| GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies JS Kim, D Senol Cali, H Xin, D Lee, S Ghose, M Alser, H Hassan, O Ergin, ... BMC genomics 19 (2), 23-40, 2018 | 169 | 2018 |
| Critical assessment of metagenome interpretation: the second round of challenges F Meyer, A Fritz, ZL Deng, D Koslicki, TR Lesker, A Gurevich, G Robertson, ... Nature methods 19 (4), 429-440, 2022 | 130 | 2022 |
| GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping M Alser, H Hassan, H Xin, O Ergin, O Mutlu, C Alkan Bioinformatics, 2017 | 111 | 2017 |
| SIMDRAM: a framework for bit-serial SIMD processing using DRAM N Hajinazar, GF Oliveira, S Gregorio, JD Ferreira, NM Ghiasi, M Patel, ... Proceedings of the 26th ACM International Conference on Architectural …, 2021 | 109 | 2021 |
| 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 | 103 | 2020 |
| Technology dictates algorithms: recent developments in read alignment M Alser, J Rotman, D Deshpande, K Taraszka, H Shi, PI Baykal, HT Yang, ... Genome biology 22 (1), 249, 2021 | 76 | 2021 |
| Shouji: a fast and efficient pre-alignment filter for sequence alignment M Alser, H Hassan, A Kumar, O Mutlu, C Alkan Bioinformatics 35 (21), 4255-4263, 2019 | 72 | 2019 |
| NATSA: a near-data processing accelerator for time series analysis I Fernandez, R Quislant, E Gutiérrez, O Plata, C Giannoula, M Alser, ... 2020 IEEE 38th International Conference on Computer Design (ICCD), 120-129, 2020 | 68 | 2020 |
| Accelerating genome analysis: A primer on an ongoing journey M Alser, Z Bingöl, DS Cali, J Kim, S Ghose, C Alkan, O Mutlu IEEE Micro 40 (5), 65-75, 2020 | 67 | 2020 |
| FPGA-based near-memory acceleration of modern data-intensive applications G Singh, M Alser, DS Cali, D Diamantopoulos, J Gómez-Luna, ... IEEE Micro 41 (4), 39-48, 2021 | 61 | 2021 |
| SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs M Alser, T Shahroodi, J Gómez-Luna, C Alkan, O Mutlu Bioinformatics 36 (22-23), 5282-5290, 2020 | 57 | 2020 |
| Metalign: efficient alignment-based metagenomic profiling via containment min hash N LaPierre, M Alser, E Eskin, D Koslicki, S Mangul Genome biology 21 (1), 1-15, 2020 | 43 | 2020 |
| 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 | 43 | 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 | 38 | 2022 |
| SysScale: Exploiting multi-domain dynamic voltage and frequency scaling for energy efficient mobile processors J Haj-Yahya, M Alser, J Kim, AG Yağlıkçı, N Vijaykumar, E Rotem, O Mutlu 2020 ACM/IEEE 47th Annual International Symposium on Computer Architecture …, 2020 | 34 | 2020 |
| MAGNET: understanding and improving the accuracy of genome pre-alignment filtering M Alser, O Mutlu, C Alkan arXiv preprint arXiv:1707.01631, 2017 | 32 | 2017 |
| pluto: In-dram lookup tables to enable massively parallel general-purpose computation JD Ferreira, G Falcao, J Gómez-Luna, M Alser, L Orosa, M Sadrosadati, ... arXiv preprint arXiv:2104.07699, 2021 | 31 | 2021 |
| 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 | 27 | 2022 |
| MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples N LaPierre, S Mangul, M Alser, I Mandric, NC Wu, D Koslicki, E Eskin BMC genomics 20, 1-10, 2019 | 27 | 2019 |
| High-throughput pairwise alignment with the wavefront algorithm using processing-in-memory S Diab, A Nassereldine, M Alser, JG Luna, O Mutlu, IE Hajj arXiv preprint arXiv:2204.02085, 2022 | 23 | 2022 |
Onur MutluETH Zürich and Carnegie Mellon UniversityVerified email at inf.ethz.ch
