MOTIVATION: Gene set enrichment analysis (GSEA) has been widely used to identify gene sets with statistically significant difference between cases and controls against a large gene set. GSEA needs both phenotype labels and expression of genes. Howeve...
Unsupervised methods, such as clustering methods, are essential to the analysis of single-cell genomic data. The most current clustering methods are designed for one data type only, such as single-cell RNA sequencing (scRNA-seq), single-cell ATAC seq...
A promoter is a region in the DNA sequence that defines where the transcription of a gene by RNA polymerase initiates, which is typically located proximal to the transcription start site (TSS). How to correctly identify the gene TSS and the core prom...
Origins of replication sites (ORIs), which refers to the initiative locations of genomic DNA replication, play essential roles in DNA replication process. Detection of ORIs' distribution in genome scale is one of key steps to in-depth understanding t...
Proceedings of the National Academy of Sciences of the United States of America
Jul 13, 2021
Forward genetic studies use meiotic mapping to adduce evidence that a particular mutation, normally induced by a germline mutagen, is causative of a particular phenotype. Particularly in small pedigrees, cosegregation of multiple mutations, occasiona...
MOTIVATION: Mapping distal regulatory elements, such as enhancers, is a cornerstone for elucidating how genetic variations may influence diseases. Previous enhancer-prediction methods have used either unsupervised approaches or supervised methods wit...
PURPOSE: To design a robust and automated estimation method for measuring the retinal nerve fiber layer (RNFL) thickness using spectral domain optical coherence tomography (SD-OCT).
Profiling molecular features associated with the morphological landscape of tissue is crucial for investigating the structural and spatial patterns that underlie the biological function of tissues. In this study, we present a new method, spatial gene...
Speckle noises widely exist in optical coherence tomography (OCT) images. We propose an improved double-path parallel convolutional neural network (called DPNet) to reduce speckles. We increase the network width to replace the network depth to extrac...
MOTIVATION: Over the past years, many computational methods have been developed to incorporate information about phenotypes for disease-gene prioritization task. These methods generally compute the similarity between a patient's phenotypes and a data...
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