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The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is…
Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the…
A substantial disadvantage of traditional learning is that all students follow the same learning sequence, but not all of them have the same background of knowledge, the same preferences, the same learning goals, and the same needs.…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
Motivation: Modern genomics laboratories generate massive volumes of sequencing data, often resulting in significant storage costs. Genomics storage consists of duplicate files, temporary processing files, and redundant intermediate data.…
Computer-aided diagnosis (CADx) algorithms in medicine provide patient-specific decision support for physicians. These algorithms are usually applied after full acquisition of high-dimensional multimodal examination data, and often assume…
Mapper, a topological algorithm, is frequently used as an exploratory tool to build a graphical representation of data. This representation can help to gain a better understanding of the intrinsic shape of high-dimensional genomic data and…
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…
Molecular property calculations are the bedrock of chemical physics. High-fidelity \textit{ab initio} modeling techniques for computing the molecular properties can be prohibitively expensive, and motivate the development of…
De novo assembly enables investigations of unknown genomes, paving the way for personalized medicine and disease management. However, it faces immense computational challenges arising from the excessive data volumes and algorithmic…
With the popularity of deep learning, the hardware implementation platform of deep learning has received increasing interest. Unlike the general purpose devices, e.g., CPU, or GPU, where the deep learning algorithms are executed at the…
We present PEANUT (ParallEl AligNment UTility), a highly parallel GPU-based read mapper with several distinguishing features, including a novel q-gram index (called the q-group index) with small memory footprint built on-the-fly over the…
Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it…
Darwin is a genomics co-processor that achieved a 15000x acceleration on long read assembly through innovative hardware and algorithm co-design. Darwins algorithms and hardware implementation were specifically designed for DNA analysis…
The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications. We propose a rigorous and flexible algorithmic solution to mapping SOLiD…
Achieving faster execution with shorter compilation time can foster further diversity and innovation in neural networks. However, the current paradigm of executing neural networks either relies on hand-optimized libraries, traditional…
While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
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…
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…