Nonadditive genetic effects pose significant challenges to traditional genomic selection methods for quantitative traits. Machine learning approaches, particularly kernel-based methods, offer promising solutions to overcome these limitations. In this...
Taihang is an indigenous breed in Hebei Province and has a long history of evolution. To uncover the genetic basis and protect the genetic resources, it is important to develop accurate markers to identify Taihang at the molecular level. In this stud...
Machine learning (ML) methods have rapidly developed in various theoretical and practical research areas, including predicting genomic breeding values for large livestock animals. However, few studies have investigated the application of ML in broile...
The 3D structure of the genome is an important mediator of gene expression. As phenotypic divergence is largely driven by gene regulatory variation, comparing genome 3D contacts across species can further understanding of the molecular basis of speci...
IEEE/ACM transactions on computational biology and bioinformatics
39361454
In this paper, we propose a Learning-based gEnome Codec (LEC), which is designed for high efficiency and enhanced flexibility. The LEC integrates several advanced technologies, including Group of Bases (GoB) compression, multi-stride coding and bidir...
Current opinion in genetics & development
39862604
Three-dimensional genome folding plays roles in gene regulation and disease. In this review, we compare and contrast recent deep learning models for predicting genome contact maps. We survey preprocessing, architecture, training, evaluation, and inte...
Deep learning classification models based on Convolutional Neural Networks (CNNs) are increasingly used in population genetic inference for detecting signatures of natural selection. Prevailing detection methods treat the design of the classifier as ...
Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of natural language processing is to understand sequences of words, a major objective i...
Methods in molecular biology (Clifton, N.J.)
39283464
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...
The critical stage of every de novo genome assembler is identifying paths in assembly graphs that correspond to the reconstructed genomic sequences. The existing algorithmic methods struggle with this, primarily due to repetitive regions causing comp...