Joël Lindegger

According to our database, Joël Lindegger authored at least 18 papers between 2022 and 2024.

Collaborative distances:

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

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

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

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

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, Nishil Talati, Onur Mutlu, Osman S. Unsal, Mateo Valero, Adrián Cristal

Proceedings of the 51st ACM/IEEE Annual International Symposium on Computer Architecture, 2024

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, Onur Mutlu

Proceedings of the 51st ACM/IEEE Annual International Symposium on Computer Architecture, 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

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, 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

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

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

RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes.

Can Firtina, Nika Mansouri-Ghiasi, Joël Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu

Bioinform., 2023

Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors.

Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi, Haiyu Mao, Joël Lindegger, Can Firtina, Stephan Wong, Onur Mutlu, Said Hamdioui

Proceedings of the 56th Annual IEEE/ACM International Symposium on Microarchitecture, 2023

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

Proceedings of the 50th Annual International Symposium on Computer Architecture, 2023

2022

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering.

Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser, Can Firtina, Joël Lindegger, Mohammad Sadrosadati, Nika Mansouri-Ghiasi, Can Alkan, Onur Mutlu

CoRR, 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, Juan Gómez-Luna, Onur Mutlu

CoRR, 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, Jisung Park, Juan Gómez-Luna, Onur Mutlu, Hamid Sarbazi-Azad

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