Genetics and molecular research : GMR
Jul 25, 2016
Identifying biomarker genes and characterizing interaction pathways with high-dimensional and low-sample size microarray data is a major challenge in computational biology. In this field, the construction of protein-protein interaction (PPI) networks...
BMC medical informatics and decision making
Jul 25, 2016
BACKGROUND: The study on disease-disease association has been increasingly viewed and analyzed as a network, in which the connections between diseases are configured using the source information on interactome maps of biomolecules such as genes, prot...
In this paper we apply machine learning methods for predicting protein interactions in fungal secretion pathways. We assume an inter-species transfer setting, where training data is obtained from a single species and the objective is to predict prote...
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...
BACKGROUND: Intellectual disability (ID), autism, and epilepsy share frequent yet variable comorbidities with one another. In order to better understand potential genetic divergence underlying this variable risk, we studied genes responsible for mono...
Arteriosclerosis, thrombosis, and vascular biology
Mar 10, 2016
OBJECTIVE: Recent genome-wide association studies of coronary artery disease (CAD) have revealed 58 genome-wide significant and 148 suggestive genetic loci. However, the molecular mechanisms through which they contribute to CAD and the clinical impli...
A major challenge of systems biology is to capture the rewiring of biological functions (e.g. signaling pathways) in a molecular network. To address this problem, we proposed a novel computational framework, namely network stratification analysis (Ne...
BACKGROUND: Protein-protein interactions (PPIs) are involved in various biological processes, and underlying mechanism of the interactions plays a crucial role in therapeutics and protein engineering. Most machine learning approaches have been develo...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 7, 2015
One of the goals of relation extraction is to identify protein-protein interactions (PPIs) in biomedical literature. Current systems are capturing binary relations and also the direction and type of an interaction. Besides assisting in the curation P...
Computational and mathematical methods in medicine
Oct 7, 2015
Informatics methods, such as text mining and natural language processing, are always involved in bioinformatics research. In this study, we discuss text mining and natural language processing methods in bioinformatics from two perspectives. First, we...
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