AIMC Topic: Genomics

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CrossAttOmics: multiomics data integration with cross-attention.

Bioinformatics (Oxford, England)
MOTIVATION: Advances in high throughput technologies enabled large access to various types of omics. Each omics provides a partial view of the underlying biological process. Integrating multiple omics layers would help have a more accurate diagnosis....

Environment ensemble models for genomic prediction in common bean (Phaseolus vulgaris L.).

The plant genome
For important food crops such as the common bean (Phaseolus vulgaris, L.), global demand continues to outpace the rate of genetic gain for quantitative traits. In this study, we leveraged the multi-environment trial (MET) dataset from the cooperative...

Integrating Multiple Data Sources With Interactions in Multi-Omics Using Cooperative Learning.

Statistics in medicine
Modeling with multiomics data presents multiple challenges, such as the high dimensionality of the problem ( ), the presence of interactions between features, and the need for integration between multiple data sources. We establish an interaction mo...

Enhancing prediction accuracy of key biomass partitioning traits in wheat using multi-kernel genomic prediction models integrating secondary traits and environmental covariates.

The plant genome
Achieving significant genetic gains in grain yield (GY) in wheat (Triticum aestivum L.) requires optimization of the key biomass partitioning traits such as spike partitioning index (SPI) and fruiting efficiency (FE). However, traditional manual phen...

Genomic selection: Essence, applications, and prospects.

The plant genome
Genomic selection (GS) emerged as a key part of the solution to ensure the food supply for the growing human population thanks to advances in genotyping and other enabling technologies and improved understanding of the genotype-phenotype relationship...

AI and omics technologies in biobanking: Applications and challenges for public health.

Public health
OBJECTIVES: Considering the growing intersection of biobanks, artificial intelligence (AI) and omics research, and their critical impact on public health, this study aimed to explore the current and future public health implications and challenges of...

Deep learning and genomic best linear unbiased prediction integration: An approach to identify potential nonlinear genetic relationships between traits.

Journal of dairy science
Genomic prediction (GP) aims to predict the breeding values of multiple complex traits, usually assumed to be multivariate normally distributed by the largely used statistical methods, thus imposing linear genetic relationships between traits. Althou...

scDMSC: Deep Multi-View Subspace Clustering for Single-Cell Multi-Omics Data.

IEEE journal of biomedical and health informatics
Single-cell multi-omics sequencing technology comprehensively considers various molecular features to reveal the complexity of cells information. The clustering analysis of multi-omics data provides new insight into cellular heterogeneity. However, m...

MLOmics: Cancer Multi-Omics Database for Machine Learning.

Scientific data
Framing the investigation of diverse cancers as a machine learning problem has recently shown significant potential in multi-omics analysis and cancer research. Empowering these successful machine learning models are the high-quality training dataset...

scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links.

Nature communications
Recent advancements in single-cell technologies have enabled comprehensive characterization of cellular states through transcriptomic, epigenomic, and proteomic profiling at single-cell resolution. These technologies have significantly deepened our u...