Can Firtina
Citata da
Citata da
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
On Genomic Repeats and Reproducibility
C Firtina, C Alkan
Bioinformatics 32 (15), 2243-2247, 2016
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
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
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
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
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
GLANET: genomic loci annotation and enrichment tool
B Otlu, C Firtina, S Keleş, O Tastan
Bioinformatics 33 (18), 2818-2828, 2017
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, 2022
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
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
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
Modeling economic activities and random catastrophic failures of financial networks via Gibbs random fields
L Onural, MÇ Pınar, C Fırtına
Computational Economics 58, 203-232, 2021
ApHMM: Accelerating profile hidden markov models for fast and energy-efficient genome analysis
C Firtina, K Pillai, GS Kalsi, B Suresh, DS Cali, J Kim, T Shahroodi, ...
arXiv preprint arXiv:2207.09765, 2022
A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers
G Singh, M Alser, A Khodamoradi, K Denolf, C Firtina, MB Cavlak, ...
bioRxiv, 2022.11. 20.517297, 2022
Utopia: Efficient Address Translation using Hybrid Virtual-to-Physical Address Mapping
K Kanellopoulos, R Bera, K Stojiljkovic, C Firtina, R Ausavarungnirun, ...
arXiv preprint arXiv:2211.12205, 2022
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
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
MB Cavlak, G Singh, M Alser, C Firtina, J Lindegger, M Sadrosadati, ...
bioRxiv, 2022.12. 09.519749, 2022
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
C Firtina, NM Ghiasi, J Lindegger, G Singh, MB Cavlak, H Mao, O Mutlu
bioRxiv, 2023.01. 22.525080, 2023
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities
M Alser, S Waymost, R Ayyala, B Lawlor, RJ Abdill, N Rajkumar, ...
arXiv preprint arXiv:2203.16261, 2022
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