AIMC Topic: Computational Biology

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ESM-BBB-Pred: a fine-tuned ESM 2.0 and deep neural networks for the identification of blood-brain barrier peptides.

Briefings in bioinformatics
Blood-brain barrier peptides (BBBP) could significantly improve the delivery of drugs to the brain, paving the way for new treatments for central nervous system (CNS) disorders. The primary challenge in treating CNS disorders lies in the difficulty p...

Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP.

Briefings in bioinformatics
Existing algorithms for assessing tumor purity are limited to a single omics data, such as gene expression, somatic copy number variations, somatic mutations, and DNA methylation. Here we proposed the machine learning Multi-omics Tumor Purity predict...

Introducing TEC-LncMir for prediction of lncRNA-miRNA interactions through deep learning of RNA sequences.

Briefings in bioinformatics
The interactions between long noncoding RNA (lncRNA) and microRNA (miRNA) play critical roles in life processes, highlighting the necessity to enhance the performance of state-of-the-art models. Here, we introduced TEC-LncMir, a novel approach for pr...

Deconvolution of spatial transcriptomics data via graph contrastive learning and partial least square regression.

Briefings in bioinformatics
Deciphering the cellular abundance in spatial transcriptomics (ST) is crucial for revealing the spatial architecture of cellular heterogeneity within tissues. However, some of the current spatial sequencing technologies are in low resolutions, leadin...

DeepPFP: a multi-task-aware architecture for protein function prediction.

Briefings in bioinformatics
Deriving protein function from protein sequences poses a significant challenge due to the intricate relationship between sequence and function. Deep learning has made remarkable strides in predicting sequence-function relationships. However, models t...

Multi-view multi-level contrastive graph convolutional network for cancer subtyping on multi-omics data.

Briefings in bioinformatics
Cancer is a highly diverse group of diseases, and each type of cancer can be further divided into various subtypes according to specific characteristics, cellular origins, and molecular markers. Subtyping helps in tailoring treatment and prognosis ac...

Attention-aware differential learning for predicting peptide-MHC class I binding and T cell receptor recognition.

Briefings in bioinformatics
The identification of neoantigens is crucial for advancing vaccines, diagnostics, and immunotherapies. Despite this importance, a fundamental question remains: how to model the presentation of neoantigens by major histocompatibility complex class I m...

Classification-based pathway analysis using GPNet with novel P-value computation.

Briefings in bioinformatics
Pathway analysis plays a critical role in bioinformatics, enabling researchers to identify biological pathways associated with various conditions by analyzing gene expression data. However, the rise of large, multi-center datasets has highlighted lim...

BioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction.

Briefings in bioinformatics
The automatic and accurate extraction of diverse biomedical relations from literature constitutes the core elements of medical knowledge graphs, which are indispensable for healthcare artificial intelligence. Currently, fine-tuning through stacking v...

Deep learning-based design and experimental validation of a medicine-like human antibody library.

Briefings in bioinformatics
Antibody generation requires the use of one or more time-consuming methods, namely animal immunization, and in vitro display technologies. However, the recent availability of large amounts of antibody sequence and structural data in the public domain...