38 citations · 47 across the 4 of their papers we have counts for
4 papers
LCPan: efficient variation graph construction using Locally Consistent Parsing
Akmuhammet Ashyralyyev, Zülal Bingöl, Begüm Filiz Öz +5
Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input…
Revisiting Main Memory-Based Covert and Side Channel Attacks in the Context of Processing-in-Memory
F. Nisa Bostanci, Konstantinos Kanellopoulos, Ataberk Olgun +6
We introduce IMPACT, a set of high-throughput main memory-based timing attacks that leverage characteristics of processing-in-memory (PiM) architectures to establish covert and sid…
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.,…
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping
Zülal Bingöl, Mohammed Alser, Onur Mutlu +2
At the last step of short read mapping, the candidate locations of the reads on the reference genome are verified to compute their differences from the corresponding reference segm…