Network-based methods for predicting essential genes or proteins: a survey

X Li, W Li, M Zeng, R Zheng, M Li - Briefings in bioinformatics, 2020 - academic.oup.com
network topological and biological properties. In Dynamic … provide a more comprehensive
gene expression profile. More … Accordingly, identifying the domains that occur within proteins

[HTML][HTML] A novel essential protein identification method based on PPI networks and gene expression data

J Zhong, C Tang, W Peng, M Xie, Y Sun, Q Tang… - BMC …, 2021 - Springer
… methods for identifying essential proteins have better results by using biological information.
… characterize the probability of two proteins being in a cluster from a topology perspective (2) …

A deep learning framework for gene ontology annotations with sequence-and network-based information

F Zhang, H Song, M Zeng, FX Wu, Y Li… - … /ACM transactions on …, 2020 - ieeexplore.ieee.org
… biological problems and network topological features are very important in the study …
identifying essential proteins based on proteinprotein interaction network and gene expression data

Determining proteinprotein functional associations by functional rules based on gene ontology and KEGG pathway

YH Zhang, T Zeng, L Chen, T Huang, YD Cai - … Acta (BBA)-Proteins and …, 2021 - Elsevier
gene expression profiling data [15] or cellular co-localization … that a lot of features were
essential for majority datasets. These … : 0006412 is definitely an effective parameter for identifying

[HTML][HTML] Glioblastoma gene network reconstruction and ontology analysis by online bioinformatics tools

NV Gubanova, NG Orlova, AI Dergilev… - Journal of integrative …, 2021 - degruyter.com
… sequencing, analysis of gene expression on microarrays, and … Despite the development in
early detection, and treatment, 5-… The study of the structure of the gene network shows a high …

An integrated systems biology and network-based approaches to identify novel biomarkers in breast cancer cell lines using gene expression data

A Khan, Z Rehman, HF Hashmi, AA Khan… - Interdisciplinary …, 2020 - Springer
Proteinprotein interaction network is a very important … the data set of microarray gene
expression and identifying … of PPI and TF network assessment as a powerful structure for gaining …

Computational methods for identifying the critical nodes in biological networks

X Liu, Z Hong, J Liu, Y Lin… - Briefings in …, 2020 - academic.oup.com
… new essential proteins based on network topology. CEPPK detects new essential proteins by
integrating network … the gene expression data with the static PPI network to build a dynamic …

[HTML][HTML] Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data

V Bourgeais, F Zehraoui, M Ben Hamdoune… - BMC …, 2021 - Springer
… by identifying the most important neurons and … based on a MLP constrained by the GO
structure. The constraints are introduced into the network using an adaptive regularization term

An effective link-based clustering algorithm for detecting overlapping protein complexes in protein-protein interaction networks

L Hu, J Zhang, X Pan, X Luo… - … Transactions on Network …, 2021 - ieeexplore.ieee.org
detect overlapping protein complexes. It first measures the similarity between pairwise
interactions from the perspectives of network topology and Gene Ontology. … form complete protein

Identifying protein complexes from protein-protein interaction networks based on fuzzy clustering and GO semantic information

X Pan, L Hu, P Hu, ZH You - IEEE/ACM Transactions on …, 2021 - ieeexplore.ieee.org
… order to complete the task of identifying overlapping protein … consider both of the network
structure and GO, we observed … transcompel®: Transcriptional gene regulation in eukaryotes,…