155 citations · 1k across the 40 of their papers we have counts for
11 papers · 2 filters
RUBICON: A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers
Gagandeep Singh, Mohammed Alser, Kristof Denolf +5
Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The a…
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping
Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati +6
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore seq…
Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs
Joël Lindegger, Damla Senol Cali, Mohammed Alser +3
Pairwise sequence alignment is a very time-consuming step in common bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations, and/or hardware…
A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems
Safaa Diab, Amir Nassereldine, Mohammed Alser +3
Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate thi…
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis
Can Firtina, Kamlesh Pillai, Gurpreet S. Kalsi +10
Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequen…
Exploiting Near-Data Processing to Accelerate Time Series Analysis
Ivan Fernandez, Ricardo Quislant, Christina Giannoula +5
Time series analysis is a key technique for extracting and predicting events in domains as diverse as epidemiology, genomics, neuroscience, environmental sciences, economics, and m…