AIMC Topic: Computational Biology

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BERMP: a cross-species classifier for predicting mA sites by integrating a deep learning algorithm and a random forest approach.

International journal of biological sciences
N-methyladenosine (mA) is a prevalent RNA methylation modification involved in several biological processes. Hundreds or thousands of mA sites identified from different species using high-throughput experiments provides a rich resource to construct ...

Digital Diabetes Data and Artificial Intelligence: A Time for Humility Not Hubris.

Journal of diabetes science and technology
In the future artificial intelligence (AI) will have the potential to improve outcomes diabetes care. With the creation of new sensors for physiological monitoring sensors and the introduction of smart insulin pens, novel data relationships based on ...

Utilizing Deep Learning and Genome Wide Association Studies for Epistatic-Driven Preterm Birth Classification in African-American Women.

IEEE/ACM transactions on computational biology and bioinformatics
Genome-Wide Association Studies (GWAS) are used to identify statistically significant genetic variants in case-control studies. The main objective is to find single nucleotide polymorphisms (SNPs) that influence a particular phenotype (i.e., disease ...

Integrating Language Model and Reading Control Gate in BLSTM-CRF for Biomedical Named Entity Recognition.

IEEE/ACM transactions on computational biology and bioinformatics
Biomedical named entity recognition (Bio-NER) is an important preliminary step for many biomedical text mining tasks. The current mainstream methods for NER are based on the neural networks to avoid the complex hand-designed features derived from var...

Novel symmetry-based gene-gene dissimilarity measures utilizing Gene Ontology: Application in gene clustering.

Gene
In recent years DNA microarray technology, leading to the generation of high-volume biological data, has gained significant attention. To analyze this high volume gene-expression data, one such powerful tool is Clustering. For any clustering algorith...

Predicting apoptosis protein subcellular localization by integrating auto-cross correlation and PSSM into Chou's PseAAC.

Journal of theoretical biology
The prediction of subcellular localization of an apoptosis protein is still a challenging task, and existing methods mainly based on protein primary sequences. In this study, we propose a novel model called MACC-PSSM by integrating Moran autocorrelat...

Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences Using Deep Neural Networks.

IEEE/ACM transactions on computational biology and bioinformatics
Gapped k-mers frequency vectors (gkm-fv) has been presented for extracting sequence features. Coupled with support vector machine (gkm-SVM), gkm-fvs have been used to achieve effective sequence-based predictions. However, the huge computation of a la...

CEA: Combination-based gene set functional enrichment analysis.

Scientific reports
Functional enrichment analysis is a fundamental and challenging task in bioinformatics. Most of the current enrichment analysis approaches individually evaluate functional terms and often output a list of enriched terms with high similarity and redun...

Integration of virtual screening and susceptibility test to discover active-site subpocket-specific biogenic inhibitors of Helicobacter pylori shikimate dehydrogenase.

International microbiology : the official journal of the Spanish Society for Microbiology
Shikimate dehydrogenase (HpSDH) (EC 1.1.1.25) is a key enzyme in the shikimate pathway of Helicobacter pylori (H. pylori), which catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. Targeting HpSDH has been recognize...

Combinatorial Scoring of Phylogenetic Trees and Networks Based on Homoplasy-Free Characters.

Journal of computational biology : a journal of computational molecular cell biology
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for tree/netw...