OBJECTIVES: We propose a communication-efficient transfer learning approach (COMMUTE) that effectively incorporates multi-site healthcare data for training a risk prediction model in a target population of interest, accounting for challenges includin...
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...
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...
There are currently >1.3 million human -omics samples that are publicly available. This valuable resource remains acutely underused because discovering particular samples from this ever-growing data collection remains a significant challenge. The maj...
Mathematical biosciences and engineering : MBE
Oct 24, 2022
DNase I hypersensitive sites (DHSs) are a specific genomic region, which is critical to detect or understand cis-regulatory elements. Although there are many methods developed to detect DHSs, there is a big gap in practice. We presented a deep learni...
Multi-task deep learning (DL) models can accurately predict diverse genomic marks from sequence, but whether these models learn the causal relationships between genomic marks is unknown. Here, we describe Deep Mendelian Randomization (DeepMR), a meth...
BACKGROUND: Identifying splice site regions is an important step in the genomic DNA sequencing pipelines of biomedical and pharmaceutical research. Within this research purview, efficient and accurate splice site detection is highly desirable, and a ...
IEEE journal of biomedical and health informatics
Oct 4, 2022
With the number of phage genomes increasing, it is urgent to develop new bioinformatics methods for phage genome annotation. Promoter, a DNA region, is important for gene transcriptional regulation. In the era of post-genomics, the availability of da...
Artificial intelligence (AI) models based on deep learning now represent the state of the art for making functional predictions in genomics research. However, the underlying basis on which predictive models make such predictions is often unknown. For...
Cancer prognosis analysis is of essential interest in clinical practice. In order to explore the prognostic power of computational histopathology and genomics, this paper constructs a multi-modality prognostic model for survival prediction. We collec...