SUMMARY: Although many quantitative structure-activity relationship (QSAR) models are trained and evaluated for their predictive merits, understanding what models have been learning is of critical importance. However, the interpretation and visualiza...
MOTIVATION: In precision medicine, next-generation sequencing and novel preclinical reports have led to an increasingly large amount of results, published in the scientific literature. However, identifying novel treatments or predicting a drug respon...
SUMMARY: We present the first tool of gene prediction, PlasGUN, for plasmid metagenomic short-read data. The tool, developed based on deep learning algorithm of multiple input Convolutional Neural Network, demonstrates much better performance when te...
MOTIVATION: Imaging mass spectrometry (imaging MS) is a prominent technique for capturing distributions of molecules in tissue sections. Various computational methods for imaging MS rely on quantifying spatial correlations between ion images, referre...
SUMMARY: In the last decade, increasing attention has been paid to the study of gene fusions. However, the problem of determining whether a gene fusion is a cancer driver or just a passenger mutation is still an open issue. Here we present DEEPrior, ...
MOTIVATION: Gene sets over-representation analysis (GSOA) is a common technique of enrichment analysis that measures the overlap between a gene set and selected instances (e.g. pathways). Despite its popularity, there is currently no established stan...
Phylogenetic inference is of fundamental importance to evolutionary as well as other fields of biology, and molecular sequences have emerged as the primary data for this task. Although many phylogenetic methods have been developed to explicitly take ...
MOTIVATION: Understanding the mechanisms and structural mappings between molecules and pathway classes are critical for design of reaction predictors for synthesizing new molecules. This article studies the problem of prediction of classes of metabol...
A system based on the use of two artificial neural networks (ANNs) to determine the location of the scleral spur of the human eye in ocular images generated by an ultrasound biomicroscopy is presented in this paper. The two ANNs establish a relations...
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