Modern computing systems are overwhelmingly designed to move data to computation. This
design choice goes directly against at least three key trends in computing that cause …

Motivation Sequence alignment is a memory bound computation whose performance in
modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory …

Sequence alignment remains a fundamental problem in computer science with practical
applications ranging from pattern matching to computational biology. The ever-increasing …

Generating the hash values of short subsequences, called seeds, enables quickly
identifying similarities between genomic sequences by matching seeds with a single lookup …

In the last years, advances in genome sequencing technologies have enabled the
proliferation of genomic applications that guide personalized medicine. These applications …

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 …

Motivation Pairwise sequence alignment is a very time-consuming step in common
bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations …

Fast and accurate climate simulations and weather predictions are critical for understanding
and preparing for the impact of climate change. Real-world climate and weather simulations …

High-throughput sequencing (HTS) technologies have revolutionized the field of genomics,
enabling rapid and cost-effective genome analysis for various applications. However, the …

The end of Moore's Law and Dennard Scaling has combined with advances in agile
hardware design to foster a golden age of domain-specific acceleration. However, this new …