A5052807455- Algorithms and Data Compression
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Advanced Data Storage Technologies
- Caching and Content Delivery
- Distributed and Parallel Computing Systems
- Microbial Community Ecology and Physiology
- Machine Learning in Bioinformatics
- Cloud Computing and Resource Management
ETH Zurich
2022
Read mapping is a fundamental step in many genomics applications. It used to identify potential matches and differences between fragments (called reads) of sequenced genome an already known reference genome). costly because it needs perform approximate string matching (ASM) on large amounts data. To address the computational challenges analysis, prior works propose various approaches such as accurate filters that select reads within dataset genomic read set) must undergo expensive...
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It used to identify potential matches and differences between fragments (called reads) of sequenced genome an already known reference genome). To address the computational challenges analysis, prior works propose various approaches such as filters that select reads must undergo expensive computation, efficient heuristics, hardware acceleration. While effective at reducing computation overhead,...
Metagenomics has led to significant advances in many fields. Metagenomic analysis commonly involves the key tasks of determining species present a sample and their relative abundances. These require searching large metagenomic databases. suffers from data movement overhead due moving amounts low-reuse storage system. In-storage processing can be fundamental solution for reducing this overhead. However, designing an in-storage system metagenomics is challenging because existing approaches...
Genome sequence analysis, which analyzes the DNA sequences of organisms, is important for many applications in personalized medicine [1]–[8], outbreak tracing [9]–[14], and evolutionary studies [15]–[21]. The information an organism's converted to digital data via a process called sequencing. A sequencing machine extracts molecules from sample form strings consisting four base pairs <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$(bps)$</tex> ,...
Metagenomics, the study of genome sequences diverse organisms cohabiting in a shared environment, has experienced significant advancements across various medical and biological fields. Metagenomic analysis is crucial, for instance, clinical applications such as infectious disease screening diagnosis early detection diseases cancer. A key task metagenomics to determine species present sample their relative abundances. Currently, field dominated by either alignment-based tools, which offer...
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 sequences one most fundamental steps in Due to its high complexity, optimized exact and algorithms are still being developed. We find these highly sensitive underlying data, quality, various hyperparameters. Despite their wide use, no in-depth analysis has been performed, potentially falsely...
Metagenomics has led to significant advancements in many fields. Metagenomic analysis commonly involves the key tasks of determining species present a sample and their relative abundances. These require searching large metagenomic databases containing information on different species' genomes. suffers from data movement overhead due moving amounts low-reuse storage system rest system. In-storage processing can be fundamental solution for reducing overhead. However, designing an in-storage...