MOTIVATION: Biological network querying is a problem requiring a considerable computational effort to be solved. Given a target and a query network, it aims to find occurrences of the query in the target by considering topological and node similariti...
MOTIVATION: Bioimages of subcellular protein distribution as a new data source have attracted much attention in the field of automated prediction of proteins subcellular localization. Performance of existing systems is significantly limited by the sm...
UNLABELLED: We present a new R package for training gapped-kmer SVM classifiers for DNA and protein sequences. We describe an improved algorithm for kernel matrix calculation that speeds run time by about 2 to 5-fold over our original gkmSVM algorith...
MOTIVATION: Probability distributions play a central role in mathematical and statistical modelling. The encoding, annotation and exchange of such models could be greatly simplified by a resource providing a common reference for the definition of pro...
MOTIVATION: Accurate segmentation of brain electron microscopy (EM) images is a critical step in dense circuit reconstruction. Although deep neural networks (DNNs) have been widely used in a number of applications in computer vision, most of these mo...
UNLABELLED: gkm-SVM is a sequence-based method for predicting and detecting the regulatory vocabulary encoded in functional DNA elements, and is a commonly used tool for studying gene regulatory mechanisms. Here we introduce new software, LS-GKM, whi...
MOTIVATION: Similarity-based methods have been widely used in order to infer the properties of genes and gene products containing little or no experimental annotation. New approaches that overcome the limitations of methods that rely solely upon sequ...
MOTIVATION: Supervised machine learning is widely applied to transcriptomic data to predict disease diagnosis, prognosis or survival. Robust and interpretable classifiers with high accuracy are usually favored for their clinical and translational pot...
MOTIVATION: Measures of protein functional similarity are essential tools for function prediction, evaluation of protein-protein interactions (PPIs) and other applications. Several existing methods perform comparisons between proteins based on the se...
MOTIVATION: PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly abundant in the germline. One important role of piRNAs is to defend genome integrity by guiding PIWI proteins to silence transposable elements (TEs), whic...