Related papers: Accelerating Genome Sequence Analysis via Efficien…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
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., sequence-to-sequence mapping). Recent works replace the…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
Genome sequence analysis, which examines the DNA sequences of organisms, drives advances in many critical medical and biotechnological fields. Given its importance and the exponentially growing volumes of genomic sequence data, there are…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a critical bottleneck in bioinformatics analysis. The existing…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\times$ and the number of…
Genome sequence analysis is a powerful tool in medical and scientific research. Considering the inevitable sequencing errors and genetic variations, approximate string matching (ASM) has been adopted in practice for genome sequencing.…
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 relief. Comparing genomic sequences is one of the most…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
Dynamic programming (DP) algorithms, such as All-Pairs Shortest Path (APSP) and genomic sequence alignment, are fundamental to many scientific domains but are severely bottlenecked by data movement on conventional architectures. While…
Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
Pairwise sequence alignment is a very time-consuming step in common bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations, and/or hardware acceleration. A promising candidate for all of the above is…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
Genomics is the critical key to enabling precision medicine, ensuring global food security and enforcing wildlife conservation. The massive genomic data produced by various genome sequencing technologies presents a significant challenge for…