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Can Firtina
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GenASM: A high-performance, low-power approximate string matching acceleration framework for genome sequence analysis
DS Cali, GS Kalsi, Z Bingöl, C Firtina, L Subramanian, JS Kim, ...
2020 53rd Annual IEEE/ACM International Symposium on Microarchitecture …, 2020
1232020
GenStore: a high-performance in-storage processing system for genome sequence analysis
N Mansouri Ghiasi, J Park, H Mustafa, J Kim, A Olgun, A Gollwitzer, ...
Proceedings of the 27th ACM International Conference on Architectural …, 2022
73*2022
On Genomic Repeats and Reproducibility
C Firtina, C Alkan
Bioinformatics 32 (15), 2243-2247, 2016
472016
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm
C Firtina, JS Kim, M Alser, D Senol Cali, AE Cicek, C Alkan, O Mutlu
Bioinformatics 36 (12), 3669-3679, 2020
462020
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
C Firtina, Z Bar-Joseph, C Alkan, AE Cicek
Nucleic acids research 46 (21), e125-e125, 2018
402018
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
M Alser, J Lindegger, C Firtina, N Almadhoun, H Mao, G Singh, ...
Computational and Structural Biotechnology Journal 20, 4579-4599, 2022
37*2022
SeGraM: A universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping
DS Cali, K Kanellopoulos, J Lindegger, Z Bingöl, GS Kalsi, Z Zuo, ...
Proceedings of the 49th Annual International Symposium on Computer …, 2022
312022
BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis
C Firtina, J Park, M Alser, JS Kim, DS Cali, T Shahroodi, NM Ghiasi, ...
NAR Genomics and Bioinformatics 5 (1), lqad004, 2023
22*2023
Demeter: A fast and energy-efficient food profiler using hyperdimensional computing in memory
T Shahroodi, M Zahedi, C Firtina, M Alser, S Wong, O Mutlu, S Hamdioui
IEEE Access 10, 82493-82510, 2022
202022
AirLift: A Fast and Comprehensive Technique for Translating Alignments between Reference Genomes
JS Kim, C Firtina, DS Cali, M Alser, N Hajinazar, C Alkan, O Mutlu
arXiv preprint arXiv:1912.08735, 2019
182019
GLANET: genomic loci annotation and enrichment tool
B Otlu, C Firtina, S Keleş, O Tastan
Bioinformatics 33 (18), 2818-2828, 2017
172017
Genpip: In-memory acceleration of genome analysis via tight integration of basecalling and read mapping
H Mao, M Alser, M Sadrosadati, C Firtina, A Baranwal, DS Cali, A Manglik, ...
2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO), 710-726, 2022
122022
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes
C Firtina, N Mansouri Ghiasi, J Lindegger, G Singh, MB Cavlak, H Mao, ...
Bioinformatics 39 (Supplement_1), i297-i307, 2023
112023
RUBICON: a framework for designing efficient deep learning-based genomic basecallers
G Singh, M Alser, K Denolf, C Firtina, A Khodamoradi, MB Cavlak, ...
Genome Biology 25 (1), 49, 2024
6*2024
FastRemap: a tool for quickly remapping reads between genome assemblies
JS Kim, C Firtina, MB Cavlak, D Senol Cali, C Alkan, O Mutlu
Bioinformatics 38 (19), 4633-4635, 2022
62022
Accelerating Genome Analysis via Algorithm-Architecture Co-Design
O Mutlu, C Firtina
2023 60th ACM/IEEE Design Automation Conference (DAC), 1-4, 2023
52023
Modeling economic activities and random catastrophic failures of financial networks via Gibbs random fields
L Onural, MÇ Pınar, C Fırtına
Computational Economics 58 (2), 203-232, 2021
52021
ApHMM: Accelerating profile hidden markov models for fast and energy-efficient genome analysis
C Firtina, K Pillai, GS Kalsi, B Suresh, DS Cali, JS Kim, T Shahroodi, ...
ACM Transactions on Architecture and Code Optimization 21 (1), 1-29, 2024
42024
Targetcall: Eliminating the wasted computation in basecalling via pre-basecalling filtering
MB Cavlak, G Singh, M Alser, C Firtina, J Lindegger, M Sadrosadati, ...
arXiv preprint arXiv:2212.04953, 2022
32022
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors
T Shahroodi, G Singh, M Zahedi, H Mao, J Lindegger, C Firtina, S Wong, ...
Proceedings of the 56th Annual IEEE/ACM International Symposium on …, 2023
22023
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