Joël Lindegger

29 papers A* 6Journal 22Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.
Bioinform.
Can Firtina, Maximilian Mordig, Harun Mustafa, Sayan Goswami, Nika Mansouri-Ghiasi, Stefano Mercogliano, Furkan Eris, Joël Lindegger, André Kahles, 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
2024 A* conf
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing.
ISCA
Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Harun Mustafa, Arvid Gollwitzer, Can Firtina, Julien Eudine, Haiyu Mao, Joël Lindegger, Meryem Banu Cavlak, Mohammed Alser, Jisung Park, Onur Mutlu
2024 J jnl
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing.
CoRR
Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Harun Mustafa, Arvid Gollwitzer, Can Firtina, Julien Eudine, Haiyu Mao, Joël Lindegger, Meryem Banu Cavlak, Mohammed Alser, Jisung Park, Onur Mutlu
2024 A* conf
QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms.
ISCA
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, Nishil Talati, Onur Mutlu, Osman S. Unsal, Mateo Valero, Adrián Cristal
2024 J jnl
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment.
IEEE Access
Joël Lindegger, Can Firtina, Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu
2024 J jnl
RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization.
Bioinform.
Can Firtina, Melina Soysal, Joël Lindegger, Onur Mutlu
2024 J jnl
RowPress Vulnerability in Modern DRAM Chips.
CoRR
Haocong Luo, Ataberk Olgun, A. Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, Onur Mutlu
2024 J jnl
RowPress Vulnerability in Modern DRAM Chips.
IEEE Micro
Haocong Luo, Ataberk Olgun, Abdullah Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, Onur Mutlu
2023 J jnl
An In-Memory Architecture for High-Performance Long-Read Pre-Alignment Filtering.
CoRR
Taha Shahroodi, Michael Miao, Joël Lindegger, Stephan Wong, Onur Mutlu, Said Hamdioui
2023 J jnl
MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation.
CoRR
Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joël Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu
2023 J jnl
MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing.
CoRR
Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Harun Mustafa, Arvid Gollwitzer, Can Firtina, Julien Eudine, Haiyu Mao, Joël Lindegger, Meryem Banu Cavlak, Mohammed Alser, Jisung Park, Onur Mutlu
2023 J jnl
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes.
Bioinform.
Can Firtina, Nika Mansouri-Ghiasi, Joël Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu
2023 A* conf
RowPress: Amplifying Read Disturbance in Modern DRAM Chips.
ISCA
Haocong Luo, Ataberk Olgun, Abdullah Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, Onur Mutlu
2023 J jnl
RowPress: Amplifying Read Disturbance in Modern DRAM Chips.
CoRR
Haocong Luo, Ataberk Olgun, Abdullah Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, 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
2023 J jnl
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences.
CoRR
Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joël Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu
2023 A* conf
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors.
MICRO
Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joël Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui
2023 J jnl
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors.
CoRR
Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joël Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui
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
Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis.
CoRR
Mohammed Alser, Joël Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gómez-Luna, Onur Mutlu
2022 A* conf
Morpheus: Extending the Last Level Cache Capacity in GPU Systems Using Idle GPU Core Resources.
MICRO
Sina Darabi, Mohammad Sadrosadati, Negar Akbarzadeh, Joël Lindegger, Mohammad Hosseini, Jisung Park, Juan Gómez-Luna, Onur Mutlu, Hamid Sarbazi-Azad
2022 J jnl
Morpheus: Extending the Last Level Cache Capacity in GPU Systems Using Idle GPU Core Resources.
CoRR
Sina Darabi, Mohammad Sadrosadati, Joël Lindegger, Negar Akbarzadeh, Mohammad Hosseini, Jisung Park, Juan Gómez-Luna, Hamid Sarbazi-Azad, 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
2022 J jnl
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering.
CoRR
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu