AIMC Topic: Computational Biology

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Text mining for precision medicine: automating disease-mutation relationship extraction from biomedical literature.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: Identifying disease-mutation relationships is a significant challenge in the advancement of precision medicine. The aim of this work is to design a tool that automates the extraction of disease-related mutations from biomedical text to adv...

From frames to OWL2: Converting the Foundational Model of Anatomy.

Artificial intelligence in medicine
OBJECTIVE: The Foundational Model of Anatomy (FMA) [Rosse C, Mejino JLV. A reference ontology for bioinformatics: the Foundational Model of Anatomy. J. Biomed. Inform. 2003;36:478-500] is an ontology that represents canonical anatomy at levels rangin...

Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction.

Bioinformatics (Oxford, England)
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...

A New Feature Vector Based on Gene Ontology Terms for Protein-Protein Interaction Prediction.

IEEE/ACM transactions on computational biology and bioinformatics
Protein-protein interaction (PPI) plays a key role in understanding cellular mechanisms in different organisms. Many supervised classifiers like Random Forest (RF) and Support Vector Machine (SVM) have been used for intra or inter-species interaction...

Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning.

Database : the journal of biological databases and curation
Medicinal chemistry patents contain rich information about chemical compounds. Although much effort has been devoted to extracting chemical entities from scientific literature, limited numbers of patent mining systems are publically available, probab...

DiMeX: A Text Mining System for Mutation-Disease Association Extraction.

PloS one
The number of published articles describing associations between mutations and diseases is increasing at a fast pace. There is a pressing need to gather such mutation-disease associations into public knowledge bases, but manual curation slows down th...

A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts.

PLoS computational biology
O-linked glycosylation is an important post-translational modification of mucin-type protein, changes to which are important biomarkers of cancer. For this study of the enzymes of O-glycosylation, we developed a shorthand notation for representing Ga...

Neural model of gene regulatory network: a survey on supportive meta-heuristics.

Theory in biosciences = Theorie in den Biowissenschaften
Gene regulatory network (GRN) is produced as a result of regulatory interactions between different genes through their coded proteins in cellular context. Having immense importance in disease detection and drug finding, GRN has been modelled through ...

ProbOnto: ontology and knowledge base of probability distributions.

Bioinformatics (Oxford, England)
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...

The Virtual Screening of the Drug Protein with a Few Crystal Structures Based on the Adaboost-SVM.

Computational and mathematical methods in medicine
Using the theory of machine learning to assist the virtual screening (VS) has been an effective plan. However, the quality of the training set may reduce because of mixing with the wrong docking poses and it will affect the screening efficiencies. To...