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Efficient randomization of biological networks while preserving functional characterization of individual nodes

https://doi.org/10.1101/069245
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What this work says

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

inferredcites →https://doi.org/10.1007/978-3-642-30541-2_12openalex-snapshot
Are We There Yet? When to Stop a Markov Chain while Generating Random Graphs
inferredcites →https://doi.org/10.1007/s004420100717openalex-snapshot
Swap and fill algorithms in null model analysis: rethinking the knight's tour
inferredcites →https://doi.org/10.1016/0097-3165(78)90059-6openalex-snapshot
The asymptotic number of labeled graphs with given degree sequences
inferredcites →https://doi.org/10.1016/j.cell.2015.05.056openalex-snapshot
Elucidating Compound Mechanism of Action by Network Perturbation Analysis
inferredcites →https://doi.org/10.1016/j.drudis.2012.11.001openalex-snapshot
Biological network inference for drug discovery
inferredcites →https://doi.org/10.1038/ncomms5114openalex-snapshot
A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals
inferredcites →https://doi.org/10.1038/nmeth.3773openalex-snapshot
Inferring causal molecular networks: empirical assessment through a community-based effort
inferredcites →https://doi.org/10.1038/nrg3552openalex-snapshot
Integrative approaches for finding modular structure in biological networks
inferredcites →https://doi.org/10.1089/cmb.2010.0265openalex-snapshot
Algorithms for Detecting Significantly Mutated Pathways in Cancer
inferredcites →https://doi.org/10.1093/bioinformatics/18.suppl_1.s233openalex-snapshot
Discovering regulatory and signalling circuits in molecular interaction networks
inferredcites →https://doi.org/10.1093/bioinformatics/btn161openalex-snapshot
Identifying functional modules in protein–protein interaction networks: an integrated exact approach
inferredcites →https://doi.org/10.1093/bioinformatics/btq089openalex-snapshot
BioNet: an R-Package for the functional analysis of biological networks
inferredcites →https://doi.org/10.1093/bioinformatics/btr028openalex-snapshot
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens
inferredcites →https://doi.org/10.1093/bioinformatics/btr145openalex-snapshot
Mass-balanced randomization of metabolic networks
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/bioinformatics/btu474openalex-snapshot
Fast randomization of large genomic datasets while preserving alteration counts
inferredcites →https://doi.org/10.1093/nar/gkj141openalex-snapshot
Human protein reference database--2006 update
inferredcites →https://doi.org/10.1103/physreve.85.046103openalex-snapshot
Unbiased degree-preserving randomization of directed binary networks
inferredcites →https://doi.org/10.1126/scisignal.2001965openalex-snapshot
Introduction to Network Analysis in Systems Biology
inferredcites →https://doi.org/10.1142/2446openalex-snapshot
Graph Theory and Its Engineering Applications
inferredcites →https://doi.org/10.1145/2133803.2330086openalex-snapshot
Constructing and sampling graphs with a prescribed joint degree distribution
inferredcites →https://doi.org/10.1146/annurev-bioeng-071813-104927openalex-snapshot
Modeling Signaling Networks to Advance New Cancer Therapies
inferredcites →https://doi.org/10.1186/1752-0509-6-133openalex-snapshot
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
inferredcites →https://doi.org/10.1186/1752-0509-7-139openalex-snapshot
Network based elucidation of drug response: from modulators to targets
inferredcites →https://doi.org/10.1186/1756-0381-4-10openalex-snapshot
Using graph theory to analyze biological networks
inferredcites →https://doi.org/10.18632/oncotarget.7255openalex-snapshot
Integrated transcriptomic and proteomic analysis identifies protein kinase CK2 as a key signaling node in an inflammatory cytokine network in ovarian cancer cells
inferredcites →https://doi.org/10.48550/arxiv.cond-mat/0312028openalex-snapshot
On the uniform generation of random graphs with prescribed degree sequences
inferredcites →https://doi.org/10.5169/seals-266450openalex-snapshot
Étude comparative de la distribution florale dans une portion des Alpes et du Jura

What points at this work

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

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Early fate bias in neuroepithelial progenitors of hippocampal neurogenesis
inferred← citeshttps://doi.org/10.1038/s41467-022-30755-0openalex-snapshot
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data
inferred← citeshttps://doi.org/10.1038/s41593-022-01011-xopenalex-snapshot
Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics
inferred← citeshttps://doi.org/10.11606/t.95.2019.tde-09122017-001154openalex-snapshot
Estruturas de redes em ossos ao longo do desenvolvimento
inferred← citeshttps://doi.org/10.1371/journal.pgen.1008711openalex-snapshot
Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins
inferred← citeshttps://doi.org/10.7287/peerj.13016v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Functional network motifs defined through integration of protein-protein and genetic interactions (v0.1)"
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