BACKGROUND: Although the diagnostic method for coronary atherosclerosis heart disease (CAD) is constantly innovated, CAD in the early stage is still missed diagnosis for the absence of any symptoms. The gene expression levels varied during disease de...
OBJECTIVE: Hypoxia presents a salient feature investigated in most solid tumors that holds key roles in cancer progression, including glioblastoma multiforme (GBM). Here, we aimed to construct a hypoxia-derived gene signature for identifying the high...
The rapid evolution of the novel coronavirus disease (COVID-19) pandemic has resulted in an urgent need for effective clinical tools to reduce transmission and manage severe illness. Numerous teams are quickly developing artificial intelligence appro...
In the integrative analyses of omics data, it is often of interest to extract data representation from one data type that best reflect its relations with another data type. This task is traditionally fulfilled by linear methods such as canonical corr...
In recent years, exome sequencing (ES) has shown great utility in the diagnoses of Mendelian disorders. However, after rigorous filtering, a typical ES analysis still involves the interpretation of hundreds of variants, which greatly hinders the rapi...
BACKGROUND: Glioblastoma (GBM) can be divided into subtypes according to their genomic features, including Proneural (PN), Neural (NE), Classical (CL) and Mesenchymal (ME). However, it is a difficult task to unify various genomic expression profiles ...
Publicly available gene expression datasets were analyzed to develop a chromophobe and oncocytoma related gene signature (COGS) to distinguish chRCC from RO. The datasets GSE11151, GSE19982, GSE2109, GSE8271 and GSE11024 were combined into a discover...
Identifying relevant disease modules such as target cell types is a significant step for studying diseases. High-throughput single-cell RNA-Seq (scRNA-seq) technologies have advanced in recent years, enabling researchers to investigate cells individu...
Journal of computational biology : a journal of computational molecular cell biology
Jan 5, 2022
Deep neural networks (DNNs) have been recently proposed for quartet tree phylogeny estimation. Here, we present a study evaluating recently trained DNNs in comparison to a collection of standard phylogeny estimation methods on a heterogeneous collect...
Journal of computational biology : a journal of computational molecular cell biology
Jan 5, 2022
Non-negative matrix factorization (NMF) is a fundamental matrix decomposition technique that is used primarily for dimensionality reduction and is increasing in popularity in the biological domain. Although finding a unique NMF is generally not possi...