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)

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)

Understanding the Interactions of Workloads and DRAM Types: A Comprehensive Experimental Study. - Saugata Ghose; Tianshi Li 001; Nastaran Hajinazar; Damla Senol Cali; Onur Mutlu (CoRR, 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)

Demystifying Complex Workload-DRAM Interactions: An Experimental Study. - Saugata Ghose; Tianshi Li 001; Nastaran Hajinazar; Damla Senol Cali; Onur Mutlu (Proc. ACM Meas. Anal. Comput. Syst., 2019)

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; et al. (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)

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)

Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design. - Damla Senol Cali (CoRR, 2021)

FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications. - Gagandeep Singh 002; Mohammed Alser; Damla Senol Cali; Dionysios Diamantopoulos; Juan Gómez-Luna; Henk Corporaal; Onur Mutlu (IEEE Micro, 2021)

GenStore: a high-performance in-storage processing system for genome sequence analysis. - Nika Mansouri-Ghiasi; Jisung Park 001; Harun Mustafa; Jeremie S. Kim; Ataberk Olgun; Arvid Gollwitzer; Damla Senol Cali; Can Firtina; Haiyu Mao; Nour Almadhoun Alserr; Rachata Ausavarungnirun; Nandita Vijaykumar; et al. (ASPLOS, 2022)

Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. - Joël Lindegger; Damla Senol Cali; Mohammed Alser; Juan Gómez-Luna; Onur Mutlu (IPDPS Workshops, 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 002; Juan Gómez-Luna; et al. (ISCA, 2022)

GenStore: In-Storage Filtering of Genomic Data for High-Performance and Energy-Efficient Genome Analysis. - Nika Mansouri-Ghiasi; Jisung Park 001; Harun Mustafa; Jeremie S. Kim; Ataberk Olgun; Arvid Gollwitzer; Damla Senol Cali; Can Firtina; Haiyu Mao; Nour Almadhoun Alserr; Rachata Ausavarungnirun; Nandita Vijaykumar; et al. (ISVLSI, 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 (MICRO, 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)

GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis. - Nika Mansouri-Ghiasi; Jisung Park 001; Harun Mustafa; Jeremie S. Kim; Ataberk Olgun; Arvid Gollwitzer; Damla Senol Cali; Can Firtina; Haiyu Mao; Nour Almadhoun Alserr; Rachata Ausavarungnirun; Nandita Vijaykumar; et al. (CoRR, 2022)

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., 2023)

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; et al. (ACM Trans. Archit. Code Optim., 2024)