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Can Firtina
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2020 – today
- 2024
- [j7]Can Firtina
, Kamlesh R. Pillai
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis. ACM Trans. Archit. Code Optim. 21(1): 19:1-19:29 (2024) - [c9]Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Harun Mustafa
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. ISCA 2024: 660-677 - [i19]Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Harun Mustafa
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. CoRR abs/2406.19113 (2024) - 2023
- [j6]Can Firtina
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes. Bioinform. 39(Supplement-1): 297-307 (2023) - [c8]Onur Mutlu, Can Firtina:
Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design. DAC 2023: 1-4 - [c7]Konstantinos Kanellopoulos
Utopia: Fast and Efficient Address Translation via Hybrid Restrictive & Flexible Virtual-to-Physical Address Mappings. MICRO 2023: 1196-1212 - [c6]Taha Shahroodi
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors. MICRO 2023: 1437-1452 - [i18]Onur Mutlu, Can Firtina:
Accelerating Genome Analysis via Algorithm-Architecture Co-Design. CoRR abs/2305.00492 (2023) - [i17]Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joël Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui:
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors. CoRR abs/2310.04366 (2023) - [i16]Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences. CoRR abs/2310.16908 (2023) - [i15]Arvid E. Gollwitzer
MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation. CoRR abs/2311.02029 (2023) - [i14]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:
MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing. CoRR abs/2311.12527 (2023) - 2022
- [j5]Taha Shahroodi
Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in Memory. IEEE Access 10: 82493-82510 (2022) - [j4]Jeremie S. Kim
FastRemap: a tool for quickly remapping reads between genome assemblies. Bioinform. 38(19): 4633-4635 (2022) - [c5]Nika Mansouri-Ghiasi, Jisung Park
GenStore: a high-performance in-storage processing system for genome sequence analysis. ASPLOS 2022: 635-654 - [c4]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:
SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping. ISCA 2022: 638-655 - [c3]Nika Mansouri-Ghiasi, Jisung Park, Harun Mustafa, Jeremie S. Kim, Ataberk Olgun, Arvid Gollwitzer
GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis. ISVLSI 2022: 283-287 - [c2]Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu:
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. MICRO 2022: 710-726 - [i13]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:
GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis. CoRR abs/2202.10400 (2022) - [i12]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:
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities. CoRR abs/2203.16261 (2022) - [i11]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:
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping. CoRR abs/2205.05883 (2022) - [i10]Mohammed Alser, Joël Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gómez-Luna, Onur Mutlu:
Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis. CoRR abs/2205.07957 (2022) - [i9]Taha Shahroodi, Mahdi Zahedi, Can Firtina, Mohammed Alser, Stephan Wong, Onur Mutlu, Said Hamdioui:
Demeter: A Fast and Energy-Efficient Food Profiler using Hyperdimensional Computing in Memory. CoRR abs/2206.01932 (2022) - [i8]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:
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis. CoRR abs/2207.09765 (2022) - [i7]Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu:
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. CoRR abs/2209.08600 (2022) - [i6]Gagandeep Singh, Mohammed Alser, Alireza Khodamoradi, Kristof Denolf, Can Firtina, Meryem Banu Cavlak, Henk Corporaal, Onur Mutlu:
A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers. CoRR abs/2211.03079 (2022) - [i5]Konstantinos Kanellopoulos, Rahul Bera, Kosta Stojiljkovic, Can Firtina, Rachata Ausavarungnirun, Nastaran Hajinazar, Jisung Park, Nandita Vijaykumar, Onur Mutlu:
Utopia: Efficient Address Translation using Hybrid Virtual-to-Physical Address Mapping. CoRR abs/2211.12205 (2022) - [i4]Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu:
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering. CoRR abs/2212.04953 (2022) - 2020
- [j3]Can Firtina
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Bioinform. 36(12): 3669-3679 (2020) - [c1]Damla Senol Cali
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. MICRO 2020: 951-966 - [i3]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:
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. CoRR abs/2009.07692 (2020)
2010 – 2019
- 2019
- [i2]Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu:
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm. CoRR abs/1902.04341 (2019) - [i1]Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu:
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes. CoRR abs/1912.08735 (2019) - 2017
- [j2]Burçak Otlu
GLANET: genomic loci annotation and enrichment tool. Bioinform. 33(18): 2818-2828 (2017) - 2016
- [j1]Can Firtina
On genomic repeats and reproducibility. Bioinform. 32(15): 2243-2247 (2016)
Coauthor Index
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last updated on 2024-10-07 21:23 CEST by the dblp team
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