AIMC Topic: Gene Regulatory Networks

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Spatially aligned graph transfer learning for characterizing spatial regulatory heterogeneity.

Briefings in bioinformatics
Spatially resolved transcriptomics (SRT) technologies facilitate the exploration of cell fates or states within tissue microenvironments. Despite these advances, the field has not adequately addressed the regulatory heterogeneity influenced by microe...

Integrating scRNA-seq and scATAC-seq with inter-type attention heterogeneous graph neural networks.

Briefings in bioinformatics
Single-cell multi-omics techniques, which enable the simultaneous measurement of multiple modalities such as RNA gene expression and Assay for Transposase-Accessible Chromatin (ATAC) within individual cells, have become a powerful tool for decipherin...

Towards simplified graph neural networks for identifying cancer driver genes in heterophilic networks.

Briefings in bioinformatics
The identification of cancer driver genes is crucial for understanding the complex processes involved in cancer development, progression, and therapeutic strategies. Multi-omics data and biological networks provided by numerous databases enable the a...

A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks.

Briefings in bioinformatics
The interactions between transcription factors (TFs) and the target genes could provide a basis for constructing gene regulatory networks (GRNs) for mechanistic understanding of various biological complex processes. From gene expression data, particu...

FunlncModel: integrating multi-omic features from upstream and downstream regulatory networks into a machine learning framework to identify functional lncRNAs.

Briefings in bioinformatics
Accumulating evidence indicates that long noncoding RNAs (lncRNAs) play important roles in molecular and cellular biology. Although many algorithms have been developed to reveal their associations with complex diseases by using downstream targets, th...

BioDSNN: a dual-stream neural network with hybrid biological knowledge integration for multi-gene perturbation response prediction.

Briefings in bioinformatics
Studying the outcomes of genetic perturbation based on single-cell RNA-seq data is crucial for understanding genetic regulation of cells. However, the high cost of cellular experiments and single-cell sequencing restrict us from measuring the full co...

Identification and validation of oxidative stress-related genes in primary open-angle glaucoma by weighted gene co-expression network analysis and machine learning.

Medicine
Primary open-angle glaucoma (POAG) is a common ocular disease, and there is currently no effective treatment for POAG therapy. Thus, identifying some effective diagnostic markers is beneficial to the treatment of patients. The expression profile was ...

Evolving Novel Gene Regulatory Networks for Structural Engineering Designs.

Artificial life
Engineering design optimization poses a significant challenge, usually requiring human expertise to discover superior solutions. Although various search techniques have been employed to generate diverse designs, their effectiveness is often limited b...

A multichannel graph neural network based on multisimilarity modality hypergraph contrastive learning for predicting unknown types of cancer biomarkers.

Briefings in bioinformatics
Identifying potential cancer biomarkers is a key task in biomedical research, providing a promising avenue for the diagnosis and treatment of human tumors and cancers. In recent years, several machine learning-based RNA-disease association prediction...

Multi-view learning framework for predicting unknown types of cancer markers via directed graph neural networks fitting regulatory networks.

Briefings in bioinformatics
The discovery of diagnostic and therapeutic biomarkers for complex diseases, especially cancer, has always been a central and long-term challenge in molecular association prediction research, offering promising avenues for advancing the understanding...