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Motivation: Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. Results: We introduce context schemes: a method that allows the unambiguous recognition of a…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
Brain-inspired computing proposes a set of algorithmic principles that hold promise for advancing artificial intelligence. They endow systems with self learning capabilities, efficient energy usage, and high storage capacity. A core concept…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Over the years, many frameworks and optimization techniques have been proposed to accelerate graph neural networks (GNNs). Compared to the optimizations explored in these systems, we observe that different matrix re-associations of GNN…
Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…
This paper investigates sequencing policies for file reading requests in linear storage devices, such as magnetic tapes. Tapes are the technology of choice for long-term storage in data centers due to their low cost and reliability.…
This paper presents a genetic algorithm (GA) approach to cost-optimal task scheduling in a production line. The system consists of a set of serial processing tasks, each with a given duration, unit execution cost, and precedence…
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…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which…
Modern applications commonly leverage large, multi-modal foundation models. These applications often feature complex workflows that demand the storage and usage of similar models in multiple precisions. A straightforward approach is to…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
Living in the age of the digital media explosion, the amount of data that is being stored increases dramatically. However, even if existing storage systems suggest efficiency in capacity, they are lacking in durability. Hard disks, flash,…
This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node…
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…
Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce…
This paper presents an accurate short-read mapper for next-generation sequencing data which is widely used in the 1000 Genomes Project, and human clinical and other species genome studies.