46 citations · 107 across the 9 of their papers we have counts for
11 papers
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…
RowPress Vulnerability in Modern DRAM Chips
Haocong Luo, Ataberk Olgun, A. Giray Yağlıkçı +6
Memory isolation is a critical property for system reliability, security, and safety. We demonstrate RowPress, a DRAM read disturbance phenomenon different from the well-known RowH…
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…
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…
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser +6
Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art…
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…
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…
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping
Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger +15
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e.,…
FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak +3
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a…
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak +5
AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another simil…