AIMC Topic: Computational Biology

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DeepIsoFun: a deep domain adaptation approach to predict isoform functions.

Bioinformatics (Oxford, England)
MOTIVATION: Isoforms are mRNAs produced from the same gene locus by alternative splicing and may have different functions. Although gene functions have been studied extensively, little is known about the specific functions of isoforms. Recently, some...

Where to search top-K biomedical ontologies?

Briefings in bioinformatics
MOTIVATION: Searching for precise terms and terminological definitions in the biomedical data space is problematic, as researchers find overlapping, closely related and even equivalent concepts in a single or multiple ontologies. Search engines that ...

Artificial intelligence in drug combination therapy.

Briefings in bioinformatics
Currently, the development of medicines for complex diseases requires the development of combination drug therapies. It is necessary because in many cases, one drug cannot target all necessary points of intervention. For example, in cancer therapy, a...

Drug knowledge bases and their applications in biomedical informatics research.

Briefings in bioinformatics
Recent advances in biomedical research have generated a large volume of drug-related data. To effectively handle this flood of data, many initiatives have been taken to help researchers make good use of them. As the results of these initiatives, many...

BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches.

Briefings in bioinformatics
With the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems is how to computationally analyze their structures and functions. Machine learning techniques are playing key roles in this field. Typi...

Multi-omics integration-a comparison of unsupervised clustering methodologies.

Briefings in bioinformatics
With the recent developments in the field of multi-omics integration, the interest in factors such as data preprocessing, choice of the integration method and the number of different omics considered had increased. In this work, the impact of these f...

Multifaceted protein-protein interaction prediction based on Siamese residual RCNN.

Bioinformatics (Oxford, England)
MOTIVATION: Sequence-based protein-protein interaction (PPI) prediction represents a fundamental computational biology problem. To address this problem, extensive research efforts have been made to extract predefined features from the sequences. Base...

Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks.

Bioinformatics (Oxford, England)
MOTIVATION: Sequence-based prediction of one dimensional structural properties of proteins has been a long-standing subproblem of protein structure prediction. Recently, prediction accuracy has been significantly improved due to the rapid expansion o...

Computational functional genomics-based reduction of disease-related gene sets to their key components.

Bioinformatics (Oxford, England)
MOTIVATION: The genetic architecture of diseases becomes increasingly known. This raises difficulties in picking suitable targets for further research among an increasing number of candidates. Although expression based methods of gene set reduction a...

DeepMRMP: A new predictor for multiple types of RNA modification sites using deep learning.

Mathematical biosciences and engineering : MBE
RNA modification plays an indispensable role in the regulation of organisms. RNA modification site prediction offers an insight into diverse cellular processing. Regarding different types of RNA modification site prediction, it is difficult to tell t...