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ORCIDJoël Lindegger
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2020 – today
- 2024
[j5]Joël Lindegger, Can Firtina
, Nika Mansouri-Ghiasi, Mohammad Sadrosadati, Mohammed Alser, Onur Mutlu:
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment. IEEE Access 12: 196855-196865 (2024)- [j4]Haocong Luo, Ataberk Olgun, Abdullah Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, Onur Mutlu:
RowPress Vulnerability in Modern DRAM Chips. IEEE Micro 44(4): 60-69 (2024) - [j3]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:
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis. ACM Trans. Archit. Code Optim. 21(1): 19:1-19:29 (2024) - [c7]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:
QUETZAL: Vector Acceleration Framework for Modern Genome Sequence Analysis Algorithms. ISCA 2024: 597-612 - [c6]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:
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. ISCA 2024: 660-677 - [i15]Haocong Luo, Ataberk Olgun, A. Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, Onur Mutlu:
RowPress Vulnerability in Modern DRAM Chips. CoRR abs/2406.16153 (2024) - [i14]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:
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing. CoRR abs/2406.19113 (2024) - 2023
- [j2]Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu:
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs. Bioinform. 39(5) (2023) - [j1]Can Firtina, Nika Mansouri-Ghiasi, Joël Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu:
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes. Bioinform. 39(Supplement-1): 297-307 (2023) - [c5]Haocong Luo, Ataberk Olgun, Abdullah Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, Onur Mutlu:
RowPress: Amplifying Read Disturbance in Modern DRAM Chips. ISCA 2023: 28:1-28:18 - [c4]Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joël Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui:
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors. MICRO 2023: 1437-1452 - [i13]Haocong Luo, Ataberk Olgun, Abdullah Giray Yaglikçi, Yahya Can Tugrul, Steve Rhyner, Meryem Banu Cavlak, Joël Lindegger, Mohammad Sadrosadati, Onur Mutlu:
RowPress: Amplifying Read Disturbance in Modern DRAM Chips. CoRR abs/2306.17061 (2023) - [i12]Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joël Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui:
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors. CoRR abs/2310.04366 (2023) - [i11]Taha Shahroodi, Michael Miao, Joël Lindegger, Stephan Wong, Onur Mutlu, Said Hamdioui:
An In-Memory Architecture for High-Performance Long-Read Pre-Alignment Filtering. CoRR abs/2310.15634 (2023) - [i10]Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer, Joël Lindegger, Nour Almadhoun, Can Firtina, Serghei Mangul, Onur Mutlu:
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences. CoRR abs/2310.16908 (2023) - [i9]Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt, Joël Lindegger, Maximilian-David Rumpf, Can Firtina, Serghei Mangul, Onur Mutlu:
MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation. CoRR abs/2311.02029 (2023) - [i8]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:
MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing. CoRR abs/2311.12527 (2023) - 2022
- [c3]Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu:
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. IPDPS Workshops 2022: 162 - [c2]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:
SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping. ISCA 2022: 638-655 - [c1]Sina Darabi, Mohammad Sadrosadati, Negar Akbarzadeh, Joël Lindegger, Mohammad Hosseini, Jisung Park, Juan Gómez-Luna, Onur Mutlu, Hamid Sarbazi-Azad:
Morpheus: Extending the Last Level Cache Capacity in GPU Systems Using Idle GPU Core Resources. MICRO 2022: 228-244 - [i7]Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu:
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm. CoRR abs/2203.15561 (2022) - [i6]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:
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping. CoRR abs/2205.05883 (2022) - [i5]Mohammed Alser, Joël Lindegger, Can Firtina, Nour Almadhoun, Haiyu Mao, Gagandeep Singh, Juan Gómez-Luna, Onur Mutlu:
Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis. CoRR abs/2205.07957 (2022) - [i4]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:
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis. CoRR abs/2207.09765 (2022) - [i3]Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Nika Mansouri-Ghiasi, Onur Mutlu:
Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs. CoRR abs/2208.09985 (2022) - [i2]Sina Darabi, Mohammad Sadrosadati, Joël Lindegger, Negar Akbarzadeh, Mohammad Hosseini, Jisung Park, Juan Gómez-Luna, Hamid Sarbazi-Azad, Onur Mutlu:
Morpheus: Extending the Last Level Cache Capacity in GPU Systems Using Idle GPU Core Resources. CoRR abs/2209.10914 (2022) - [i1]Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu:
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering. CoRR abs/2212.04953 (2022)
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