Damla Senol Cali

According to our database, Damla Senol Cali authored at least 19 papers between 2018 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis.

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

ACM Trans. Archit. Code Optim., March, 2024

2023

Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs.

Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu

Bioinform., May, 2023

2022

GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis.

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

CoRR, 2022

FastRemap: a tool for quickly remapping reads between genome assemblies.

Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu

Bioinform., 2022

GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping.

Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati, Can Firtina, Akanksha Baranwal, Damla Senol Cali, Aditya Manglik, Nour Almadhoun Alserr, Onur Mutlu

Proceedings of the 55th IEEE/ACM International Symposium on Microarchitecture, 2022

GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis.

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

Proceedings of the IEEE Computer Society Annual Symposium on VLSI, 2022

SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping.

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

Proceedings of the ISCA '22: The 49th Annual International Symposium on Computer Architecture, New York, New York, USA, June 18, 2022

Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm.

Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022

GenStore: a high-performance in-storage processing system for genome sequence analysis.

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

Proceedings of the ASPLOS '22: 27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems, Lausanne, Switzerland, 28 February 2022, 2022

2021

FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications.

Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, Onur Mutlu

IEEE Micro, 2021

Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design.

Damla Senol Cali

CoRR, 2021

2020

Accelerating Genome Analysis: A Primer on an Ongoing Journey.

Mohammed Alser, Zülal Bingöl, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu

IEEE Micro, 2020

Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm.

Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercüment Çiçek, Can Alkan, Onur Mutlu

Bioinform., 2020

GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis.

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

Proceedings of the 53rd Annual IEEE/ACM International Symposium on Microarchitecture, 2020

2019

Demystifying Complex Workload-DRAM Interactions: An Experimental Study.

Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, Onur Mutlu

Proc. ACM Meas. Anal. Comput. Syst., 2019

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes.

Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Mohammed Alser, Nastaran Hajinazar, Can Alkan, Onur Mutlu

CoRR, 2019

Understanding the Interactions of Workloads and DRAM Types: A Comprehensive Experimental Study.

Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, Onur Mutlu

CoRR, 2019

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu

Briefings Bioinform., 2019

2018

GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.

Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu

BMC Genom., 2018