Damla Senol Cali

31 papers A* 4Journal 24Unranked 3

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	AirLift: A Fast and Comprehensive Technique for Remapping Alignments Between Reference Genomes. IEEE Trans. Comput. Biol. Bioinform. Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, Onur Mutlu
2024	J	`jnl`	ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis. ACM Trans. Archit. Code Optim. 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
2023	J	`jnl`	Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs. Bioinform. Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu
2022	—	`conf`	Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. IPDPS Workshops Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu
2022	J	`jnl`	Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. CoRR Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu
2022	J	`jnl`	ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis. CoRR 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
2022	J	`jnl`	FastRemap: a tool for quickly remapping reads between genome assemblies. Bioinform. Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu
2022	A*	`conf`	GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. MICRO Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu
2022	J	`jnl`	GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping. CoRR Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu
2022	J	`jnl`	GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis. CoRR 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
2022	—	`conf`	GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis. ISVLSI 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
2022	A*	`conf`	GenStore: a high-performance in-storage processing system for genome sequence analysis. ASPLOS 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
2022	J	`jnl`	Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs. CoRR Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu
2022	J	`jnl`	SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping. CoRR 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
2022	A*	`conf`	SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping. ISCA 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
2021	J	`jnl`	Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design. CoRR Damla Senol Cali
2021	J	`jnl`	FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications. IEEE Micro Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, Onur Mutlu
2021	J	`jnl`	FPGA-based Near-Memory Acceleration of Modern Data-Intensive Applications. CoRR Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, Onur Mutlu
2020	J	`jnl`	Accelerating Genome Analysis: A Primer on an Ongoing Journey. CoRR Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
2020	J	`jnl`	Accelerating Genome Analysis: A Primer on an Ongoing Journey. IEEE Micro Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
2020	J	`jnl`	Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm. Bioinform. Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
2020	A*	`conf`	GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. MICRO 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
2020	J	`jnl`	GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. CoRR 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
2019	J	`jnl`	AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes. CoRR Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu
2019	J	`jnl`	Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm. CoRR Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu
2019	—	`conf`	Demystifying Complex Workload-DRAM Interactions: An Experimental Study. SIGMETRICS (Abstracts) Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, Onur Mutlu
2019	J	`jnl`	Demystifying Complex Workload-DRAM Interactions: An Experimental Study. Proc. ACM Meas. Anal. Comput. Syst. Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, Onur Mutlu
2019	J	`jnl`	Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions. Briefings Bioinform. Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
2019	J	`jnl`	Understanding the Interactions of Workloads and DRAM Types: A Comprehensive Experimental Study. CoRR Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, Onur Mutlu
2018	J	`jnl`	GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies. BMC Genom. Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
2017	J	`jnl`	GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies. CoRR Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu