Next-generation sequencing (NGS) methods lie at the heart of large parts of biological and medical research. Their fundamental importance has created a continuously increasing demand for processing and analysis methods of the data sets produced, addr...
BACKGROUND: It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new ref...
Chinese Sichuan Paocai (CSP) is one of the world's best-known fermented vegetables with a large presence in the Chinese market. The dynamic microbial community is the main contributor to Paocai fermentation. However, little is known about the ecologi...
The rise in metagenomics has led to an exponential growth in virus discovery. However, the majority of these new virus sequences have no assigned host. Current machine learning approaches to predicting virus host interactions have a tendency to focus...
The fast accumulation of viral metagenomic data has contributed significantly to new RNA virus discovery. However, the short read size, complex composition, and large data size can all make taxonomic analysis difficult. In particular, commonly used a...
In the past decade, there has been a tremendous increase in studies on the link between oral microbiome and systemic diseases. However, variations in study design and confounding variables across studies often lead to inconsistent observations. In th...
IEEE journal of biomedical and health informatics
May 11, 2020
Accurate prediction of the host phenotype from a metagenomic sample and identification of the associated microbial markers are important in understanding potential host-microbiome interactions related to disease initiation and progression. We introdu...
The microbiome is a new frontier for building predictors of human phenotypes. However, machine learning in the microbiome is fraught with issues of reproducibility, driven in large part by the wide range of analytic models and metagenomic data types ...
IBD is a complex multifactorial inflammatory disease of the gut driven by extrinsic and intrinsic factors, including host genetics, the immune system, environmental factors and the gut microbiome. Technological advancements such as next-generation se...
The release of wastewater from textile dyeing industrial sectors is a huge concern with regard to pollution as the treatment of these waters is truly a challenging process. Hence, this study investigates the triazo bond Direct Blue 71 (DB71) dye deco...
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