Research graph
References from Heterogeneous network approaches to protein pathway prediction. Local targets link to admitted publications; unresolved targets remain external evidence.
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10.1016/j.jtbi.2014.05.031 · External reference
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10.1155/2010/924529 · External reference
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2014 · External reference
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Graph neural networks: a review of methods and applications
10.1016/j.aiopen.2021.01.001 · 2020 · External reference
Graph convolutional networks: a comprehensive review
10.1186/s40649-019-0069-y · 2019 · External reference
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10.1145/3442381.3449914 · External reference
Protein-protein interaction networks (PPI) and complex diseases
2014 · External reference
Scale-free networks are rare
10.1038/s41467-019-08746-5 · 2019 · External reference
Identifying hubs in protein interaction networks
10.1371/journal.pone.0005344 · 2009 · External reference
A systematic survey of centrality measures for protein-protein interaction networks
10.1186/s12918-018-0598-2 · 2018 · External reference
10.5936/csbj.201302006 · 2013 · Admitted local publication
Network “small-world-ness”: a quantitative method for determining canonical network equivalence
10.1371/journal.pone.0002051 · 2008 · External reference
Disease networks. Uncovering disease-disease relationships through the incomplete interactome
10.1126/science.1257601 · 2015 · External reference
Approximating the largest eigenvalue of the modified adjacency matrix of networks with heterogeneous node biases
2009 · External reference
Heterogeneous graph structure learning for graph neural networks
10.1609/aaai.v35i5.16600 · 2021 · External reference
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10.1109/tbdata.2022.3177455 · External reference
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10.1145/3340531.3411983 · 2020 · External reference
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2017 · External reference
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10.1002/pro.3978
10.1002/pro.3978 · External reference
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10.1093/nar/gkw985 · External reference
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10.1093/nar/29.1.242 · 2001 · External reference
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10.1093/nar/gkac1015 · External reference
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10.1093/nar/gky1131 · External reference
Human protein reference database--2009 update
10.1093/nar/gkn892 · 2009 · External reference
10.1093/database/baz005
10.1093/database/baz005 · External reference
Co-immunoprecipitation and semi-quantitative immunoblotting for the analysis of protein-protein interactions
10.1016/j.xpro.2021.100644 · 2021 · External reference
10.1074/mcp.o116.065920
10.1074/mcp.o116.065920 · External reference
Filtering high-throughput protein-protein interaction data using a combination of genomic features
10.1186/1471-2105-6-100 · 2005 · External reference
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Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor
10.1371/journal.pcbi.1008890 · 2021 · External reference
Towards reproducibility in large-scale analysis of protein-protein interactions
10.1038/s41592-021-01202-7 · 2021 · External reference
Towards a characterization of apparent contradictions in the biomedical literature using context analysis
10.1016/j.jbi.2019.103275 · 2019 · External reference
Recording negative results of protein-protein interaction assays: an easy way to deal with the biases and errors of interactomic data sets
2017 · External reference
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10.3390/molecules27010041 · External reference
10.1038/s41580-022-00507-5
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10.1101/gr.276059.121
10.1101/gr.276059.121 · External reference
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10.1038/nbt1385 · External reference
A next generation connectivity map: L1000 platform and the first 1,000,000 profiles
10.1016/j.cell.2017.10.049 · 2017 · External reference
The gene expression omnibus database
10.1007/978-1-4939-3578-9_5 · 2016 · External reference
10.1002/pro.3307
10.1002/pro.3307 · External reference
10.1101/2022.07.06.499022
10.1101/2022.07.06.499022 · External reference
10.1038/nature10098
10.1038/nature10098 · External reference
Experimental reproducibility limits the correlation between mRNA and protein abundances in tumor proteomic profiles
2022 · External reference
Cautions about the reliability of pairwise gene correlations based on expression data
10.3389/fmicb.2015.00650 · 2015 · External reference
To embed or not: network embedding as a paradigm in computational biology
10.3389/fgene.2019.00381 · 2019 · External reference
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Graph-based prediction of Protein-protein interactions with attributed signed graph embedding
10.1186/s12859-020-03646-8 · 2020 · External reference
On protocols and measures for the validation of supervised methods for the inference of biological networks
10.3389/fgene.2013.00262 · 2013 · External reference
10.1093/bib/bbad189
10.1093/bib/bbad189 · External reference
10.1016/j.cels.2021.05.012
10.1016/j.cels.2021.05.012 · External reference
10.1016/j.csbj.2022.06.040 · Admitted local publication
10.1038/s41592-022-01616-x
10.1038/s41592-022-01616-x · External reference
Large-scale analysis of disease pathways in the human interactome. Pac Symp
2018 · External reference
10.1007/s41019-022-00188-2
10.1007/s41019-022-00188-2 · External reference
A systematic analysis of community detection in complex networks
10.1016/j.procs.2022.03.046 · 2022 · External reference
Detection of dynamic protein complexes through Markov Clustering based on Elephant Herd Optimization Approach
2019 · External reference
10.1093/bioinformatics/bty787
10.1093/bioinformatics/bty787 · External reference
10.1038/s41592-022-01454-x
10.1038/s41592-022-01454-x · External reference
Individualized pathway activity algorithm identifies oncogenic pathways in pan-cancer analysis
2022 · External reference
Identification of gastric cancer subtypes based on pathway clustering
10.1038/s41698-021-00186-z · 2021 · External reference
Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST
10.1038/s41467-023-36796-3 · 2023 · External reference
10.1074/mcp.tir118.001263
10.1074/mcp.tir118.001263 · External reference
Genomic data integration systematically biases interactome mapping
10.1371/journal.pcbi.1006474 · 2018 · External reference
Gene annotation bias impedes biomedical research
10.1038/s41598-018-19333-x · 2018 · External reference
Benefits and challenges of pre-clustered network-based pathway analysis
10.3389/fgene.2022.855766 · 2022 · External reference
10.1093/bioinformatics/btn164
10.1093/bioinformatics/btn164 · External reference
Predicting protein complex in protein interaction network - a supervised learning based method
2014 · External reference
Identifying protein complexes based on node embeddings obtained from protein-protein interaction networks
10.1186/s12859-018-2364-2 · 2018 · External reference
Predicting protein complexes using a supervised learning method combined with local structural information
10.1371/journal.pone.0194124 · 2018 · External reference
10.1007/978-3-030-26142-9_15
10.1007/978-3-030-26142-9_15 · External reference
10.1109/tcbb.2019.2944809
10.1109/tcbb.2019.2944809 · External reference
Super.Complex: a supervised machine learning pipeline for molecular complex detection in protein-interaction networks
10.1371/journal.pone.0262056 · 2021 · External reference
Network-based prediction of protein interactions
10.1038/s41467-019-09177-y · 2019 · External reference
Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding
10.7717/peerj.15815 · 2023 · External reference
10.3390/molecules27186135
10.3390/molecules27186135 · External reference
Efficient link prediction in the protein-protein interaction network using topological information in a generative adversarial network machine learning model
10.1186/s12859-022-04598-x · 2022 · External reference
10.1093/bib/bbab491
10.1093/bib/bbab491 · External reference
10.1021/acs.chemrev.5b00548
10.1021/acs.chemrev.5b00548 · External reference
Dynamic changes in protein functional linkage networks revealed by integration with gene expression data
10.1371/journal.pcbi.1000237 · 2008 · External reference
Graph algorithms for predicting subcellular localization at the pathway level
2023 · External reference
10.3390/sym14102218
10.3390/sym14102218 · External reference
BERTwalk for integrating gene networks to predict gene- to pathway-level properties
10.1093/bioadv/vbad086 · 2023 · External reference
Graph-BERT and language model-based framework for protein-protein interaction identification
10.1038/s41598-023-31612-w · 2023 · External reference
Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes
2016 · External reference
10.1002/gepi.21794
10.1002/gepi.21794 · External reference
Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study
10.1093/bioinformatics/btaa483 · 2020 · External reference
Characterizing genetic interactions in human disease association studies using statistical epistasis networks
10.1186/1471-2105-12-364 · 2011 · External reference
A systematic analysis of gene-gene interaction in multiple sclerosis
10.1186/s12920-022-01247-3 · 2022 · External reference
The post GWAS era: strategies to identify gene-gene and gene-environment interactions in urinary bladder cancer
2014 · External reference
Assessment of community efforts to advance network-based prediction of protein-protein interactions
10.1038/s41467-023-37079-7 · 2023 · External reference
From communities to protein complexes: a local community detection algorithm on PPI networks
10.1371/journal.pone.0260484 · 2022 · External reference
A closer look at cross-validation for assessing the accuracy of gene regulatory networks and models
10.1038/s41598-018-24937-4 · 2018 · External reference
Identifying significantly impacted pathways: a comprehensive review and assessment
10.1186/s13059-019-1790-4 · 2019 · External reference
DANUBE: Data-driven meta-ANalysis using UnBiased Empirical distributions-applied to biological pathway analysis
10.1109/jproc.2015.2507119 · 2017 · External reference
Statistics and network-based approaches to identify molecular mechanisms that drive the progression of breast cancer
2022 · External reference
Predicting biological pathways of chemical compounds with a profile-inspired approach
10.1186/s12859-021-04252-y · 2021 · External reference
Causal disturbance analysis: a novel graph centrality based method for pathway enrichment analysis
10.1109/tcbb.2019.2907246 · 2020 · External reference
A comparative study of topology-based pathway enrichment analysis methods
10.1186/s12859-019-3146-1 · 2019 · External reference
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10.1126/science.286.5439.509
10.1126/science.286.5439.509 · External reference
Recent advances in machine learning applications in metabolic engineering
10.1016/j.biotechadv.2022.108069 · 2023 · External reference
Current successes and remaining challenges in protein function prediction
10.3389/fbinf.2023.1222182 · 2023 · External reference
10.1016/j.cbpa.2008.07.024
10.1016/j.cbpa.2008.07.024 · External reference
10.3390/ijms22073327
10.3390/ijms22073327 · External reference
Assigning protein function from domain-function associations using DomFun
10.1186/s12859-022-04565-6 · 2022 · External reference
Pathway-specific protein domains are predictive for human diseases
2019 · External reference
Identification of pathway-specific protein domain by incorporating hyperparameter optimization based on 2d convolutional neural network
10.1109/access.2020.3027887 · 2020 · External reference
10.1016/j.ejca.2022.08.033
10.1016/j.ejca.2022.08.033 · External reference
