| Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions D Senol Cali, JS Kim, S Ghose, C Alkan, O Mutlu Briefings in Bioinformatics, 2018 | 216 | 2018 |
| 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 | 213* | 2018 |
| GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis D Senol Cali, GS Kalsi, Z Bingöl, C Firtina, L Subramanian, JS Kim, ... 2020 53rd Annual IEEE/ACM International Symposium on Microarchitecture …, 2020 | 153 | 2020 |
| Demystifying complex workload-DRAM interactions: An experimental study S Ghose, T Li, N Hajinazar, D Senol Cali, O Mutlu Proceedings of the ACM on Measurement and Analysis of Computing Systems 3 (3 …, 2019 | 108* | 2019 |
| Accelerating Genome Analysis: A Primer on an Ongoing Journey M Alser, Z Bingöl, D Senol Cali, J Kim, S Ghose, C Alkan, O Mutlu IEEE Micro 40 (5), 65-75, 2020 | 94 | 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 | 89* | 2022 |
| FPGA-based Near-Memory Acceleration of Modern Data-Intensive Applications G Singh, M Alser, D Senol Cali, D Diamantopoulos, J Gomez-Luna, ... IEEE Micro, 2021 | 81 | 2021 |
| 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 | 55 | 2020 |
| SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping D Senol Cali, K Kanellopoulos, J Lindegger, Z Bingöl, GS Kalsi, Z Zuo, ... arXiv preprint arXiv:2205.05883, 2022 | 44* | 2022 |
| BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches C Firtina, J Park, JS Kim, M Alser, D Senol Cali, T Shahroodi, NM Ghiasi, ... arXiv preprint arXiv:2112.08687, 2021 | 34* | 2021 |
| AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes JS Kim, C Firtina, MB Cavlak, D Senol Cali, N Hajinazar, M Alser, C Alkan, ... bioRxiv, 2021 | 17* | 2021 |
| 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 |
| 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, D Senol Cali, ... arXiv preprint arXiv:2209.08600, 2022 | 14 | 2022 |
| ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis C Firtina, K Pillai, GS Kalsi, B Suresh, D Senol Cali, J Kim, T Shahroodi, ... arXiv preprint arXiv:2207.09765, 2022 | 6 | 2022 |
| Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm J Lindegger, D Senol Cali, M Alser, J Gómez-Luna, O Mutlu arXiv preprint arXiv:2203.15561, 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 arXiv preprint arXiv:2201.06255, 2022 | 6 | 2022 |
| Genome Sequence Alignment System and Method GS Kalsi, AV Nori, CJ Hughes, S Subramoney, D Senol US Patent App. 16/729,379, 2021 | 3 | 2021 |
| Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design D Senol Cali Carnegie Mellon University, 2021 | 1 | 2021 |
| Accelerated Optical Genome Mapping Analysis with Stratys Compute and Guided Assembly D Senol Cali, T Anantharaman, M Muggli, S Al-Saffar, C Schoonover, ... Cancer Research 84 (6_Supplement), 2337-2337, 2024 | | 2024 |
| P850: Accelerated Optical Genome Mapping Analysis with Stratys Compute and Guided Assembly D Senol Cali, T Anantharaman, M Muggli, S Al-Saffar, C Schoonover, ... Genetics in Medicine Open 2, 2024 | | 2024 |
Onur MutluETH Zürich and Carnegie Mellon UniversityVerified email at inf.ethz.ch
