Research graph
References from Network-based approaches for modeling disease regulation and progression. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1093/nar/gky1079
10.1093/nar/gky1079 · External reference
10.1093/nar/gkaa1074
10.1093/nar/gkaa1074 · External reference
Learning from co-expression networks: possibilities and challenges
2016 · External reference
10.1146/annurev-genet-112414-055257
10.1146/annurev-genet-112414-055257 · External reference
10.1038/nrm1570
10.1038/nrm1570 · External reference
Profiling cell signaling networks at single-cell resolution
10.1074/mcp.r119.001790 · 2020 · External reference
Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks
10.3389/fcell.2014.00038 · 2014 · External reference
Network approaches for modeling the effect of drugs and diseases
10.1093/bib/bbac229 · 2022 · External reference
10.1038/nrg2918
10.1038/nrg2918 · External reference
10.1093/hmg/ddv001
10.1093/hmg/ddv001 · External reference
10.1073/pnas.0701361104
10.1073/pnas.0701361104 · External reference
Uncovering disease-disease relationships through the incomplete interactome
10.1126/science.1257601 · 2015 · External reference
10.1038/nchembio.118
10.1038/nchembio.118 · External reference
10.1016/j.tips.2021.11.004
10.1016/j.tips.2021.11.004 · External reference
10.1073/pnas.0506580102
10.1073/pnas.0506580102 · External reference
Toward a gold standard for benchmarking gene set enrichment analysis
2020 · External reference
On the performance of de novo pathway enrichment
10.1038/s41540-017-0007-2 · 2017 · External reference
10.1093/bioinformatics/btx004
10.1093/bioinformatics/btx004 · External reference
Unresolved reference
External reference
PCSF: an R-package for network-based interpretation of high-throughput data
10.1371/journal.pcbi.1005694 · 2017 · External reference
10.1371/journal.pcbi.1004879
10.1371/journal.pcbi.1004879 · External reference
10.1038/s41467-021-27138-2
10.1038/s41467-021-27138-2 · External reference
Robust disease module mining via enumeration of diverse prize-collecting Steiner trees
10.1093/bioinformatics/btab876 · 2022 · External reference
DOMINO: a novel algorithm for network-based identification of active modules with reduced rate of false calls
10.15252/msb.20209593 · 2021 · External reference
10.12688/f1000research.9054.1
10.12688/f1000research.9054.1 · External reference
Modulediscoverer: Identification of regulatory modules in protein-protein interaction networks
10.1038/s41598-017-18370-2 · 2018 · External reference
NoMAS: a computational approach to find mutated subnetworks associated with survival in genome-wide cancer studies
10.3389/fgene.2019.00265 · 2019 · External reference
10.1016/j.cels.2017.09.003
10.1016/j.cels.2017.09.003 · External reference
10.1093/nar/gkw166
10.1093/nar/gkw166 · External reference
10.1038/ng.3168
10.1038/ng.3168 · External reference
10.1093/bioinformatics/bty613
10.1093/bioinformatics/bty613 · External reference
10.1089/sysm.2019.0008
10.1089/sysm.2019.0008 · External reference
Disease Module Identification Based on Representation Learning of Complex Networks Integrated From GWAS, eQTL Summaries, and Human Interactome
10.3389/fbioe.2020.00418 · 2020 · External reference
BiCoN: Network-constrained biclustering of patients and omics data
10.1101/2020.01.31.926345 · 2020 · External reference
10.1089/sysm.2018.0013
10.1089/sysm.2018.0013 · External reference
10.1016/j.xcrm.2021.100424
10.1016/j.xcrm.2021.100424 · External reference
10.1016/j.cels.2016.12.011
10.1016/j.cels.2016.12.011 · External reference
Individuating Possibly Repurposable Drugs and Drug Targets for COVID-19 Treatment Through Hypothesis-Driven Systems Medicine Using CoVex
10.1089/adt.2020.1010 · 2020 · External reference
Systematic analysis of alternative splicing in time course data using Spycone
2022 · External reference
Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection
10.1038/s41540-021-00181-x · 2021 · External reference
Mesenchymal stromal cells mitigate liver damage after extended resection in the pig by modulating thrombospondin-1/TGF-β
10.1038/s41536-021-00194-4 · 2021 · External reference
Modular network mechanism of CCN1-associated resistance to HSV-1-derived oncolytic immunovirotherapies for glioblastomas
10.1038/s41598-021-90718-1 · 2021 · External reference
Genomic analyses identify molecular subtypes of pancreatic cancer
10.1038/nature16965 · 2016 · External reference
10.1038/s41586-021-03493-4
10.1038/s41586-021-03493-4 · External reference
Transcriptome and lipidome profile of human mesenchymal stem cells with reduced senescence and increased trilineage differentiation ability upon drug treatment
10.18632/aging.202759 · 2021 · External reference
10.1038/nmeth.3773
10.1038/nmeth.3773 · External reference
Towards a rigorous assessment of systems biology models: the DREAM3 challenges
10.1371/journal.pone.0009202 · 2010 · External reference
10.1186/1471-2105-9-559
10.1186/1471-2105-9-559 · External reference
Network inference in systems biology: recent developments, challenges, and applications
10.1016/j.copbio.2019.12.002 · 2020 · External reference
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
10.1186/1471-2105-7-s1-s7 · 2006 · External reference
10.1093/bioinformatics/btw216
10.1093/bioinformatics/btw216 · External reference
10.1371/journal.pbio.0050008
10.1371/journal.pbio.0050008 · External reference
Improving gene regulatory network structure using redundancy reduction in the MRNET algorithm
10.1039/c7ra01557g · 2017 · External reference
Inferring regulatory networks from expression data using tree-based methods
2010 · External reference
10.1093/bioinformatics/bty916
10.1093/bioinformatics/bty916 · External reference
Gene regulatory network inference using PLS-based methods
10.1186/s12859-016-1398-6 · 2016 · External reference
10.1093/biostatistics/kxm045
10.1093/biostatistics/kxm045 · External reference
FastGGM: an efficient algorithm for the inference of Gaussian graphical model in biological networks
10.1371/journal.pcbi.1004755 · 2016 · External reference
Asymptotic normality and optimalities in estimation of large Gaussian graphical models
2015 · External reference
Unresolved reference
2009 · External reference
Learning the structure of bayesian networks: a quantitative assessment of the effect of different algorithmic schemes
10.1155/2018/1591878 · 2018 · External reference
10.7551/mitpress/1754.001.0001
10.7551/mitpress/1754.001.0001 · External reference
Mutational interactions define novel cancer subgroups
10.1038/s41467-018-06867-x · 2018 · External reference
Unresolved reference
External reference
Inference of gene regulatory network based on local bayesian networks
10.1371/journal.pcbi.1005024 · 2016 · External reference
Unresolved reference
External reference
10.1145/3527154
10.1145/3527154 · External reference
Supervised learning of gene-regulatory networks based on graph distance profiles of transcriptomics data
10.1038/s41540-020-0140-1 · 2020 · External reference
10.1073/pnas.1911536116
10.1073/pnas.1911536116 · External reference
DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data
10.1093/bib/bbab325 · 2021 · External reference
Unresolved reference
External reference
10.1038/s43588-021-00099-8
10.1038/s43588-021-00099-8 · External reference
10.1038/nature10110
10.1038/nature10110 · External reference
10.1038/s41593-020-00748-7
10.1038/s41593-020-00748-7 · External reference
10.1161/circresaha.110.226357
10.1161/circresaha.110.226357 · External reference
10.1126/scisignal.2002282
10.1126/scisignal.2002282 · External reference
Information-theoretic inference of large transcriptional regulatory networks
2007 · External reference
10.1038/ncomms7683
10.1038/ncomms7683 · External reference
10.1038/s41586-020-2941-1
10.1038/s41586-020-2941-1 · External reference
Computational identification of new potential transcriptional partners of ERRα in breast cancer cells: specific partners for specific targets
10.1038/s41598-022-07744-w · 2022 · External reference
Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks
2022 · External reference
ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics
10.1093/bioinformatics/btz563 · 2020 · External reference
10.1093/bioinformatics/bty584
10.1093/bioinformatics/bty584 · External reference
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior
10.1126/sciadv.abc3781 · 2021 · External reference
10.1038/s41598-018-21715-0
10.1038/s41598-018-21715-0 · External reference
10.15252/msb.20156236
10.15252/msb.20156236 · External reference
High performance single-cell gene regulatory network inference at scale: the inferelator 3.0
2022 · External reference
10.1186/gb-2006-7-5-r36
10.1186/gb-2006-7-5-r36 · External reference
The inferelator 2.0: a scalable framework for reconstruction of dynamic regulatory network models
2009 · External reference
10.1093/bioinformatics/btaa032
10.1093/bioinformatics/btaa032 · External reference
Causal network inference from gene transcriptional time-series response to glucocorticoids
10.1371/journal.pcbi.1008223 · 2021 · External reference
Windowed Granger causal inference strategy improves discovery of gene regulatory networks
10.1073/pnas.1710936115 · 2018 · External reference
Clinical proteomic tumor analysis consortium, integrated proteogenomic characterization of clear cell renal cell carcinoma
10.1016/j.cell.2019.12.026 · 2020 · External reference
10.1093/bioinformatics/btv268
10.1093/bioinformatics/btv268 · External reference
10.1093/bioinformatics/btx748
10.1093/bioinformatics/btx748 · External reference
10.1186/s12918-014-0118-y
10.1186/s12918-014-0118-y · External reference
10.1371/journal.pone.0064832
10.1371/journal.pone.0064832 · External reference
Changes in the gene expression profile during spontaneous migraine attacks
10.1038/s41598-021-87503-5 · 2021 · External reference
10.1371/journal.pcbi.1003983
10.1371/journal.pcbi.1003983 · External reference
10.1016/j.cels.2019.05.012
10.1016/j.cels.2019.05.012 · External reference
A prior-based integrative framework for functional transcriptional regulatory network inference
10.1093/nar/gkw1160 · 2017 · External reference
Enhancing gene regulatory network inference through data integration with markov random fields
10.1038/srep41174 · 2017 · External reference
Network embedding across multiple tissues and data modalities elucidates the context of host factors important for COVID-19 infection
10.3389/fgene.2022.909714 · 2022 · External reference
Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data
10.1038/s41598-021-85544-4 · 2021 · External reference
10.1038/s41586-021-03933-1
10.1038/s41586-021-03933-1 · External reference
10.1371/journal.pcbi.1006591
10.1371/journal.pcbi.1006591 · External reference
Regulation of early host immune responses shapes the pathogenicity of avian influenza A virus
10.3389/fmicb.2019.02007 · 2019 · External reference
Gene regulatory network inference using fused LASSO on multiple data sets
10.1038/srep20533 · 2016 · External reference
10.1101/2021.03.31.437978
10.1101/2021.03.31.437978 · External reference
10.1038/s41592-021-01252-x
10.1038/s41592-021-01252-x · External reference
Leveraging supervised learning for functionally informed fine-mapping of cis-eQTLs identifies an additional 20,913 putative causal eQTLs
10.1038/s41467-021-23134-8 · 2021 · External reference
10.1101/gr.227819.117
10.1101/gr.227819.117 · External reference
10.1016/j.csbj.2022.06.035
10.1016/j.csbj.2022.06.035 · External reference
10.1371/journal.pone.0171097
10.1371/journal.pone.0171097 · External reference
10.1016/j.heliyon.2022.e10222
10.1016/j.heliyon.2022.e10222 · External reference
Bayesian network models for incomplete and dynamic data
10.1111/stan.12197 · 2020 · External reference
Measuring the wisdom of the crowds in network-based gene function inference
10.1093/bioinformatics/btu715 · 2015 · External reference
10.1101/gr.127191.111
10.1101/gr.127191.111 · External reference
10.1016/j.biosystems.2008.12.004
10.1016/j.biosystems.2008.12.004 · External reference
10.1038/nmeth.2810
10.1038/nmeth.2810 · External reference
Estimating gene regulatory networks with pandaR
10.1093/bioinformatics/btx139 · 2017 · External reference
Unresolved reference
External reference
Survey on graph neural networks
10.1109/tnnls.2020.2978386 · 2021 · External reference
The graph neural network model
10.1109/tnn.2008.2005605 · 2009 · External reference
Unresolved reference
External reference
A general survey on attention mechanisms in deep learning
2021 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
A statistical method for identifying differential gene-gene co-expression patterns
10.1093/bioinformatics/bth379 · 2004 · External reference
Gene co-expression network topology provides a framework for molecular characterization of cellular state
10.1093/bioinformatics/bth234 · 2004 · External reference
Finding disease specific alterations in the co-expression of genes
10.1093/bioinformatics/bth909 · 2004 · External reference
10.1038/msb.2011.99
10.1038/msb.2011.99 · External reference
10.1007/s00018-017-2679-6
10.1007/s00018-017-2679-6 · External reference
10.1093/bioinformatics/bty538
10.1093/bioinformatics/bty538 · External reference
10.1371/journal.pone.0109569
10.1371/journal.pone.0109569 · External reference
The joint graphical lasso for inverse covariance estimation across multiple classes
10.1111/rssb.12033 · 2014 · External reference
10.1093/biomet/asx049
10.1093/biomet/asx049 · External reference
10.1371/journal.pcbi.1002955
10.1371/journal.pcbi.1002955 · External reference
10.1126/science.1073374
10.1126/science.1073374 · External reference
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
10.1186/1471-2105-11-497 · 2010 · External reference
Detecting phenotype-driven transitions in regulatory network structure
10.1038/s41540-018-0052-5 · 2018 · External reference
10.1186/s13059-019-1851-8
10.1186/s13059-019-1851-8 · External reference
Differential network analysis: a statistical perspective
10.1002/wics.1508 · 2021 · External reference
10.1186/s13024-017-0219-3
10.1186/s13024-017-0219-3 · External reference
10.1186/s12918-016-0349-1
10.1186/s12918-016-0349-1 · External reference
Dissecting the interface between signaling and transcriptional regulation in human B cells
2009 · External reference
10.1038/nbt.1563
10.1038/nbt.1563 · External reference
10.1016/j.cell.2020.11.045
10.1016/j.cell.2020.11.045 · External reference
10.1111/1462-2920.13463
10.1111/1462-2920.13463 · External reference
Regulatory network of PD1 signaling is associated with prognosis in glioblastoma multiforme
10.1158/0008-5472.can-21-0730 · 2021 · External reference
10.1371/journal.ppat.1004869
10.1371/journal.ppat.1004869 · External reference
10.1093/nar/gkw772
10.1093/nar/gkw772 · External reference
Disease characterization using a partial correlation-based sample-specific network
10.1093/bib/bbaa062 · 2021 · External reference
10.2139/ssrn.3253573
10.2139/ssrn.3253573 · External reference
10.1101/gr.275107.120
10.1101/gr.275107.120 · External reference
10.1186/s12967-019-1908-1
10.1186/s12967-019-1908-1 · External reference
10.1016/j.celrep.2020.107795
10.1016/j.celrep.2020.107795 · External reference
Molecular networks in Network Medicine: Development and applications
10.1002/wsbm.1489 · 2020 · External reference
On the limits of active module identification
10.1093/bib/bbab066 · 2021 · External reference
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases
10.1093/nar/gkt1115 · 2014 · External reference
Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types
10.3389/fgene.2015.00260 · 2015 · External reference
10.1038/s41586-021-03819-2
10.1038/s41586-021-03819-2 · External reference
10.1073/pnas.0913357107
10.1073/pnas.0913357107 · External reference
10.1038/s41592-019-0509-5
10.1038/s41592-019-0509-5 · External reference
Statistical inference and reverse engineering of gene regulatory networks from observational expression data
10.3389/fgene.2012.00008 · 2012 · External reference
A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data
10.1093/bib/bbaa190 · 2021 · External reference
10.15252/msb.20188746
10.15252/msb.20188746 · External reference
Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data
10.1038/s41592-019-0690-6 · 2020 · External reference
Network modeling of single-cell omics data: challenges, opportunities, and progresses
10.1042/etls20180176 · 2019 · External reference
10.1016/j.coisb.2020.09.005
10.1016/j.coisb.2020.09.005 · External reference
Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data
2018 · External reference
The cancer genome atlas network, comprehensive molecular portraits of human breast tumours
10.1038/nature11412 · 2012 · External reference
The genotype-tissue expression (GTEx) project
10.1038/ng.2653 · 2013 · External reference
10.1038/s41467-020-14743-w
10.1038/s41467-020-14743-w · External reference
Large-scale inference of competing endogenous RNA networks with sparse partial correlation
10.1093/bioinformatics/btz314 · 2019 · External reference
Inferring interaction networks from multi-omics data
10.3389/fgene.2019.00535 · 2019 · External reference
Interpretation of deep learning in genomics and epigenomics
10.1093/bib/bbaa177 · 2021 · External reference
10.3389/fmolb.2021.673363
10.3389/fmolb.2021.673363 · External reference
Assessment and optimization of explainable machine learning models applied to transcriptomic data
10.1016/j.gpb.2022.07.003 · 2022 · External reference
The DisGeNET knowledge platform for disease genomics: 2019 update
2020 · External reference
10.1093/nar/28.1.27
10.1093/nar/28.1.27 · External reference
The reactome pathway knowledgebase
2020 · External reference
WikiPathways: pathway editing for the people
10.1371/journal.pbio.0060184 · 2008 · External reference
10.1016/j.cels.2021.05.015
10.1016/j.cels.2021.05.015 · External reference
10.1038/msb.2011.70
10.1038/msb.2011.70 · External reference
Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
10.7554/elife.51254 · 2020 · External reference
Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens
10.1126/sciadv.abf5733 · 2021 · External reference
High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer
10.1038/s41467-021-23213-w · 2021 · External reference
Using CRISPR to understand and manipulate gene regulation
10.1242/dev.182667 · 2021 · External reference
10.1016/j.jmb.2018.06.016
10.1016/j.jmb.2018.06.016 · External reference
10.1016/j.csbj.2021.05.001 · Admitted local publication
