| 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 | 82 | 2020 |
| On Genomic Repeats and Reproducibility C Firtina, C Alkan Bioinformatics 32 (15), 2243-2247, 2016 | 43 | 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 | 38 | 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 | 33* | 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 | 31 | 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 | 15 | 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 | 15 | 2019 |
| GLANET: genomic loci annotation and enrichment tool B Otlu, C Firtina, S Keleş, O Tastan Bioinformatics 33 (18), 2818-2828, 2017 | 15 | 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 | 12* | 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 | 7* | 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 | 6 | 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 | 5 | 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 | 4 | 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 | 3 | 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 | 2 | 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 | 1 | 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 | 1 | 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 | 1 | 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 | | 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 | | 2022 |
Onur MutluETH Zürich and Carnegie Mellon UniversityEmail verificata su inf.ethz.ch
