65 citations · 376 across the 32 of their papers we have counts for
14 papers · 1 filter
Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors
Taha Shahroodi, Gagandeep Singh, Mahdi Zahedi +6
Basecalling, an essential step in many genome analysis studies, relies on large Deep Neural Networks (DNNs) to achieve high accuracy. Unfortunately, these DNNs are computationally…
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…
MetaTrinity: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance Approximation
Arvid E. Gollwitzer, Mohammed Alser, Joel Bergtholdt +5
Metagenomics, the study of genome sequences of diverse organisms cohabiting in a shared environment, has experienced significant advancements across various medical and biological…
An In-Memory Architecture for High-Performance Long-Read Pre-Alignment Filtering
Taha Shahroodi, Michael Miao, Joel Lindegger +3
With the recent move towards sequencing of accurate long reads, finding solutions that support efficient analysis of these reads becomes more necessary. The long execution time req…
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic Sequences
Maximilian-David Rumpf, Mohammed Alser, Arvid E. Gollwitzer +5
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational…
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
Joël Lindegger, Can Firtina, Nika Mansouri Ghiasi +3
Nanopore sequencers generate raw electrical signals representing the contents of a biological sequence molecule passing through the nanopore. These signals can be analyzed directly…