| Rowpress: Amplifying read disturbance in modern dram chips H Luo, A Olgun, AG Yağlıkçı, YC Tuğrul, S Rhyner, MB Cavlak, ... Proceedings of the 50th Annual International Symposium on Computer …, 2023 | 54 | 2023 |
| 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 | 49 | 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 | 48 | 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 | 20 | 2023 |
| Morpheus: Extending the last level cache capacity in GPU systems using idle GPU core resources S Darabi, M Sadrosadati, N Akbarzadeh, J Lindegger, M Hosseini, J Park, ... 2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO), 228-244, 2022 | 17 | 2022 |
| Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs J Lindegger, D Senol Cali, M Alser, J Gómez-Luna, NM Ghiasi, O Mutlu Bioinformatics 39 (5), btad151, 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 | 9 | 2023 |
| 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 | 7 | 2024 |
| Going from molecules to genomic variations to scientific discovery: Intelligent algorithms and architectures for intelligent genome analysis M Alser, J Lindegger, C Firtina, N Almadhoun, H Mao, G Singh, ... arXiv preprint arXiv:2205.07957, 2022 | 7 | 2022 |
| 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 | 6 | 2024 |
| Algorithmic improvement and GPU acceleration of the GenASM algorithm J Lindegger, DS Cali, M Alser, J Gómez-Luna, O Mutlu 2022 IEEE International Parallel and Distributed Processing Symposium …, 2022 | 6 | 2022 |
| 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 | 5 | 2024 |
| RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization C Firtina, M Soysal, J Lindegger, O Mutlu Bioinformatics 40 (8), btae478, 2024 | 3 | 2024 |
| MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing NM Ghiasi, M Sadrosadati, H Mustafa, A Gollwitzer, C Firtina, J Eudine, ... 2024 ACM/IEEE 51st Annual International Symposium on Computer Architecture …, 2024 | 2 | 2024 |
| An In-Memory Architecture for High-Performance Long-Read Pre-Alignment Filtering T Shahroodi, M Miao, J Lindegger, S Wong, O Mutlu, S Hamdioui arXiv preprint arXiv:2310.15634, 2023 | 2 | 2023 |
| RawHash2: Accurate and fast mapping of raw nanopore signals using a hash-based seeding mechanism C Firtina, M Soysal, J Lindegger, O Mutlu arXiv preprint arXiv:2309.05771, 2023 | 2 | 2023 |
| RowPress Vulnerability in Modern DRAM Chips H Luo, A Olgun, AG Yağlıkçı, YC Tuğrul, S Rhyner, MB Cavlak, ... IEEE Micro, 2024 | 1 | 2024 |
| SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences MD Rumpf, M Alser, AE Gollwitzer, J Lindegger, N Almadhoun, C Firtina, ... arXiv preprint arXiv:2310.16908, 2023 | 1 | 2023 |
| Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism C Firtina, M Mordig, H Mustafa, S Goswami, NM Ghiasi, S Mercogliano, ... arXiv preprint arXiv:2410.17801, 2024 | | 2024 |
| QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms J Pavon, IV Valdivieso, C Rojas, C Hernandez, M Aslan, R Figueras, ... 2024 ACM/IEEE 51st Annual International Symposium on Computer Architecture …, 2024 | | 2024 |
