Advancements in biological and biomedical research are fueled by the analysis of vast, complex, integrated datasets, made possible through large-scale computational resources. While bioinformatics has revolutionized our understanding of diseases such as cancer or COVID-19, there are costs associated with the computing requirements. On one hand, computational power requires financial process, but it may...
In metagenomics, biological specimens are sometimes collected from host tissue that contains a high ratio of host to bacterial DNA. When shotgun metagenomics sequencing data are generated for these specimens, they normally contain a large fraction of host reads compared to microbial reads. Analyzing microbiome data with a high host ratio of reads can lead...
A complete analysis of the microbiome should combine taxonomic profiling with functional characterization to discover the full potential of an entire community of microorganisms. However, research teams often require specialized training and extensive computational infrastructure to establish an in-house suite of tools for processing shotgun metagenomic data – and even with the right know-how, the...
Over the last decade, the field of metagenomics has grown extensively, leading to an exponential increase in sequencing data in public data repositories. Availability of this huge collection of data has accelerated the discovery of novel microbiome-related biomarkers and microbiome-based novel biomedical therapeutics. One of the key steps in identifying potential biomarkers or lead candidates...
Introduction The advent of metagenomic sequencing has led to significant advancements in our understanding of the microbiome in a wide variety of contexts, from the human body1 to farm animals2,3, soil, and marine environments4. Each unique environment provides its own set of challenges in accurate microbial identification, including low microbial biomass in ocean samples, PCR...
By Barış Özdinç Dogs have been man’s best friend for centuries — and continue to be popular pets today. According to the American Pet Products Association National Pet Owners Survey, 53.4% of American households own a dog. People treat their dogs like family members, including looking after and investigating ways in which to improve...
Mobile phones have become essential to modern-day living; they are the main communication device for two-thirds of the human population (Kemp 2020). People handle their mobile phones up to 2000 times per day, which can total up to 3h and 37 minutes (Winnick 2016). Consequently, mobile phones have emerged as a fomite that could play...
Written by Nayeim Khan The process of sequencing determines the DNA or RNA nucleotide bases within a sample. A sequence, also referred to as a read, is generated for each fragment in the nucleotide library and reveals the sequence they are aligned in. Modern sequencing technologies can generate a massive number of sequence reads in a single...
Written by Nayeim Khan The investigation of microbial communities and microbiomes has been revolutionized by the development of high-throughput sequencing. There are two main methods that most researchers use to analyze samples – sequencing all of the DNA in a sample (whole genome sequencing, WGS) or targeting a specific marker gene (amplicon sequencing). The premise...
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