The cost of sequencing a genome has become affordable for many research groups. However, with the growing number of sequenced genomes from non-model organisms, manually building functional genome annotation knowledge databases for each species is no ...
Transposable elements (TEs) are repetitive DNA sequences that move within genomes and play important roles in gene regulation and genome evolution. Accurate TE annotation in genomes is crucial for downstream analyses but challenging due to their sequ...
How does genomic information unfold, to give rise to self-constructing living organisms with problem-solving capacities at all levels of organization? We review recent progress that unifies work in developmental genetics and machine learning (ML) to ...
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...
Current opinion in genetics & development
Jan 24, 2025
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...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 10, 2024
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...
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...
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