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Prioritizing network communities

https://doi.org/10.1101/315903
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Stable Community Cores in Complex Networks
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Voting schemes for which it can be difficult to tell who won the election
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Defining and evaluating network communities based on ground-truth
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TYROBP in Alzheimer’s Disease
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Journal of the American Statistical Association
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A Proteome-Scale Map of the Human Interactome Network
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Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis
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Systematic Functional Annotation and Visualization of Biological Networks
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Graph clustering
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Community detection in graphs
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Testing order constraints: Qualitative differences between Bayes factors and normalized maximum likelihood
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Disentangling Interactions in the Microbiome: A Network Perspective
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Efficacy of galantamine in probable vascular dementia and Alzheimer's disease combined with cerebrovascular disease: a randomised trial
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Clustering attributed graphs: Models, measures and methods
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Gene Ontology: tool for the unification of biology
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Spatial reconstruction of single-cell gene expression data
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Network-based in silico drug efficacy screening
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Structure and inference in annotated networks
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Massively parallel digital transcriptional profiling of single cells
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Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients
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Human symptoms–disease network
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Understanding multicellular function and disease with human tissue-specific networks
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Network-based stratification of tumor mutations
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Selecting causal genes from genome-wide association studies via functionally coherent subnetworks
inferredcites →https://doi.org/10.1038/nmeth.3971openalex-snapshot
Diffusion pseudotime robustly reconstructs lineage branching
inferredcites →https://doi.org/10.1038/nrg.2016.87openalex-snapshot
Network biology concepts in complex disease comorbidities
inferredcites →https://doi.org/10.1038/nrg2363openalex-snapshot
Use and misuse of the gene ontology annotations
inferredcites →https://doi.org/10.1038/nrg2884openalex-snapshot
Analysing biological pathways in genome-wide association studies
inferredcites →https://doi.org/10.1038/nrg2918openalex-snapshot
Network medicine: a network-based approach to human disease
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Computational tools for prioritizing candidate genes: boosting disease gene discovery
inferredcites →https://doi.org/10.1038/s41540-017-0009-0openalex-snapshot
Integrating personalized gene expression profiles into predictive disease-associated gene pools
inferredcites →https://doi.org/10.1038/s41570-017-0054openalex-snapshot
Global chemical analysis of biology by mass spectrometry
inferredcites →https://doi.org/10.1073/pnas.0506580102openalex-snapshot
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
inferredcites →https://doi.org/10.1073/pnas.0601602103openalex-snapshot
Modularity and community structure in networks
inferredcites →https://doi.org/10.1073/pnas.0811511106openalex-snapshot
Assessing the relevance of node features for network structure
inferredcites →https://doi.org/10.1073/pnas.1221839110openalex-snapshot
Efficient discovery of overlapping communities in massive networks
inferredcites →https://doi.org/10.1073/pnas.1318948111openalex-snapshot
Defining functional DNA elements in the human genome
inferredcites →https://doi.org/10.1073/pnas.1409770111openalex-snapshot
Scalable detection of statistically significant communities and hierarchies, using message passing for modularity
inferredcites →https://doi.org/10.1073/pnas.1516878112openalex-snapshot
Illuminating the dark matter in metabolomics
inferredcites →https://doi.org/10.1073/pnas.1701464114openalex-snapshot
Diverse regulation of mammary epithelial growth and branching morphogenesis through noncanonical Wnt signaling
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Bayes Factors
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The Intrinsic Bayes Factor for Model Selection and Prediction
inferredcites →https://doi.org/10.1080/01621459.1997.10474045openalex-snapshot
Computing Bayes Factors by Combining Simulation and Asymptotic Approximations
inferredcites →https://doi.org/10.1080/01621459.2012.682530openalex-snapshot
A Multiscale Community Blockmodel for Network Exploration
inferredcites →https://doi.org/10.1093/bioinformatics/btr678openalex-snapshot
seeQTL: a searchable database for human eQTLs
inferredcites →https://doi.org/10.1093/bioinformatics/bts389openalex-snapshot
EnrichNet: network-based gene set enrichment analysis
inferredcites →https://doi.org/10.1093/nar/gkr251openalex-snapshot
NOA: a novel Network Ontology Analysis method
inferredcites →https://doi.org/10.1093/nar/gks1094openalex-snapshot
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
inferredcites →https://doi.org/10.1093/nar/gkt1068openalex-snapshot
DrugBank 4.0: shedding new light on drug metabolism
inferredcites →https://doi.org/10.1093/nar/gkt1115openalex-snapshot
The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases
inferredcites →https://doi.org/10.1093/nar/gkt1207openalex-snapshot
STITCH 4: integration of protein–chemical interactions with user data
inferredcites →https://doi.org/10.1093/nar/gkt533openalex-snapshot
GeneMANIA Prediction Server 2013 Update
inferredcites →https://doi.org/10.1093/nar/gku1204openalex-snapshot
The BioGRID interaction database: 2015 update
inferredcites →https://doi.org/10.1093/nar/gku935openalex-snapshot
The Comparative Toxicogenomics Database's 10th year anniversary: update 2015
inferredcites →https://doi.org/10.1093/nar/gkv1194openalex-snapshot
PANTHER version 10: expanded protein families and functions, and analysis tools
inferredcites →https://doi.org/10.1093/nar/gkv1351openalex-snapshot
The Reactome pathway Knowledgebase
inferredcites →https://doi.org/10.1101/265553openalex-snapshot
Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases
inferredcites →https://doi.org/10.1101/gr.118992.110openalex-snapshot
Prioritizing candidate disease genes by network-based boosting of genome-wide association data
inferredcites →https://doi.org/10.1101/gr.190595.115openalex-snapshot
Defining cell types and states with single-cell genomics
inferredcites →https://doi.org/10.1101/gr.6202607openalex-snapshot
A systems biology approach for pathway level analysis
inferredcites →https://doi.org/10.1103/physreve.72.056135openalex-snapshot
Finding instabilities in the community structure of complex networks
inferredcites →https://doi.org/10.1103/physreve.74.016110openalex-snapshot
Statistical mechanics of community detection
inferredcites →https://doi.org/10.1103/physreve.76.015102openalex-snapshot
Partitioning and modularity of graphs with arbitrary degree distribution
inferredcites →https://doi.org/10.1103/physreve.77.046119openalex-snapshot
Robustness of community structure in networks
inferredcites →https://doi.org/10.1103/physreve.82.066106openalex-snapshot
Measuring the significance of community structure in complex networks
inferredcites →https://doi.org/10.1103/physreve.83.016107openalex-snapshot
Stochastic blockmodels and community structure in networks
inferredcites →https://doi.org/10.1103/physreve.84.036103openalex-snapshot
Efficient and principled method for detecting communities in networks
inferredcites →https://doi.org/10.1109/icdm.2013.167openalex-snapshot
Community Detection in Networks with Node Attributes
inferredcites →https://doi.org/10.1109/mlsp.2011.6064546openalex-snapshot
Infinite multiple membership relational modeling for complex networks
inferredcites →https://doi.org/10.1126/sciadv.1602548openalex-snapshot
The ground truth about metadata and community detection in networks
inferredcites →https://doi.org/10.1126/science.1180823openalex-snapshot
The Genetic Landscape of a Cell
inferredcites →https://doi.org/10.1126/science.1257601openalex-snapshot
Uncovering disease-disease relationships through the incomplete interactome
inferredcites →https://doi.org/10.1126/science.aaa1934openalex-snapshot
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
inferredcites →https://doi.org/10.1126/science.aad9029openalex-snapshot
Higher-order organization of complex networks
inferredcites →https://doi.org/10.1126/science.aaf1420openalex-snapshot
A global genetic interaction network maps a wiring diagram of cellular function
inferredcites →https://doi.org/10.1137/1.9781611972894.4openalex-snapshot
Rank Aggregation: Together We're Strong
inferredcites →https://doi.org/10.1140/epjb/e2004-00125-xopenalex-snapshot
Finding communities in linear time: a physics approach
inferredcites →https://doi.org/10.1142/9789813235533_0011openalex-snapshot
Large-scale analysis of disease pathways in the human interactome
inferredcites →https://doi.org/10.1145/1109557.1109642openalex-snapshot
Ordering by weighted number of wins gives a good ranking for weighted tournaments
inferredcites →https://doi.org/10.1145/1411509.1411513openalex-snapshot
Aggregating inconsistent information
inferredcites →https://doi.org/10.1145/1553374.1553416openalex-snapshot
Dynamic mixed membership blockmodel for evolving networks
inferredcites →https://doi.org/10.1145/1835804.1835906openalex-snapshot
Modeling relational events via latent classes
inferredcites →https://doi.org/10.1145/2433396.2433471openalex-snapshot
Overlapping community detection at scale
inferredcites →https://doi.org/10.1145/2556195.2556243openalex-snapshot
Detecting cohesive and 2-mode communities indirected and undirected networks
inferredcites →https://doi.org/10.1145/2623330.2623707openalex-snapshot
On the permanence of vertices in network communities
inferredcites →https://doi.org/10.1145/371920.372165openalex-snapshot
Rank aggregation methods for the Web
inferredcites →https://doi.org/10.1145/872757.872795openalex-snapshot
Efficient similarity search and classification via rank aggregation
inferredcites →https://doi.org/10.1186/1471-2105-13-226openalex-snapshot
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
inferredcites →https://doi.org/10.1198/016214507000001337openalex-snapshot
Mixtures of g Priors for Bayesian Variable Selection
inferredcites →https://doi.org/10.1198/jasa.2009.tm08106openalex-snapshot
Assessing Robustness of Intrinsic Tests of Independence in Two-Way Contingency Tables
inferredcites →https://doi.org/10.1201/9780429258411openalex-snapshot
Bayesian Data Analysis
inferredcites →https://doi.org/10.1371/journal.pcbi.1002375openalex-snapshot
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
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A Neural Probabilistic Model for Context Based Citation Recommendation
inferredcites →https://doi.org/10.2174/1389557513666131119201353openalex-snapshot
Donepezil: An Important Prototype to the Design of New Drug Candidates for Alzheimer’s Disease
inferredcites →https://doi.org/10.2307/2291091openalex-snapshot
Bayes Factors
inferredcites →https://doi.org/10.2307/2986349openalex-snapshot
Algorithm AS 296: Optimal Median Smoothing
inferredcites →https://doi.org/10.48550/arxiv.1302.2684openalex-snapshot
A Tensor Approach to Learning Mixed Membership Community Models
inferredcites →https://doi.org/10.48550/arxiv.1401.7375openalex-snapshot
Detecting Cohesive and 2-mode Communities in Directed and Undirected Networks
inferredcites →https://doi.org/10.5555/1109557.1109642openalex-snapshot
Ordering by weighted number of wins gives a good ranking for weighted tournaments

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Learning Strong Graph Neural Networks with Weak Information
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