相关论文: From features to expression: High-density oligonuc…
Late diagnosis and high costs are key factors that negatively impact the care of cancer patients worldwide. Although the availability of biological markers for the diagnosis of cancer type is increasing, costs and reliability of tests…
Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we consider an extension of Efron's single-study two-groups model to allow joint analysis of multiple…
Even though there is a plethora of research in Microarray gene expression data analysis, still, it poses challenges for researchers to effectively and efficiently analyze the large yet complex expression of genes. The feature (gene)…
Toxicity evaluation of chemical compounds has traditionally relied on animal experiments;however, the demand for non-animal-based prediction methods for toxicology of compounds is increasing worldwide. Our aim was to provide a…
Evaluation metrics in image synthesis play a key role to measure performances of generative models. However, most metrics mainly focus on image fidelity. Existing diversity metrics are derived by comparing distributions, and thus they…
In the early days of gene expression data, researchers have focused on gene-level analysis, and particularly on finding differentially expressed genes. This usually involved making a simplifying assumption that genes are independent, which…
Prediction of mRNA gene-expression profiles directly from routine whole-slide images (WSIs) using deep learning models could potentially offer cost-effective and widely accessible molecular phenotyping. While such WSI-based gene-expression…
In a mouse intercross with more than 500 animals and genome-wide gene expression data on six tissues, we identified a high proportion (18%) of sample mix-ups in the genotype data. Local expression quantitative trait loci (eQTL; genetic loci…
Optical Coherence Tomography allows ophthalmologist to obtain cross-section imaging of eye retina. Assisted with digital image analysis methods, effective disease detection could be performed. Various methods exist to extract feature from…
Identifying disease-associated genes enables the development of precision medicine and the understanding of biological processes. Genome-wide association studies (GWAS), gene expression data, biological pathway analysis, and protein network…
Ensembles of deep neural networks demonstrate improved performance over single models. For enhancing the diversity of ensemble members while keeping their performance, particle-based inference methods offer a promising approach from a…
Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution…
Epilepsy is a chronic neurological condition characterized by recurrent seizures, with global prevalence estimated at 50 million people worldwide. While progress in high-throughput sequencing has allowed for broad-based transcriptomic…
MOTIVATION: The use of oligonucleotide microarray technology requires a very detailed attention to the design of specific probes spotted on the solid phase. These problems are far from being commonplace since they refer to complex…
Next-generation sequencing (NGS) is a key technique for studying the DNA and RNA of organisms. However, identifying quality problems in NGS data across different experimental settings remains challenging. To develop automated…
Thin-film solar cells are predominately designed similar to a stacked structure. Optimizing the layer thicknesses in this stack structure is crucial to extract the best efficiency of the solar cell. The commonplace method used in…
We perform differential expression analysis of high-throughput sequencing count data under a Bayesian nonparametric framework, removing sophisticated ad-hoc pre-processing steps commonly required in existing algorithms. We propose to use…
Phenotypic heterogeneity is a most fascinating property of a population of cells, which shows the differences among individuals even with the same genetic background and extracellular environmental conditions. However, the lack of…
In this paper, a robust weighted score for unbalanced data (ROWSU) is proposed for selecting the most discriminative feature for high dimensional gene expression binary classification with class-imbalance problem. The method addresses one…
Microarrays have become extremely useful for analysing genetic phenomena, but establishing a relation between microarray analysis results (typically a list of genes) and their biological significance is often difficult. Currently, the…