AIMC Topic: Computational Biology

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Ongoing brain rhythms shape I-wave properties in a computational model.

Brain stimulation
BACKGROUND: Responses to transcranial magnetic stimulation (TMS) are notoriously variable. Previous studies have observed a dependence of TMS-induced responses on ongoing brain activity, for instance sensorimotor rhythms. This suggests an opportunity...

Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach.

BMC systems biology
BACKGROUND: Gene Ontology (GO) is one of the most popular bioinformatics resources. In the past decade, Gene Ontology-based gene semantic similarity has been effectively used to model gene-to-gene interactions in multiple research areas. However, mos...

ANTENNA, a Multi-Rank, Multi-Layered Recommender System for Inferring Reliable Drug-Gene-Disease Associations: Repurposing Diazoxide as a Targeted Anti-Cancer Therapy.

IEEE/ACM transactions on computational biology and bioinformatics
Existing drug discovery processes follow a reductionist model of "one-drug-one-gene-one-disease," which is inadequate to tackle complex diseases involving multiple malfunctioned genes. The availability of big omics data offers opportunities to transf...

Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies.

IEEE/ACM transactions on computational biology and bioinformatics
Sigma factor, as a unit of RNA polymerase holoenzyme, is a critical factor in the process of gene transcriptional regulation. It recognizes the specific DNA sites and brings the core enzyme of RNA polymerase to the upstream regions of target genes. T...

Development of an information retrieval tool for biomedical patents.

Computer methods and programs in biomedicine
BACKGROUND AND OBJECTIVE: The volume of biomedical literature has been increasing in the last years. Patent documents have also followed this trend, being important sources of biomedical knowledge, technical details and curated data, which are put to...

iRSpot-PDI: Identification of recombination spots by incorporating dinucleotide property diversity information into Chou's pseudo components.

Genomics
Recombination spot identification plays an important role in revealing genome evolution and developing DNA function study. Although some computational methods have been proposed, extracting discriminatory information embedded in DNA properties has no...

Prediction of Apoptosis Protein's Subcellular Localization by Fusing Two Different Descriptors Based on Evolutionary Information.

Acta biotheoretica
The apoptosis protein has a central role in the development and the homeostasis of an organism. Obtaining information about the subcellular localization of apoptosis protein is very helpful to understand the apoptosis mechanism and the function of th...

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein-Protein Network Mapping.

Journal of molecular biology
Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO,...

Inferring MicroRNA Targets Based on Restricted Boltzmann Machines.

IEEE journal of biomedical and health informatics
Predicting the miRNA-target interactions (MTIs) is a critical task for elucidating mechanistic roles of miRNAs in pathophysiology. However, most existing techniques have a higher false positive because the precise miRNA target mechanisms are poorly k...

Bat detective-Deep learning tools for bat acoustic signal detection.

PLoS computational biology
Passive acoustic sensing has emerged as a powerful tool for quantifying anthropogenic impacts on biodiversity, especially for echolocating bat species. To better assess bat population trends there is a critical need for accurate, reliable, and open s...