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Genomics

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Geno-GCN: A Genome-specific Graph Convolutional Network for Diabetes Prediction.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Drawing inspiration from convolutional neural networks, graph convolutional networks (GCNs) have been implemented in various applications. Yet, the integration of GCNs into clinical settings, particularly in the context of complex health conditions l...

Multi-task Learning Graph Neural Networks for Cancer Prognosis Prediction with Genomic Data.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
Providing robust prognosis predictions for cancers with limited data samples remains a challenge for precision oncology. In this study, we propose a novel approach that combines multi-task learning (MTL) and graph neural networks (GNNs) to address th...

Deep learning-based cell-specific gene regulatory networks inferred from single-cell multiome data.

Nucleic acids research
Gene regulatory networks (GRNs) provide a global representation of how genetic/genomic information is transferred in living systems and are a key component in understanding genome regulation. Single-cell multiome data provide unprecedented opportunit...

A compendium of human gene functions derived from evolutionary modelling.

Nature
A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this g...

Toward an integrated omics approach for plant biosynthetic pathway discovery in the age of AI.

Trends in biochemical sciences
Elucidating plant biosynthetic pathways is key to advancing a sustainable bioeconomy by enabling access to complex natural products through synthetic biology. Despite progress from genomic, transcriptomic, and metabolomic approaches, much multiomics ...

SVLearn: a dual-reference machine learning approach enables accurate cross-species genotyping of structural variants.

Nature communications
Structural variations (SVs) are diverse forms of genetic alterations and drive a wide range of human diseases. Accurately genotyping SVs, particularly occurring at repetitive genomic regions, from short-read sequencing data remains challenging. Here,...

Genomic selection in pig breeding: comparative analysis of machine learning algorithms.

Genetics, selection, evolution : GSE
BACKGROUND: The effectiveness of genomic prediction (GP) significantly influences breeding progress, and employing SNP markers to predict phenotypic values is a pivotal aspect of pig breeding. Machine learning (ML) methods are usually used to predict...

Equitable machine learning counteracts ancestral bias in precision medicine.

Nature communications
Gold standard genomic datasets severely under-represent non-European populations, leading to inequities and a limited understanding of human disease. Therapeutics and outcomes remain hidden because we lack insights that could be gained from analyzing...

Interpretable Multimodal Fusion Model for Bridged Histology and Genomics Survival Prediction in Pan-Cancer.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Understanding the prognosis of cancer patients is crucial for enabling precise diagnosis and treatment by clinical practitioners. Multimodal fusion models based on artificial intelligence (AI) offer a comprehensive depiction of the tumor heterogeneit...

Leveraging Automated Machine Learning for Environmental Data-Driven Genetic Analysis and Genomic Prediction in Maize Hybrids.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Genotype, environment, and genotype-by-environment (G×E) interactions play a critical role in shaping crop phenotypes. Here, a large-scale, multi-environment hybrid maize dataset is used to construct and validate an automated machine learning framewo...