AIMC Topic: Computational Biology

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Interpretation of deep learning in genomics and epigenomics.

Briefings in bioinformatics
Machine learning methods have been widely applied to big data analysis in genomics and epigenomics research. Although accuracy and efficiency are common goals in many modeling tasks, model interpretability is especially important to these studies tow...

State-of-the-art web services for de novo protein structure prediction.

Briefings in bioinformatics
Residue coevolution estimations coupled to machine learning methods are revolutionizing the ability of protein structure prediction approaches to model proteins that lack clear homologous templates in the Protein Data Bank (PDB). This has been patent...

DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method.

Briefings in bioinformatics
Identifying drug-target interactions (DTIs) is an important step for drug discovery and drug repositioning. To reduce the experimental cost, a large number of computational approaches have been proposed for this task. The machine learning-based model...

Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework.

Briefings in bioinformatics
DNA N6-methyladenine (6mA) represents important epigenetic modifications, which are responsible for various cellular processes. The accurate identification of 6mA sites is one of the challenging tasks in genome analysis, which leads to an understandi...

ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm.

Briefings in bioinformatics
As one of the most important tasks in protein structure prediction, protein fold recognition has attracted more and more attention. In this regard, some computational predictors have been proposed with the development of machine learning and artifici...

RNA-binding protein recognition based on multi-view deep feature and multi-label learning.

Briefings in bioinformatics
RNA-binding protein (RBP) is a class of proteins that bind to and accompany RNAs in regulating biological processes. An RBP may have multiple target RNAs, and its aberrant expression can cause multiple diseases. Methods have been designed to predict ...

Integrative biomarker detection on high-dimensional gene expression data sets: a survey on prior knowledge approaches.

Briefings in bioinformatics
Gene expression data provide the expression levels of tens of thousands of genes from several hundred samples. These data are analyzed to detect biomarkers that can be of prognostic or diagnostic use. Traditionally, biomarker detection for gene expre...

Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning.

Briefings in bioinformatics
DNA N4-methylcytosine (4mC) modification represents a novel epigenetic regulation. It involves in various cellular processes, including DNA replication, cell cycle and gene expression, among others. In addition to experimental identification of 4mC s...

Dr AFC: drug repositioning through anti-fibrosis characteristic.

Briefings in bioinformatics
Fibrosis is a key component in the pathogenic mechanism of a variety of diseases. These diseases involving fibrosis may share common mechanisms and therapeutic targets, and therefore common intervention strategies and medicines may be applicable for ...

Survey and comparative assessments of computational multi-omics integrative methods with multiple regulatory networks identifying distinct tumor compositions across pan-cancer data sets.

Briefings in bioinformatics
The significance of pan-cancer categories has recently been recognized as widespread in cancer research. Pan-cancer categorizes a cancer based on its molecular pathology rather than an organ. The molecular similarities among multi-omics data found in...