There is a growing interest among quantitative geneticists and animal breeders in the use of deep learning (DL) for genomic prediction. However, the performance of DL is affected by hyperparameters that are typically manually set by users. These hype...
SUMMARY: Prediction of genomic annotations from DNA sequences using deep learning is today becoming a flourishing field with many applications. Nevertheless, there are still difficulties in handling data in order to conveniently build and train model...
MOTIVATION: The genome-wide discovery of microRNAs (miRNAs) involves identifying sequences having the highest chance of being a novel miRNA precursor (pre-miRNA), within all the possible sequences in a complete genome. The known pre-miRNAs are usuall...
MOTIVATION: The recently proposed knockoff filter is a general framework for controlling the false discovery rate (FDR) when performing variable selection. This powerful new approach generates a 'knockoff' of each variable tested for exact FDR contro...
Journal of gastroenterology and hepatology
Feb 1, 2021
Machine learning, a subset of artificial intelligence (AI), is a set of computational tools that can be used to enhance provision of clinical care in all areas of medicine. Gastroenterology and hepatology utilize multiple sources of information, incl...
The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for ...
The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic and genomic basis for human health and disease. ...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
Advances in molecular genetics through high-throughput gene mutagenesis and genetic crossing have enabled gene interaction mapping across whole genomes. Detecting gene interactions in even small microbial genomes relies on measuring growth phenotypes...
Epigenetics is a field of biological sciences focused on the study of reversible, heritable changes in gene function, not due to modifications of the genomic sequence. These changes are the result of a complex cross-talk between several molecular mec...
MOTIVATION: Predictive models of DNA chromatin profile (i.e. epigenetic state), such as transcription factor binding, are essential for understanding regulatory processes and developing gene therapies. It is known that the 3D genome, or spatial struc...
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