Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. M...
Disease gene identification is a critical step towards uncovering the molecular mechanisms of diseases and systematically investigating complex disease phenotypes. Despite considerable efforts to develop powerful computing methods, candidate gene ide...
Essential gene prediction helps to find minimal genes indispensable for the survival of any organism. Machine learning (ML) algorithms have been useful for the prediction of gene essentiality. However, currently available ML pipelines perform poorly ...
Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual curation, we identified 64,643 pathway figu...
Metabolic inference from genomic sequence information is a necessary step in determining the capacity of cells to make a living in the world at different levels of biological organization. A common method for determining the metabolic potential encod...
Through advanced mechanistic modeling and the generation of large high-quality datasets, machine learning is becoming an integral part of understanding and engineering living systems. Here we show that mechanistic and machine learning models can be c...
The numerous interconnected biochemical pathways that make up the metabolism of a living cell comprise a fuzzy logic system because of its high level of complexity and our inability to fully understand, predict, and model the many activities, how the...
OBJECTIVE: Familial adenomatous polyposis (FAP) is one major type of inherited duodenal cancer. The estimate of duodenal cancer risk in patients with FAP is critical for selecting the optimal treatment strategy.
Plant science : an international journal of experimental plant biology
May 23, 2020
Gene or pathway functional similarities are important information for researchers. However, these similarities are often described sparsely and qualitatively. The latent semantic analysis of Arabidopsis thaliana (Arabidopsis) Gene Ontology (GO) data ...
Metabolomics : Official journal of the Metabolomic Society
Mar 25, 2020
INTRODUCTION: To interpret metabolomic and lipidomic profiles, it is necessary to identify the metabolic reactions that connect the measured molecules. This can be achieved by putting them in the context of genome-scale metabolic network reconstructi...
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