Related papers: Accelerating Genome Sequence Analysis via Efficien…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
Neural architectures and hardware accelerators have been two driving forces for the progress in deep learning. Previous works typically attempt to optimize hardware given a fixed model architecture or model architecture given fixed…
High quality AI solutions require joint optimization of AI algorithms, such as deep neural networks (DNNs), and their hardware accelerators. To improve the overall solution quality as well as to boost the design productivity, efficient…
Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds of such systems. Such high-throughput and low-cost…
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…
The decreasing costs and increasing speed and accuracy of DNA sample collection, preparation, and sequencing has rapidly produced an enormous volume of genetic data. However, fast and accurate analysis of the samples remains a bottleneck.…
Genome sequencing is essential to decode genetic information, identify organisms, understand diseases and advance personalized medicine. A critical step in any genome sequencing technique is genome assembly. However, de novo genome…
The advent of next-generation sequencing (NGS) has revolutionized genomic research by enabling cost-effective, high-throughput sequencing of a diverse range of organisms. This breakthrough has unleashed a "Cambrian explosion" in genomic…
The surge in availability of genomic data holds promise for enabling determination of genetic causes of observed individual traits, with applications to problems such as discovery of the genetic roots of phenotypes, be they molecular…
Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be…
The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…
Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing…
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…
Motivation: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and…
With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden…
Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the…
Genomic sequence alignment is an important research topic in bioinformatics and continues to attract significant efforts. As genomic data grow exponentially, however, most of alignment methods face challenges due to their huge computational…