina, Ziv Bar-Joseph, Can Alkan, and A. Ercument Cicek.
  “Hercules: a profile HMM-based hybrid error correction algorithm for long reads”
  Nucleic Acids Research (NAR), November 2018.
  Paper online pdf code

• Burçak Otlu, Can Firtina, Sündüz Keleş, and Oznur Tastan.
  “GLANET: genomic loci annotation and enrichment tool”
  Bioinformatics, September 2017.
  Paper online code

• Can Firtina and Can Alkan.
  “On genomic repeats and reproducibility”
  Bioinformatics, August 2016.
  Paper online code