AIMC Topic: Computational Biology

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ACP-CapsPred: an explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network.

Briefings in bioinformatics
Cancer is a severe illness that significantly threatens human life and health. Anticancer peptides (ACPs) represent a promising therapeutic strategy for combating cancer. In silico methods enable rapid and accurate identification of ACPs without exte...

Designing interpretable deep learning applications for functional genomics: a quantitative analysis.

Briefings in bioinformatics
Deep learning applications have had a profound impact on many scientific fields, including functional genomics. Deep learning models can learn complex interactions between and within omics data; however, interpreting and explaining these models can b...

Multimodal functional deep learning for multiomics data.

Briefings in bioinformatics
With rapidly evolving high-throughput technologies and consistently decreasing costs, collecting multimodal omics data in large-scale studies has become feasible. Although studying multiomics provides a new comprehensive approach in understanding the...

scHyper: reconstructing cell-cell communication through hypergraph neural networks.

Briefings in bioinformatics
Cell-cell communications is crucial for the regulation of cellular life and the establishment of cellular relationships. Most approaches of inferring intercellular communications from single-cell RNA sequencing (scRNA-seq) data lack a comprehensive g...

Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects.

Briefings in bioinformatics
Recent advancements in high-throughput sequencing technologies have significantly enhanced our ability to unravel the intricacies of gene regulatory processes. A critical challenge in this endeavor is the identification of variant effects, a key fact...

DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs.

Briefings in bioinformatics
The internal ribosome entry site (IRES) is a cis-regulatory element that can initiate translation in a cap-independent manner. It is often related to cellular processes and many diseases. Thus, identifying the IRES is important for understanding its ...