CRANE: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models
Simon Ambrozak, Ulysse McConnell, Bhargav Srinivasan, Burak Ozkan, Ernest Zhang, Can Firtina
arXiv, March 2026.
ISMB 2026 (HiTSeq) Talk[Slides (pptx)][Slides (pdf)]
Publications
Author copies are provided for personal, academic use. Each entry includes artifacts (code, data, slides) where available.
2026
Rawsamble: Overlapping Raw Nanopore Signals using a Hash-based Seeding Mechanism
Can Firtina, Maximilian Mordig, Harun Mustafa, Sayan Goswami, Nika Mansouri Ghiasi, Stefano Mercogliano, Furkan Eris, Joel Lindegger, Andre Kahles, Onur Mutlu
Bioinformatics, February 2026.
ISMB 2024 Talk[Video][Slides (pptx)][Slides (pdf)]
CSHL 2024 (Biological Data Science) Talk[Video][Slides (pptx)][Slides (pdf)]
Social media thread[Twitter (X)][LinkedIn]
GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping
Julien Eudine, Chu Li, Zhuo Cheng, Renzo Andri, Onur Mutlu, Can Firtina, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Konstantina Koliogeorgi, Anirban Nag, Arash Tavakkol, Haiyu Mao, Shai Bergman, Ji Zhang
Proceedings of the 32nd International Symposium on High-Performance Computer Architecture (HPCA 2026), Sydney, Australia, January 2026.
SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Sequence Analysis
Nika Mansouri Ghiasi, Talu Güloglu, Harun Mustafa, Can Firtina, Konstantina Koliogeorgi, Konstantinos Kanellopoulos, Haiyu Mao, Rakesh Nadig, Mohammad Sadrosadati, Jisung Park, Onur Mutlu
Proceedings of the 32nd International Symposium on High-Performance Computer Architecture (HPCA 2026), Sydney, Australia, January 2026.
2025
RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques
Furkan Eris, Ulysse McConnell, Can Firtina, Onur Mutlu
Proceedings of the 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2025), Philadelphia, PA, USA, October 2025.
Conference talk[Slides (pptx)][Slides (pdf)]
MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem
Melina Soysal, Konstantina Koliogeorgi, Can Firtina, Nika Mansouri Ghiasi, Rakesh Nadig, Haiyu Mao, Geraldo Francisco Oliveira Junior, Yu Liang, Klea Zambaku, Mohammad Sadrosadati, Onur Mutlu
Proceedings of the 39th International Conference on Supercomputing (ICS 2025), Salt Lake City, Utah, USA, June 2025.
Conference talk[Video][Slides (pptx)][Slides (pdf)]
2024
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
IEEE Access, December 2024.
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joel Lindegger, Mohammad Sadrosadati, Nika Mansouri Ghiasi, Can Alkan, Onur Mutlu
Frontiers in Genetics, September 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, Onur Mutlu
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), August 2024.
APBC 2023 Talk[Video][Slides (pptx)][Slides (pdf)]
RawHash2: Mapping Raw Nanopore Signals Using Hash-Based Seeding and Adaptive Quantization
Can Firtina, Melina Soysal, Joël Lindegger, Onur Mutlu
Bioinformatics, July 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 51st Annual International Symposium on Computer Architecture (ISCA 2024), Buenos Aires, Argentina, July 2024.
Conference talk[Slides (pptx)][Slides (pdf)]
Packaging and containerization of computational methods
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 (B.D) Kim, Malak S. Abedalthagafi, Onur Mutlu, Serghei Mangul
Nature Protocols, April 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, February 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 (TACO), February 2024.
HiPEAC 2024 Talk[Video][Slides (pptx)][Slides (pdf)]
2023
Swordfish: A Framework for Evaluating Deep Neural Network-Based Basecalling Using Computation-In-Memory with Non-Ideal Memristors
Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joel Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui
Proceedings of the 56th International Symposium on Microarchitecture (MICRO 2023), Toronto, ON, Canada, November 2023.
Conference talk[Slides (pptx)][Slides (pdf)]
Utopia: Fast and Efficient Address Translation via Hybrid Restrictive & Flexible Virtual-to-Physical Address Mappings
Konstantinos Kanellopoulos, Rahul Bera, Kosta Stojiljkovic, F. Nisa Bostanci, Can Firtina, Rachata Ausavarungnirun, Rakesh Kumar, Nastaran Hajinazar, Mohammad Sadrosadati, Nandita Vijaykumar, Onur Mutlu
Proceedings of the 56th International Symposium on Microarchitecture (MICRO 2023), Toronto, ON, Canada, November 2023.
MetaTrinity: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation
Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joel Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu
arXiv, November 2023.
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences
Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joel Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu
arXiv, October 2023.
Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design
Onur Mutlu, Can Firtina
Proceedings of the 60th Design Automation Conference (DAC 2023), San Francisco, CA, USA, July 2023.
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
Proceedings of the 31st Annual Conference on Intelligent Systems for Molecular Biology and the 22nd European Conference on Computational Biology (ISMB/ECCB 2023), Lyon, France, July 2023.
Conference talk[Video][Slides (pptx)][Slides (pdf)]
Social media thread[Twitter (X)]
BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis
Can Firtina, Jisung Park, Mohammed Alser, Jeremie S. Kim, Damla Senol Cali, Taha Shahroodi, Nika Mansouri Ghiasi, Gagandeep Singh, Konstantinos Kanellopoulos, Can Alkan, Onur Mutlu
NAR Genomics and Bioinformatics (NARGAB), March 2023.
RECOMB 2023 Talk[Video][Slides (pptx)][Slides (pdf)]
Social media thread[Twitter (X), publication][Twitter (X), preprint]
2022
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping
Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu
Proceedings of the 55th International Symposium on Microarchitecture (MICRO 2022), Chicago, IL, USA, October 2022.
Conference talk[Slides (pptx)][Slides (pdf)]
FastRemap: a tool for quickly remapping reads between genome assemblies
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu
Bioinformatics, September 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, Onur Mutlu
Computational and Structural Biotechnology Journal (CSBJ), August 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, Said Hamdioui
IEEE Access, August 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, Onur Mutlu
Proceedings of the 49th Annual International Symposium on Computer Architecture (ISCA 2022), New York City, NY, USA, June 2022.
Conference talk[Video][Slides (pptx)][Slides (pdf)]
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, Onur Mutlu
Proceedings of the 27th International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS 2022), Lausanne, Switzerland, February 2022.
Conference talk[Video][Slides (pptx)][Slides (pdf)]
2021
Modeling Economic Activities and Random Catastrophic Failures of Financial Networks via Gibbs Random Fields
Levent Onural, Mustafa Çelebi Pınar, Can Firtina
Computational Economics, August 2021.
2020
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, Onur Mutlu
Proceedings of the 53rd International Symposium on Microarchitecture (MICRO 2020), Virtual, October 2020.
Conference talk[Video][Slides (pptx)][Slides (pdf)]
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, Onur Mutlu
Bioinformatics, June 2020.
2018
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Can Firtina, Ziv Bar-Joseph, Can Alkan, A. Ercument Cicek
Nucleic Acids Research (NAR), November 2018.
2017
GLANET: genomic loci annotation and enrichment tool
Burçak Otlu, Can Firtina, Sündüz Keleş, Oznur Tastan
Bioinformatics, September 2017.
2016
On genomic repeats and reproducibility
Can Firtina, Can Alkan
Bioinformatics, August 2016.