Can Firtina

49 papers A* 10A 1Journal 35Unranked 2
YearRankTypeTitle / Venue / Authors
2026 J jnl
AirLift: A Fast and Comprehensive Technique for Remapping Alignments Between Reference Genomes.
IEEE Trans. Comput. Biol. Bioinform.
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, Onur Mutlu
2026 J jnl
CERN: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models.
CoRR
Simon Ambrozak, Ulysse McConnell, Bhargav Srinivasan, Burak Ozkan, Can Firtina
2026 A* conf
GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping.
HPCA
Julien Eudine, Chu Li, Zhuo Cheng, Renzo Andri, Can Firtina, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Konstantina Koliogeorgi, Anirban Nag, Arash Tavakkol, Haiyu Mao, Onur Mutlu, Shai Bergman, Ji Zhang
2026 J jnl
GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping.
CoRR
Julien Eudine, Chu Li, Zhuo Cheng, Renzo Andri, Can Firtina, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Konstantina Koliogeorgi, Anirban Nag, Arash Tavakkol, Haiyu Mao, Onur Mutlu, Shai Bergman, Ji Zhang
2026 J jnl
Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.
Bioinform.
Can Firtina, Maximilian Mordig, Harun Mustafa, Sayan Goswami, Nika Mansouri-Ghiasi, Stefano Mercogliano, Furkan Eris, Joël Lindegger, André Kahles, Onur Mutlu
2026 A* conf
SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Sequence Analysis.
HPCA
Nika Mansouri-Ghiasi, Talu Güloglu, Harun Mustafa, Can Firtina, Konstantina Koliogeorgi, Konstantinos Kanellopoulos, Haiyu Mao, Rakesh Nadig, Mohammad Sadrosadati, Jisung Park, Onur Mutlu
2025 J jnl
Enabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and Techniques.
CoRR
Can Firtina
2025 A conf
MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem.
ICS
Melina Soysal, Konstantina Koliogeorgi, Can Firtina, Nika Mansouri-Ghiasi, Rakesh Nadig, Haiyu Mao, Geraldo Francisco de Oliveira Junior, Yu Liang, Klea Zambaku, Mohammad Sadrosadati, Onur Mutlu
2025 J jnl
MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem.
CoRR
Melina Soysal, Konstantina Koliogeorgi, Can Firtina, Nika Mansouri-Ghiasi, Rakesh Nadig, Haiyu Mao, Geraldo F. Oliveira, Yu Liang, Klea Zambaku, Mohammad Sadrosadati, Onur Mutlu
2025 — conf
RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques.
BCB
Furkan Eris, Ulysse McConnell, Can Firtina, Onur Mutlu
2025 J jnl
SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Analysis.
CoRR
Nika Mansouri-Ghiasi, Talu Güloglu, Harun Mustafa, Can Firtina, Konstantina Koliogeorgi, Konstantinos Kanellopoulos, Haiyu Mao, Rakesh Nadig, Mohammad Sadrosadati, Jisung Park, Onur Mutlu
2024 J jnl
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis.
ACM Trans. Archit. Code Optim.
Can Firtina, Kamlesh R. 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
2024 — —
Enabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and Techniques.
Can Firtina
2024 A* conf
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing.
ISCA
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
2024 J jnl
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing.
CoRR
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
2024 J jnl
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment.
IEEE Access
Joël Lindegger, Can Firtina, Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
2024 J jnl
RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization.
Bioinform.
Can Firtina, Melina Soysal, Joël Lindegger, Onur Mutlu
2023 J jnl
Accelerating Genome Analysis via Algorithm-Architecture Co-Design.
CoRR
Onur Mutlu, Can Firtina
2023 A* conf
Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design.
DAC
Onur Mutlu, Can Firtina
2023 J jnl
MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation.
CoRR
Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joël Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu
2023 J jnl
MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing.
CoRR
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
2023 J jnl
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes.
Bioinform.
Can Firtina, Nika Mansouri-Ghiasi, Joël Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu
2023 J jnl
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences.
CoRR
Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joël Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu
2023 A* conf
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors.
MICRO
Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joël Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui
2023 J jnl
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors.
CoRR
Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joël Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui
2023 A* conf
Utopia: Fast and Efficient Address Translation via Hybrid Restrictive & Flexible Virtual-to-Physical Address Mappings.
MICRO
Konstantinos Kanellopoulos, Rahul Bera, Kosta Stojiljkovic, F. Nisa Bostanci, Can Firtina, Rachata Ausavarungnirun, Rakesh Kumar, Nastaran Hajinazar, Mohammad Sadrosadati, Nandita Vijaykumar, Onur Mutlu
2022 J jnl
A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers.
CoRR
Gagandeep Singh, Mohammed Alser, Alireza Khodamoradi, Kristof Denolf, Can Firtina, Meryem Banu Cavlak, Henk Corporaal, Onur Mutlu
2022 J jnl
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis.
CoRR
Can Firtina, Kamlesh R. 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
2022 J jnl
Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory.
IEEE Access
Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser, Stephan Wong, Onur Mutlu, Said Hamdioui
2022 J jnl
Demeter: A Fast and Energy-Efficient Food Profiler using Hyperdimensional Computing in Memory.
CoRR
Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser, Stephan Wong, Onur Mutlu, Said Hamdioui
2022 J jnl
FastRemap: a tool for quickly remapping reads between genome assemblies.
Bioinform.
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu
2022 A* conf
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping.
MICRO
Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu
2022 J jnl
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping.
CoRR
Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu
2022 J jnl
GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis.
CoRR
Nika Mansouri-Ghiasi, Jisung Park, Harun Mustafa, Jeremie S. Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, Onur Mutlu
2022 — conf
GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis.
ISVLSI
Nika Mansouri-Ghiasi, Jisung Park, Harun Mustafa, Jeremie S. Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, Onur Mutlu
2022 A* conf
GenStore: a high-performance in-storage processing system for genome sequence analysis.
ASPLOS
Nika Mansouri-Ghiasi, Jisung Park, Harun Mustafa, Jeremie S. Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, Onur Mutlu
2022 J jnl
Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis.
CoRR
Mohammed Alser, Joël Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gómez-Luna, Onur Mutlu
2022 J jnl
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities.
CoRR
Mohammed Alser, Sharon Waymost, Ram Ayyala, Brendan Lawlor, Richard J. Abdill, Neha Rajkumar, Nathan LaPierre, Jaqueline J. Brito, Andre M. Ribeiro-dos-Santos, Can Firtina, Nour Almadhoun, Varuni Sarwal, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do Kim, Malak S. Abedalthagafi, Onur Mutlu, Serghei Mangul
2022 J jnl
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping.
CoRR
Damla Senol Cali, Konstantinos Kanellopoulos, Joël Lindegger, Zülal Bingöl, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie S. Kim, Nika Mansouri-Ghiasi, Gagandeep Singh, Juan Gómez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
2022 A* conf
SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping.
ISCA
Damla Senol Cali, Konstantinos Kanellopoulos, Joël Lindegger, Zülal Bingöl, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie S. Kim, Nika Mansouri-Ghiasi, Gagandeep Singh, Juan Gómez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
2022 J jnl
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering.
CoRR
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu
2022 J jnl
Utopia: Efficient Address Translation using Hybrid Virtual-to-Physical Address Mapping.
CoRR
Konstantinos Kanellopoulos, Rahul Bera, Kosta Stojiljkovic, Can Firtina, Rachata Ausavarungnirun, Nastaran Hajinazar, Jisung Park, Nandita Vijaykumar, Onur Mutlu
2020 J jnl
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm.
Bioinform.
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
2020 A* conf
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis.
MICRO
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 Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
2020 J jnl
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis.
CoRR
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 Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu
2019 J jnl
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes.
CoRR
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu
2019 J jnl
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm.
CoRR
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
2017 J jnl
GLANET: genomic loci annotation and enrichment tool.
Bioinform.
Burçak Otlu, Can Firtina, Sündüz Keles, Öznur Tastan
2016 J jnl
On genomic repeats and reproducibility.
Bioinform.
Can Firtina, Can Alkan