AIMC Topic: Computational Biology

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Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.

PloS one
The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation o...

Computational algorithms to predict Gene Ontology annotations.

BMC bioinformatics
BACKGROUND: Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones pro...

Briefing in application of machine learning methods in ion channel prediction.

TheScientificWorldJournal
In cells, ion channels are one of the most important classes of membrane proteins which allow inorganic ions to move across the membrane. A wide range of biological processes are involved and regulated by the opening and closing of ion channels. Ion ...

SimConcept: a hybrid approach for simplifying composite named entities in biomedical text.

IEEE journal of biomedical and health informatics
One particular challenge in biomedical named entity recognition (NER) and normalization is the identification and resolution of composite named entities, where a single span refers to more than one concept (e.g., BRCA1/2). Previous NER and normalizat...

Machine learning methods enable predictive modeling of antibody feature:function relationships in RV144 vaccinees.

PLoS computational biology
The adaptive immune response to vaccination or infection can lead to the production of specific antibodies to neutralize the pathogen or recruit innate immune effector cells for help. The non-neutralizing role of antibodies in stimulating effector ce...

Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

PloS one
Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog informati...

Bioinformatics, interaction network analysis, and neural networks to characterize gene expression of radicular cyst and periapical granuloma.

Journal of endodontics
INTRODUCTION: Bioinformatics has emerged as an important tool to analyze the large amount of data generated by research in different diseases. In this study, gene expression for radicular cysts (RCs) and periapical granulomas (PGs) was characterized ...

Accurate in silico identification of protein succinylation sites using an iterative semi-supervised learning technique.

Journal of theoretical biology
As a widespread type of protein post-translational modifications (PTMs), succinylation plays an important role in regulating protein conformation, function and physicochemical properties. Compared with the labor-intensive and time-consuming experimen...

Understanding user intents in online health forums.

IEEE journal of biomedical and health informatics
Online health forums provide a convenient way for patients to obtain medical information and connect with physicians and peers outside of clinical settings. However, large quantities of unstructured and diversified content generated on these forums m...