| 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 | 156 | 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 | 97* | 2022 |
| 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 | 60 | 2020 |
| 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 | 58* | 2022 |
| On Genomic Repeats and Reproducibility C Firtina, C Alkan Bioinformatics 32 (15), 2243-2247, 2016 | 52 | 2016 |
| 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 | 51 | 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 | 46 | 2018 |
| 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 | 36* | 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 | 27 | 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 | 25* | 2022 |
| 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 | 24 | 2023 |
| 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 | 20* | 2024 |
| AirLift: a fast and comprehensive technique for remapping alignments between reference genomes JS Kim, C Firtina, MB Cavlak, DS Cali, N Hajinazar, M Alser, C Alkan, ... IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2024 | 19* | 2024 |
| GLANET: genomic loci annotation and enrichment tool B Otlu, C Firtina, S Keleş, O Tastan Bioinformatics 33 (18), 2818-2828, 2017 | 18 | 2017 |
| Accelerating genome analysis via algorithm-architecture co-design O Mutlu, C Firtina 2023 60th ACM/IEEE Design Automation Conference (DAC), 1-4, 2023 | 14 | 2023 |
| 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 | 11 | 2023 |
| Utopia: Fast and efficient address translation via hybrid restrictive & flexible virtual-to-physical address mappings K Kanellopoulos, R Bera, K Stojiljkovic, FN Bostanci, C Firtina, ... Proceedings of the 56th Annual IEEE/ACM International Symposium on …, 2023 | 10 | 2023 |
| Targetcall: Eliminating the wasted computation in basecalling via pre-basecalling filtering MB Cavlak, G Singh, M Alser, C Firtina, J Lindegger, M Sadrosadati, ... Frontiers in Genetics 15, 1429306, 2024 | 9 | 2024 |
| 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 | 9 | 2024 |
| RawAlign: Accurate, fast, and scalable raw nanopore signal mapping via combining seeding and alignment J Lindegger, C Firtina, NM Ghiasi, M Sadrosadati, M Alser, O Mutlu IEEE Access, 2024 | 8 | 2024 |
Onur MutluETH Zürich and Carnegie Mellon UniversityVerified email at inf.ethz.ch
