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)

Morpheus: Extending the Last Level Cache Capacity in GPU Systems Using Idle GPU Core Resources. - Sina Darabi; Mohammad Sadrosadati; Negar Akbarzadeh; Joël Lindegger; Mohammad Hosseini 001; Jisung Park 001; Juan Gómez-Luna; Onur Mutlu; Hamid Sarbazi-Azad (MICRO, 2022)

Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis. - Mohammed Alser; Joël Lindegger; Can Firtina; Nour Almadhoun; Haiyu Mao; Gagandeep Singh 002; Juan Gómez-Luna; Onur Mutlu (CoRR, 2022)

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering. - Meryem Banu Cavlak; Gagandeep Singh 002; Mohammed Alser; Can Firtina; Joël Lindegger; Mohammad Sadrosadati; Nika Mansouri-Ghiasi; Can Alkan; Onur Mutlu (CoRR, 2022)

RowPress: Amplifying Read Disturbance in Modern DRAM Chips. - Haocong Luo; Ataberk Olgun; Abdullah Giray Yaglikçi; Yahya Can Tugrul; Steve Rhyner; Meryem Banu Cavlak; Joël Lindegger; Mohammad Sadrosadati; Onur Mutlu (ISCA, 2023)

Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors. - Taha Shahroodi; Gagandeep Singh 002; Mahdi Zahedi; Haiyu Mao; Joël Lindegger; Can Firtina; Stephan Wong; Onur Mutlu; Said Hamdioui (MICRO, 2023)

RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes. - Can Firtina; Nika Mansouri-Ghiasi; Joël Lindegger; Gagandeep Singh 002; Meryem Banu Cavlak; Haiyu Mao; Onur Mutlu (Bioinform., 2023)

An In-Memory Architecture for High-Performance Long-Read Pre-Alignment Filtering. - Taha Shahroodi; Michael Miao; Joël Lindegger; Stephan Wong; Onur Mutlu; Said Hamdioui (CoRR, 2023)

SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences. - Maximilian-David Rumpf; Mohammed Alser; Arvid E. Gollwitzer; Joël Lindegger; Nour Almadhoun; Can Firtina; Serghei Mangul; Onur Mutlu (CoRR, 2023)

MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation. - Arvid E. Gollwitzer; Mohammed Alser; Joel Bergtholdt; Joël Lindegger; Maximilian-David Rumpf; Can Firtina; Serghei Mangul; Onur Mutlu (CoRR, 2023)

MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing. - Nika Mansouri-Ghiasi; Mohammad Sadrosadati; Harun Mustafa; Arvid Gollwitzer; Can Firtina; Julien Eudine; Haiyu Mao; Joël Lindegger; Meryem Banu Cavlak; Mohammed Alser; Jisung Park 001; Onur Mutlu (CoRR, 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., 2023)

MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. - Nika Mansouri-Ghiasi; Mohammad Sadrosadati; Harun Mustafa; Arvid Gollwitzer; Can Firtina; Julien Eudine; Haiyu Mao; Joël Lindegger; Meryem Banu Cavlak; Mohammed Alser; Jisung Park 001; Onur Mutlu (ISCA, 2024)

QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms. - Julian Pavon; Iván Vargas Valdivieso; Carlos Rojas; César Hernández; Mehmet Aslan; Roger Figueras; Yichao Yuan; Joël Lindegger; Mohammed Alser; Francesc Moll; Santiago Marco-Sola; Oguz Ergin; et al. (ISCA, 2024)

RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment. - Joël Lindegger; Can Firtina; Nika Mansouri-Ghiasi; Mohammad Sadrosadati; Mohammed Alser; Onur Mutlu (IEEE Access, 2024)

RowPress Vulnerability in Modern DRAM Chips. - Haocong Luo; Ataberk Olgun; Abdullah Giray Yaglikçi; Yahya Can Tugrul; Steve Rhyner; Meryem Banu Cavlak; Joël Lindegger; Mohammad Sadrosadati; Onur Mutlu (IEEE Micro, 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; et al. (ACM Trans. Archit. Code Optim., 2024)