SUMMARY: Ontologies are widely used constructs for encoding and analyzing biomedical data, but the absence of simple and consistent tools has made exploratory and systematic analysis of such data unnecessarily difficult. Here we present three package...
MOTIVATION: Protein fold classification is a critical step in protein structure prediction. There are two possible ways to classify protein folds. One is through template-based fold assignment and the other is ab-initio prediction using machine learn...
MOTIVATION: High throughput screening by fluorescence activated cell sorting (FACS) is a common task in protein engineering and directed evolution. It can also be a rate-limiting step if high false positive or negative rates necessitate multiple roun...
MOTIVATION: Protein subcellular localization prediction has been an important research topic in computational biology over the last decade. Various automatic methods have been proposed to predict locations for large scale protein datasets, where stat...
MOTIVATION: Detection of RNA-binding proteins (RBPs) is essential since the RNA-binding proteins play critical roles in post-transcriptional regulation and have diverse roles in various biological processes. Moreover, identifying RBPs by computationa...
PURPOSE: The goal of this study was to assess the potential added benefit of accounting for partial volume effects (PVE) in an automatic coronary lumen segmentation algorithm that is used to determine the hemodynamic significance of a coronary artery...
MOTIVATION: Numerous ubiquitination sites remain undiscovered because of the limitations of mass spectrometry-based methods. Existing prediction methods use randomly selected non-validated sites as non-ubiquitination sites to train ubiquitination sit...
SUMMARY: GENIUS is a user-friendly web server that uses a novel machine learning algorithm to infer functional gene networks focused on specific genes and experimental conditions that are relevant to biological functions of interest. These functions ...
MOTIVATION: Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which algorithm and what parameters are optimal for any given dataset. In contrast, regions with and without obvious peaks can be easily l...
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