155 citations · 1k across the 40 of their papers we have counts for
24 papers · 1 filter
CiMBA: Accelerating Genome Sequencing through On-Device Basecalling via Compute-in-Memory
William Andrew Simon, Irem Boybat, Riselda Kodra +8
As genome sequencing is finding utility in a wide variety of domains beyond the confines of traditional medical settings, its computational pipeline faces two significant challenge…
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing
Nika Mansouri Ghiasi, Mohammad Sadrosadati, Harun Mustafa +9
Metagenomics has led to significant advances in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative…
MetaStore: High-Performance Metagenomic Analysis via In-Storage Computing
Nika Mansouri Ghiasi, Mohammad Sadrosadati, Harun Mustafa +9
Metagenomics has led to significant advancements in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relat…
GateSeeder: Near-memory CPU-FPGA Acceleration of Short and Long Read Mapping
Julien Eudine, Mohammed Alser, Gagandeep Singh +2
Motivation: Read mapping is a computationally expensive process and a major bottleneck in genomics analyses. The performance of read mapping is mainly limited by the performance of…
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…