Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Single-cell omics technologies have revolutionized the study of long non-coding RNAs (lncRNAs), offering unprecedented resolution in elucidating their expression dynamics, cell-type specificity, and associated gene regulatory networks (GRNs). Concurr...
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Jan 1, 2025
Precision medicine significantly enhances patients prognosis, offering personalized treatments. Particularly for metastatic cancer, incorporating primary tumor location into the diagnostic process greatly improves survival rates. However, traditional...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Three-dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, topologically associating domains (TADs), and A/B compartments, play critical roles in a wide range of cellular processes by regulating gene expressi...
Response to spatiotemporal variation in selection gradients resulted in signatures of polygenic adaptation in human genomes. We introduce RAISING, a two-stage deep learning framework that optimizes neural network architecture through hyperparameter t...
Frontiers in bioscience (Landmark edition)
Nov 28, 2024
In this comprehensive review, we delve into the transformative role of artificial intelligence (AI) in refining the application of multi-omics and spatial multi-omics within the realm of diffuse large B-cell lymphoma (DLBCL) research. We scrutinized ...
Genomic DNA breakages and the subsequent insertion and deletion mutations are important contributors to genome instability and linked diseases. Unlike the research in point mutations, the relationship between DNA sequence context and the propensity f...
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...
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...
Advances in three-dimensional (3D) genomics have revealed the spatial characteristics of chromatin interactions in gene expression regulation, which is crucial for understanding molecular mechanisms in biological processes. High-throughput technologi...
Machine learning (ML) methods offer opportunities for gaining insights into the intricate workings of complex biological systems, and their applications are increasingly prominent in the analysis of omics data to facilitate tasks, such as the identif...
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