AIMC Topic: Computational Biology

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MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs.

Briefings in bioinformatics
The long non-coding RNAs (lncRNAs) are subject of intensive recent studies due to its association with various human diseases. It is desirable to build the artificial intelligence-based models for prediction of diseases or tissues based on the lncRNA...

Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions.

Briefings in bioinformatics
In recent years, high-throughput experimental techniques have significantly enhanced the accuracy and coverage of protein-protein interaction identification, including human-pathogen protein-protein interactions (HP-PPIs). Despite this progress, expe...

A novel deep learning method for predictive modeling of microbiome data.

Briefings in bioinformatics
With the development and decreasing cost of next-generation sequencing technologies, the study of the human microbiome has become a rapid expanding research field, which provides an unprecedented opportunity in various clinical applications such as d...

iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning.

Briefings in bioinformatics
Accumulated researches have revealed that Piwi-interacting RNAs (piRNAs) are regulating the development of germ and stem cells, and they are closely associated with the progression of many diseases. As the number of the detected piRNAs is increasing ...

DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism.

Nucleic acids research
Subcellular localization of messenger RNAs (mRNAs), as a prevalent mechanism, gives precise and efficient control for the translation process. There is mounting evidence for the important roles of this process in a variety of cellular events. Computa...

Similarity Calculation, Enrichment Analysis, and Ontology Visualization of Biomedical Ontologies using UFO.

Current protocols
The rapid growth of biomedical ontologies observed in recent years has been reported to be useful in various applications. In this article, we propose two main-function protocols-term-related and entity-related-with the three most common ontology ana...

Biological network analysis with deep learning.

Briefings in bioinformatics
Recent advancements in experimental high-throughput technologies have expanded the availability and quantity of molecular data in biology. Given the importance of interactions in biological processes, such as the interactions between proteins or the ...

Deep learning for biological age estimation.

Briefings in bioinformatics
Modern machine learning techniques (such as deep learning) offer immense opportunities in the field of human biological aging research. Aging is a complex process, experienced by all living organisms. While traditional machine learning and data minin...

GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins.

Briefings in bioinformatics
As an important reversible lipid modification, S-palmitoylation mainly occurs at specific cysteine residues in proteins, participates in regulating various biological processes and is associated with human diseases. Besides experimental assays, compu...