Can Firtina

According to our database, Can Firtina authored at least 26 papers between 2016 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis.

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

ACM Trans. Archit. Code Optim., March, 2024

2023

MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing.

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

CoRR, 2023

MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation.

Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joël Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu

CoRR, 2023

SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences.

Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joël Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu

CoRR, 2023

Accelerating Genome Analysis via Algorithm-Architecture Co-Design.

Onur Mutlu, Can Firtina

CoRR, 2023

RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes.

Can Firtina, Nika Mansouri-Ghiasi, Joël Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu

Bioinform., 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, Joël Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui

Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, 2023

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 Annual IEEE/ACM International Symposium on Microarchitecture, 2023

Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design.

Onur Mutlu, Can Firtina

Proceedings of the 60th ACM/IEEE Design Automation Conference, 2023

2022

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering.

Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu

CoRR, 2022

Utopia: Efficient Address Translation using Hybrid Virtual-to-Physical Address Mapping.

Konstantinos Kanellopoulos, Rahul Bera, Kosta Stojiljkovic, Can Firtina, Rachata Ausavarungnirun, Nastaran Hajinazar, Jisung Park, Nandita Vijaykumar, Onur Mutlu

CoRR, 2022

A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers.

Gagandeep Singh, Mohammed Alser, Alireza Khodamoradi, Kristof Denolf, Can Firtina, Meryem Banu Cavlak, Henk Corporaal, Onur Mutlu

CoRR, 2022

Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis.

Mohammed Alser, Joël Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gómez-Luna, Onur Mutlu

CoRR, 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 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

CoRR, 2022

GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis.

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

CoRR, 2022

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

Bioinform., 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, 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 IEEE/ACM International Symposium on Microarchitecture, 2022

GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis.

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

Proceedings of the IEEE Computer Society Annual Symposium on VLSI, 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 S. 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 ISCA '22: The 49th Annual International Symposium on Computer Architecture, New York, New York, USA, June 18, 2022

GenStore: a high-performance in-storage processing system for genome sequence analysis.

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

Proceedings of the ASPLOS '22: 27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems, Lausanne, Switzerland, 28 February 2022, 2022

2020

Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm.

Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu

Bioinform., 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 Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu

Proceedings of the 53rd Annual IEEE/ACM International Symposium on Microarchitecture, 2020

2019

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes.

Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu

CoRR, 2019

2017

GLANET: genomic loci annotation and enrichment tool.

Burçak Otlu, Can Firtina, Sündüz Keles, Öznur Tastan

Bioinform., 2017

2016

On genomic repeats and reproducibility.

Can Firtina, Can Alkan

Bioinform., 2016