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Joel Lindegger
Joel Lindegger
PhD Student, SAFRI Research Group, ETH Zurich
Verified email at safari.ethz.ch
Title
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Cited by
Year
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
M Alser, J Lindegger, C Firtina, N Almadhoun, H Mao, G Singh, ...
Computational and Structural Biotechnology Journal 20, 4579-4599, 2022
342022
SeGraM: A universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping
DS Cali, K Kanellopoulos, J Lindegger, Z Bingöl, GS Kalsi, Z Zuo, ...
Proceedings of the 49th Annual International Symposium on Computer íK, 2022
332022
Rowpress: Amplifying read disturbance in modern dram chips
H Luo, A Olgun, AG Yağlıkçı, YC Tuğrul, S Rhyner, MB Cavlak, ...
Proceedings of the 50th Annual International Symposium on Computer íK, 2023
182023
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes
C Firtina, N Mansouri Ghiasi, J Lindegger, G Singh, MB Cavlak, H Mao, ...
Bioinformatics 39 (Supplement_1), i297-i307, 2023
112023
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs
J Lindegger, D Senol Cali, M Alser, J Gómez-Luna, NM Ghiasi, O Mutlu
Bioinformatics 39 (5), btad151, 2023
102023
Morpheus: Extending the last level cache capacity in GPU systems using idle GPU core resources
S Darabi, M Sadrosadati, N Akbarzadeh, J Lindegger, M Hosseini, J Park, ...
2022 55th IEEE/ACM International Symposium on Microarchitecture (MICRO), 228-244, 2022
82022
Going from molecules to genomic variations to scientific discovery: Intelligent algorithms and architectures for intelligent genome analysis
M Alser, J Lindegger, C Firtina, N Almadhoun, H Mao, G Singh, ...
arXiv preprint arXiv:2205.07957, 2022
72022
Algorithmic improvement and GPU acceleration of the GenASM algorithm
J Lindegger, DS Cali, M Alser, J Gómez-Luna, O Mutlu
2022 IEEE International Parallel and Distributed Processing Symposium íK, 2022
62022
ApHMM: Accelerating profile hidden markov models for fast and energy-efficient genome analysis
C Firtina, K Pillai, GS Kalsi, B Suresh, DS Cali, JS Kim, T Shahroodi, ...
ACM Transactions on Architecture and Code Optimization 21 (1), 1-29, 2024
42024
Targetcall: Eliminating the wasted computation in basecalling via pre-basecalling filtering
MB Cavlak, G Singh, M Alser, C Firtina, J Lindegger, M Sadrosadati, ...
arXiv preprint arXiv:2212.04953, 2022
32022
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors
T Shahroodi, G Singh, M Zahedi, H Mao, J Lindegger, C Firtina, S Wong, ...
Proceedings of the 56th Annual IEEE/ACM International Symposium on íK, 2023
22023
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
J Lindegger, C Firtina, NM Ghiasi, M Sadrosadati, M Alser, O Mutlu
arXiv preprint arXiv:2310.05037, 2023
22023
RawHash2: Accurate and Fast Mapping of Raw Nanopore Signals using a Hash-based Seeding Mechanism
C Firtina, M Soysal, J Lindegger, O Mutlu
arXiv preprint arXiv:2309.05771, 2023
22023
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences
MD Rumpf, M Alser, AE Gollwitzer, J Lindegger, N Almadhoun, C Firtina, ...
arXiv preprint arXiv:2310.16908, 2023
12023
An In-Memory Architecture for High-Performance Long-Read Pre-Alignment Filtering
T Shahroodi, M Miao, J Lindegger, S Wong, O Mutlu, S Hamdioui
arXiv preprint arXiv:2310.15634, 2023
12023
MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing
NM Ghiasi, M Sadrosadati, H Mustafa, A Gollwitzer, C Firtina, J Eudine, ...
arXiv preprint arXiv:2311.12527, 2023
2023
MetaFast: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation
AE Gollwitzer, M Alser, J Bergtholdt, J Lindegger, MD Rumpf, C Firtina, ...
arXiv preprint arXiv:2311.02029, 2023
2023
MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing
N Mansouri Ghiasi, M Sadrosadati, H Mustafa, A Gollwitzer, C Firtina, ...
arXiv e-prints, arXiv: 2311.12527, 2023
2023
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
M Banu Cavlak, G Singh, M Alser, C Firtina, J Lindegger, M Sadrosadati, ...
arXiv e-prints, arXiv: 2212.04953, 2022
2022
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping
D Senol Cali, K Kanellopoulos, J Lindegger, Z Bingöl, GS Kalsi, Z Zuo, ...
arXiv e-prints, arXiv: 2205.05883, 2022
2022
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