A5052330474- Advanced Data Storage Technologies
- Algorithms and Data Compression
- Genomics and Phylogenetic Studies
- Mass Spectrometry Techniques and Applications
- Bioinformatics and Genomic Networks
- Caching and Content Delivery
- Distributed and Parallel Computing Systems
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Amyotrophic Lateral Sclerosis Research
- Biochemical and Structural Characterization
- Genomics and Rare Diseases
- Advanced Database Systems and Queries
- Ion-surface interactions and analysis
- Scientific Computing and Data Management
University of California, Davis
2020-2024
Nile University
2020
King Abdulaziz City for Science and Technology
2018
Water buffalo (Bubalus bubalis) is an important source of meat and milk in countries with relatively warm weather. Compared to the cattle genome, a little has been done reveal its genome structure genomic traits. This due complications stemming from large size, complexity high repetitive content. In this paper, we introduce high-quality draft assembly Egyptian water genome. The breed used as dual purpose animal (milk/meat). It distinguished by adaptability local environment, quality feed...
Abstract Background Specialized data structures are required for online algorithms to efficiently handle large sequencing datasets. The counting quotient filter (CQF), a compact hashtable, can store k-mers with skewed distribution. Result Here, we present the mixed-counters (MQF) as new variant of CQF novel and labeling systems. system adapts wider range distributions increased space efficiency is faster than insertions queries in most tested scenarios. A buffered version MQF offload storage...
1 Abstract Long-read sequencing (LRS) enables variant calling of high-quality structural variants (SVs). Genotypers SVs utilize these precise call sets to increase the recall and precision genotyping in short-read (SRS) samples. With extensive growth availabilty SRS datasets recent years, we should be able calculate accurate population allele frequencies SV. However, reprocessing hundreds terabytes raw data genotype new is impractical for population-scale studies, a computational challenge...
Abstract Background Specialized data structures are required for online algorithms to efficiently handle large sequencing datasets. The counting quotient filter (CQF), a compact hashtable, can store k-mers with skewed distribution. Result Here, we present the mixed-counters (MQF) as new variant of CQF novel and labeling systems. system adapts wider range distributions increased space efficiency is faster than insertions queries in most tested scenarios. A buffered version MQF offload storage...
Abstract Background Ion Torrent is one of the major next generation sequencing (NGS) technologies and it frequently used in medical research diagnosis. The built-in software for machines delivers results BAM format. In addition to usual SAM/BAM fields, file includes technology-specific flow signal data. signals occupy a big portion (about 75% human genome). Compressing into CRAM format significantly reduces space needed store NGS results. However, tools generating formats are not designed...
Motivation: For a number of neurological diseases, such as Alzheimer’s disease, amyotrophic lateral sclerosis, and many others, certain genes are known to be involved in the disease mechanism. A common question is whether structural variant any gene may related drug response clinical trials how this relationship can contribute lifecycle development. Results: To end, we introduce VariantSurvival, tool that identifies changes survival relative variants within target genes. VariantSurvival...