AIMC Topic: Databases, Genetic

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SubLocEP: a novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning.

Briefings in bioinformatics
MOTIVATION: mRNA location corresponds to the location of protein translation and contributes to precise spatial and temporal management of the protein function. However, current assignment of subcellular localization of eukaryotic mRNA reveals import...

A graph auto-encoder model for miRNA-disease associations prediction.

Briefings in bioinformatics
Emerging evidence indicates that the abnormal expression of miRNAs involves in the evolution and progression of various human complex diseases. Identifying disease-related miRNAs as new biomarkers can promote the development of disease pathology and ...

CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms.

Briefings in bioinformatics
CyanoPATH is a database that curates and analyzes the common genomic functional repertoire for cyanobacteria harmful algal blooms (CyanoHABs) in eutrophic waters. Based on the literature of empirical studies and genome/protein databases, it summarize...

Disease gene prediction with privileged information and heteroscedastic dropout.

Bioinformatics (Oxford, England)
MOTIVATION: Recently, machine learning models have achieved tremendous success in prioritizing candidate genes for genetic diseases. These models are able to accurately quantify the similarity among disease and genes based on the intuition that simil...

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...

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...

Modeling multi-species RNA modification through multi-task curriculum learning.

Nucleic acids research
N6-methyladenosine (m6A) is the most pervasive modification in eukaryotic mRNAs. Numerous biological processes are regulated by this critical post-transcriptional mark, such as gene expression, RNA stability, RNA structure and translation. Recently, ...

Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology.

Nucleic acids research
The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the community model organism knowledgebase for the laboratory mouse, a widely used animal model for comparative studies of the genetic and genomic basis for human health and disease. ...

canSAR: update to the cancer translational research and drug discovery knowledgebase.

Nucleic acids research
canSAR (http://cansar.icr.ac.uk) is the largest, public, freely available, integrative translational research and drug discovery knowledgebase for oncology. canSAR integrates vast multidisciplinary data from across genomic, protein, pharmacological, ...

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.

Nucleic acids research
Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their ass...