46 citations · 139 across the 15 of their papers we have counts for
7 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…
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…
RawHash2: Mapping Raw Nanopore Signals Using Hash-Based Seeding and Adaptive Quantization
Can Firtina, Melina Soysal, Joël Lindegger +1
Summary: Raw nanopore signals can be analyzed while they are being generated, a process known as real-time analysis. Real-time analysis of raw signals is essential to utilize the u…
RowPress: Amplifying Read Disturbance in Modern DRAM Chips
Haocong Luo, Ataberk Olgun, A. Giray Yağlıkçı +6
Memory isolation is critical for system reliability, security, and safety. Unfortunately, read disturbance can break memory isolation in modern DRAM chips. For example, RowHammer i…
RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes
Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger +4
Nanopore sequencers generate electrical raw signals in real-time while sequencing long genomic strands. These raw signals can be analyzed as they are generated, providing an opport…