AIMC Topic: Computational Biology

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GENEVIC: GENetic data Exploration and Visualization via Intelligent interactive Console.

Bioinformatics (Oxford, England)
SUMMARY: The vast generation of genetic data poses a significant challenge in efficiently uncovering valuable knowledge. Introducing GENEVIC, an AI-driven chat framework that tackles this challenge by bridging the gap between genetic data generation ...

Unveiling the glycolysis in sepsis: Integrated bioinformatics and machine learning analysis identifies crucial roles for IER3, DSC2, and PPARG in disease pathogenesis.

Medicine
Sepsis, a multifaceted syndrome driven by an imbalanced host response to infection, remains a significant medical challenge. At its core lies the pivotal role of glycolysis, orchestrating immune responses especially in severe sepsis. The intertwined ...

A comprehensive review of machine learning techniques for multi-omics data integration: challenges and applications in precision oncology.

Briefings in functional genomics
Multi-omics data play a crucial role in precision medicine, mainly to understand the diverse biological interaction between different omics. Machine learning approaches have been extensively employed in this context over the years. This review aims t...

A systematic analyses of different bioinformatics pipelines for genomic data and its impact on deep learning models for chromatin loop prediction.

Briefings in functional genomics
Genomic data analysis has witnessed a surge in complexity and volume, primarily driven by the advent of high-throughput technologies. In particular, studying chromatin loops and structures has become pivotal in understanding gene regulation and genom...

Nmix: a hybrid deep learning model for precise prediction of 2'-O-methylation sites based on multi-feature fusion and ensemble learning.

Briefings in bioinformatics
RNA 2'-O-methylation (Nm) is a crucial post-transcriptional modification with significant biological implications. However, experimental identification of Nm sites is challenging and resource-intensive. While multiple computational tools have been de...

Robust self-supervised learning strategy to tackle the inherent sparsity in single-cell RNA-seq data.

Briefings in bioinformatics
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for elucidating cellular heterogeneity and tissue function in various biological contexts. However, the sparsity in scRNA-seq data limits the accuracy of cell type annotation and transcriptomi...

AIGen: an artificial intelligence software for complex genetic data analysis.

Briefings in bioinformatics
The recent development of artificial intelligence (AI) technology, especially the advance of deep neural network (DNN) technology, has revolutionized many fields. While DNN plays a central role in modern AI technology, it has rarely been used in gene...

Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Briefings in bioinformatics
Transcriptional factors (TFs) in bacteria play a crucial role in gene regulation by binding to specific DNA sequences, thereby assisting in the activation or repression of genes. Despite their central role, deciphering shape recognition of bacterial ...

Adversarial regularized autoencoder graph neural network for microbe-disease associations prediction.

Briefings in bioinformatics
BACKGROUND: Microorganisms inhabit various regions of the human body and significantly contribute to numerous diseases. Predicting the associations between microbes and diseases is crucial for understanding pathogenic mechanisms and informing prevent...

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...