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ITM Probe: analyzing information flow in protein networks.
Bioinformatics. 2009 Sep 15;25(18):2447-9. doi: 10.1093/bioinformatics/btp398. Epub 2009 Jun 27.
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CytoITMprobe: a network information flow plugin for Cytoscape.
BMC Res Notes. 2012 May 15;5:237. doi: 10.1186/1756-0500-5-237.
3
DeCoaD: determining correlations among diseases using protein interaction networks.
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PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks.
Bioinformatics. 2010 Jan 15;26(2):275-7. doi: 10.1093/bioinformatics/btp634. Epub 2009 Nov 13.
5
POINeT: protein interactome with sub-network analysis and hub prioritization.
BMC Bioinformatics. 2009 Apr 21;10:114. doi: 10.1186/1471-2105-10-114.
7
An analysis pipeline for the inference of protein-protein interaction networks.
Int J Data Min Bioinform. 2009;3(4):409-30. doi: 10.1504/ijdmb.2009.029204.
8
Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites.
Nucleic Acids Res. 2010 Jan;38(Database issue):D518-24. doi: 10.1093/nar/gkp842. Epub 2009 Oct 20.
10
MIPPIE: the mouse integrated protein-protein interaction reference.
Database (Oxford). 2020 Jan 1;2020. doi: 10.1093/database/baaa035.

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2
Identifying diseases-related metabolites using random walk.
BMC Bioinformatics. 2018 Apr 11;19(Suppl 5):116. doi: 10.1186/s12859-018-2098-1.
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InfAcrOnt: calculating cross-ontology term similarities using information flow by a random walk.
BMC Genomics. 2018 Jan 19;19(Suppl 1):919. doi: 10.1186/s12864-017-4338-6.
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Measuring disease similarity and predicting disease-related ncRNAs by a novel method.
BMC Med Genomics. 2017 Dec 28;10(Suppl 5):71. doi: 10.1186/s12920-017-0315-9.
5
Pathways on demand: automated reconstruction of human signaling networks.
NPJ Syst Biol Appl. 2016 Mar 3;2:16002. doi: 10.1038/npjsba.2016.2. eCollection 2016.
6
IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity.
Oncotarget. 2016 Jul 26;7(30):47864-47874. doi: 10.18632/oncotarget.10012.
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Using biological networks to integrate, visualize and analyze genomics data.
Genet Sel Evol. 2016 Mar 31;48:27. doi: 10.1186/s12711-016-0205-1.
8
Perturbation centrality and turbine: a novel centrality measure obtained using a versatile network dynamics tool.
PLoS One. 2013 Oct 21;8(10):e78059. doi: 10.1371/journal.pone.0078059. eCollection 2013.
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Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.
Pharmacol Ther. 2013 Jun;138(3):333-408. doi: 10.1016/j.pharmthera.2013.01.016. Epub 2013 Feb 4.
10
A single source k-shortest paths algorithm to infer regulatory pathways in a gene network.
Bioinformatics. 2012 Jun 15;28(12):i49-58. doi: 10.1093/bioinformatics/bts212.

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eQED: an efficient method for interpreting eQTL associations using protein networks.
Mol Syst Biol. 2008;4:162. doi: 10.1038/msb.2008.4. Epub 2008 Mar 4.
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Interaction networks for systems biology.
FEBS Lett. 2008 Apr 9;582(8):1220-4. doi: 10.1016/j.febslet.2008.02.015. Epub 2008 Feb 20.
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Information flow in interaction networks.
J Comput Biol. 2007 Oct;14(8):1115-43. doi: 10.1089/cmb.2007.0069.
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An integrative approach for causal gene identification and gene regulatory pathway inference.
Bioinformatics. 2006 Jul 15;22(14):e489-96. doi: 10.1093/bioinformatics/btl234.
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BioGRID: a general repository for interaction datasets.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9. doi: 10.1093/nar/gkj109.
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Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps.
Bioinformatics. 2005 Jun;21 Suppl 1:i302-10. doi: 10.1093/bioinformatics/bti1054.
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Automated modelling of signal transduction networks.
BMC Bioinformatics. 2002 Nov 1;3:34. doi: 10.1186/1471-2105-3-34.
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Acetylation of histones and transcription-related factors.
Microbiol Mol Biol Rev. 2000 Jun;64(2):435-59. doi: 10.1128/MMBR.64.2.435-459.2000.

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