Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Nearly all lineages of land plants have experienced at least one whole-genome duplication (WGD) in their history. The legacy of these ancient WGDs is still observable in the diploidized genomes of extant plants. Genes originating from WGD-paleologs-c...
MOTIVATION: Understanding the functional consequence of genetic variants, especially the non-coding ones, is important but particularly challenging. Genome-wide association studies (GWAS) or quantitative trait locus analyses may be subject to limited...
We introduce the R-package learnMET, developed as a flexible framework to enable a collection of analyses on multi-environment trial breeding data with machine learning-based models. learnMET allows the combination of genomic information with environ...
In oncology, the patient state is characterized by a whole spectrum of modalities, ranging from radiology, histology, and genomics to electronic health records. Current artificial intelligence (AI) models operate mainly in the realm of a single modal...
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...
Precision medicine uses genetic, environmental and lifestyle factors to more accurately diagnose and treat disease in specific groups of patients, and it is considered one of the most promising medical efforts of our time. The use of genetics is argu...
MOTIVATION: Accurate annotation of different genomic signals and regions (GSRs) from DNA sequences is fundamentally important for understanding gene structure, regulation and function. Numerous efforts have been made to develop machine learning-based...
The rapidly emerging field of computational pathology has demonstrated promise in developing objective prognostic models from histology images. However, most prognostic models are either based on histology or genomics alone and do not address how the...
MOTIVATION: The importance of chromatin loops in gene regulation is broadly accepted. There are mainly two approaches to predict chromatin loops: transcription factor (TF) binding-dependent approach and genomic variation-based approach. However, neit...