Publications

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)]

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)]

Preprint (bioRxiv)[Link][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.

Preprint (bioRxiv)[Link][PDF]

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.