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Damla Senol Cali
Damla Senol Cali
Bionano Genomics
Verified email at bionano.com - Homepage
Title
Cited by
Cited by
Year
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
206*2018
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
2022018
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
1372020
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
99*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
842020
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
79*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
782021
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
522020
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
35*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
23*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
18*2021
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
142022
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
102023
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
62022
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
62022
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
42022
Genome Sequence Alignment System and Method
GS Kalsi, AV Nori, CJ Hughes, S Subramoney, D Senol
US Patent App. 16/729,379, 2021
22021
Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design
D Senol Cali
Carnegie Mellon University, 2021
12021
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
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