Complex structural variants (CSVs) encompass multiple breakpoints and are often missed or misinterpreted. We developed SVision, a deep-learning-based multi-object-recognition framework, to automatically detect and haracterize CSVs from long-read sequ...
The first paradigm of plant breeding involves direct selection-based phenotypic observation, followed by predictive breeding using statistical models for quantitative traits constructed based on genetic experimental design and, more recently, by inco...
Identifying genomic regions influenced by natural selection provides fundamental insights into the genetic basis of local adaptation. However, it remains challenging to detect loci under complex spatially varying selection. We propose a deep learning...
Journal of computational biology : a journal of computational molecular cell biology
36048555
Species tree estimation is frequently based on phylogenomic approaches that use multiple genes from throughout the genome. However, for a combination of reasons (ranging from sampling biases to more biological causes, as in gene birth and loss), gene...
In recent years, major advances have been made in various chromosome conformation capture technologies to further satisfy the needs of researchers for high-quality, high-resolution contact interactions. Discriminating the loops from genome-wide conta...
The high dimensionality of genotype data available for genomic evaluations has presented a motivation for developing strategies to identify subsets of markers capable of increasing the accuracy of predictions compared to the current commercial single...
Predicting phenotypes and complex traits from genomic variations has always been a big challenge in molecular biology, at least in part because the task is often complicated by the influences of external stimuli and the environment on regulation of g...
Predicting phenotype with genomic and environmental information is critically needed and challenging. Machine learning methods have emerged as powerful tools to make accurate predictions from large and complex biological data. Here, we review the pro...
MOTIVATION: Interactions between proteins help us understand how genes are functionally related and how they contribute to phenotypes. Experiments provide imperfect 'ground truth' information about a small subset of potential interactions in a specif...
The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the Europe...