Individualized patient profiling is instrumental for personalized management in hepatocellular carcinoma (HCC). This study built a model based on bidirectional deep neural networks (BiDNNs), an unsupervised machine-learning approach, to integrate mu...
IEEE/ACM transactions on computational biology and bioinformatics
Aug 6, 2021
Reconstruction of time-varying gene regulatory networks underlying a time-series gene expression data is a fundamental challenge in the computational systems biology. The challenge increases multi-fold if the target networks need to be constructed fo...
For a patient affected by breast cancer, after tumor removal, it is necessary to decide which adjuvant therapy is able to prevent tumor relapse and formation of metastases. A prediction of the outcome of adjuvant therapy tailored for the patient is h...
Knowledge of genes that are critical to a tissue's function remains difficult to ascertain and presents a major bottleneck toward a mechanistic understanding of genotype-phenotype links. Here, we present the first machine learning model-FUGUE-combini...
BACKGROUND: Analyzing single-cell RNA sequencing (scRNAseq) data plays an important role in understanding the intrinsic and extrinsic cellular processes in biological and biomedical research. One significant effort in this area is the identification ...
BACKGROUND: The topology of metabolic networks is both well-studied and remarkably well-conserved across many species. The regulation of these networks, however, is much more poorly characterized, though it is known to be divergent across organisms-t...
is a major pathogen that causes a high mortality rate in trout farms. However, systemic responses to the pathogen and its interactions with multiple organs during the course of infection have not been well described. In this study, dual-organ transc...
We discuss the dynamical robustness of biological networks represented by directed graphs, such as neural networks and gene regulatory networks. The theoretical results indicate that networks with low indegree variance and high outdegree variance are...
Searching for possible biochemical networks that perform a certain function is a challenge in systems biology. For simple functions and small networks, this can be achieved through an exhaustive search of the network topology space. However, it is di...
In this study, we aimed to identify potential diagnostic biomarkers Parkinson's disease (PD) by exploring microarray gene expression data of PD patients. Differentially expressed genes associated with PD were screened from the GSE99039 dataset usin...
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