AIMC Topic: Computational Biology

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Feeding the human brain model.

Current opinion in neurobiology
The goal of the Human Brain Project is to develop, during the next decade, an infrastructure capable of simulating a draft human brain model based on available experimental data. One of the key issues is therefore to integrate and make accessible the...

BgN-Score and BsN-Score: bagging and boosting based ensemble neural networks scoring functions for accurate binding affinity prediction of protein-ligand complexes.

BMC bioinformatics
BACKGROUND: Accurately predicting the binding affinities of large sets of protein-ligand complexes is a key challenge in computational biomolecular science, with applications in drug discovery, chemical biology, and structural biology. Since a scorin...

Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis.

Proteomics
The main result of a great deal of the published proteomics studies is a list of identified proteins, which then needs to be interpreted in relation to the research question and existing knowledge. In the early days of proteomics this interpretation ...

Machine learning in computational docking.

Artificial intelligence in medicine
OBJECTIVE: The objective of this paper is to highlight the state-of-the-art machine learning (ML) techniques in computational docking. The use of smart computational methods in the life cycle of drug design is relatively a recent development that has...

OTO: Ontology Term Organizer.

BMC bioinformatics
BACKGROUND: The need to create controlled vocabularies such as ontologies for knowledge organization and access has been widely recognized in various domains. Despite the indispensable need of thorough domain knowledge in ontology construction, most ...

Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data.

International journal of medical microbiology : IJMM
Staphylococcus aureus (S. aureus) is a prominent human and livestock pathogen investigated widely using omic technologies. Critically, due to availability, low visibility or scattered resources, robust network and statistical contextualisation of the...

Measuring semantic similarities by combining gene ontology annotations and gene co-function networks.

BMC bioinformatics
BACKGROUND: Gene Ontology (GO) has been used widely to study functional relationships between genes. The current semantic similarity measures rely only on GO annotations and GO structure. This limits the power of GO-based similarity because of the li...

An ensemble method with hybrid features to identify extracellular matrix proteins.

PloS one
The extracellular matrix (ECM) is a dynamic composite of secreted proteins that play important roles in numerous biological processes such as tissue morphogenesis, differentiation and homeostasis. Furthermore, various diseases are caused by the dysfu...

HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology.

PloS one
BACKGROUND: Phenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods focus solely on the Online Mendelian Inheritance in Man (OMIM) database without considering the con...