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ORCIDDamla Senol Cali
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2020 – today
- 2024
[j9]Can Firtina
, Kamlesh R. Pillai, Gurpreet S. Kalsi, Bharathwaj Suresh, Damla Senol Cali, Jeremie S. Kim, Taha Shahroodi, Meryem Banu Cavlak, Joël Lindegger, Mohammed Alser, Juan Gómez-Luna, Sreenivas Subramoney, Onur Mutlu:
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis. ACM Trans. Archit. Code Optim. 21(1): 19:1-19:29 (2024)- 2023
- [j8]Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu:
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs. Bioinform. 39(5) (2023) - 2022
- [j7]Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu:
FastRemap: a tool for quickly remapping reads between genome assemblies. Bioinform. 38(19): 4633-4635 (2022) - [c7]Nika Mansouri-Ghiasi, Jisung Park, Harun Mustafa, Jeremie S. Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, Onur Mutlu:
GenStore: a high-performance in-storage processing system for genome sequence analysis. ASPLOS 2022: 635-654 - [c6]Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu:
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. IPDPS Workshops 2022: 162 - [c5]Damla Senol Cali, Konstantinos Kanellopoulos, Joël Lindegger, Zülal Bingöl, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie S. Kim, Nika Mansouri-Ghiasi, Gagandeep Singh, Juan Gómez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu:
SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping. ISCA 2022: 638-655 - [c4]Nika Mansouri-Ghiasi, Jisung Park, Harun Mustafa, Jeremie S. Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, Onur Mutlu:
GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis. ISVLSI 2022: 283-287 - [c3]Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu:
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. MICRO 2022: 710-726 - [i14]Nika Mansouri-Ghiasi, Jisung Park, Harun Mustafa, Jeremie S. Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, Onur Mutlu:
GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis. CoRR abs/2202.10400 (2022) - [i13]Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu:
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. CoRR abs/2203.15561 (2022) - [i12]Damla Senol Cali, Konstantinos Kanellopoulos, Joël Lindegger, Zülal Bingöl, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie S. Kim, Nika Mansouri-Ghiasi, Gagandeep Singh, Juan Gómez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu:
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping. CoRR abs/2205.05883 (2022) - [i11]Can Firtina, Kamlesh R. Pillai, Gurpreet S. Kalsi, Bharathwaj Suresh, Damla Senol Cali, Jeremie S. Kim, Taha Shahroodi, Meryem Banu Cavlak, Joël Lindegger, Mohammed Alser, Juan Gómez-Luna, Sreenivas Subramoney, Onur Mutlu:
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis. CoRR abs/2207.09765 (2022) - [i10]Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu:
Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs. CoRR abs/2208.09985 (2022) - [i9]Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu:
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. CoRR abs/2209.08600 (2022) - 2021
- [j6]Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, Onur Mutlu:
FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications. IEEE Micro 41(4): 39-48 (2021) - [i8]Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, Onur Mutlu:
FPGA-based Near-Memory Acceleration of Modern Data-Intensive Applications. CoRR abs/2106.06433 (2021) - [i7]Damla Senol Cali:
Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design. CoRR abs/2111.01916 (2021) - 2020
- [j5]Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu:
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Bioinform. 36(12): 3669-3679 (2020) - [j4]Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu:
Accelerating Genome Analysis: A Primer on an Ongoing Journey. IEEE Micro 40(5): 65-75 (2020) - [c2]Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gómez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu:
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. MICRO 2020: 951-966 - [i6]Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu:
Accelerating Genome Analysis: A Primer on an Ongoing Journey. CoRR abs/2008.00961 (2020) - [i5]Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gómez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, Onur Mutlu:
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. CoRR abs/2009.07692 (2020)
2010 – 2019
- 2019
- [j3]Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu:
Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Briefings Bioinform. 20(4): 1542-1559 (2019) - [j2]Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, Onur Mutlu:
Demystifying Complex Workload-DRAM Interactions: An Experimental Study. Proc. ACM Meas. Anal. Comput. Syst. 3(3): 60:1-60:50 (2019) - [c1]Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, Onur Mutlu:
Demystifying Complex Workload-DRAM Interactions: An Experimental Study. SIGMETRICS (Abstracts) 2019: 93 - [i4]Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu:
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm. CoRR abs/1902.04341 (2019) - [i3]Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, Onur Mutlu:
Understanding the Interactions of Workloads and DRAM Types: A Comprehensive Experimental Study. CoRR abs/1902.07609 (2019) - [i2]Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu:
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes. CoRR abs/1912.08735 (2019) - 2018
- [j1]Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu:
GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. BMC Genom. 19(S2) (2018) - 2017
- [i1]Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu:
GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies. CoRR abs/1711.01177 (2017)
Coauthor Index
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