Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for micr...
Single nucleotide exact amplicon sequence variants (ASV) of the human gut microbiome were used to evaluate if individuals with a depression phenotype (DEPR) could be identified from healthy reference subjects (NODEP). Microbial DNA in stool samples o...
The bacterial diversity and corresponding biological significance revealed by high-throughput sequencing contribute massive information to source tracking of fecal contamination. The performances of classification models on predicting the fecal sourc...
Journal of gastroenterology and hepatology
Apr 1, 2021
Gut microbiota has been shown to associate with the development of gastrointestinal diseases. In the last decade, development in whole metagenome sequencing and 16S rRNA sequencing technology has dramatically accelerated the gut microbiome's research...
The stomach is inhabited by diverse microbial communities, co-existing in a dynamic balance. Long-term use of drugs such as proton pump inhibitors (PPIs), or bacterial infection such as Helicobacter pylori, cause significant microbial alterations. Ye...
BACKGROUND: Diverse microbiome communities drive biogeochemical processes and evolution of animals in their ecosystems. Many microbiome projects have demonstrated the power of using metagenomics to understand the structures and factors influencing th...
BACKGROUND: 16S sequencing results are often used for Machine Learning (ML) tasks. 16S gene sequences are represented as feature counts, which are associated with taxonomic representation. Raw feature counts may not be the optimal representation for ...
BACKGROUND: The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately wh...
Low concordance between studies that examine the role of microbiota in human diseases is a pervasive challenge that limits the capacity to identify causal relationships between host-associated microorganisms and pathology. The risk of obtaining false...
The study of complex microbial communities typically entails high-throughput sequencing and downstream bioinformatics analyses. Here we expand and accelerate microbiota analysis by enabling cell type diversity quantification from multidimensional flo...