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Constructing the angiome: a global angiogenesis protein interaction network.

Chu LH, Rivera CG, Popel AS, Bader JS.

Physiol Genomics. 2012 Oct 2;44(19):915-24. doi: 10.1152/physiolgenomics.00181.2011. Epub 2012 Aug 21.


PADPIN: protein-protein interaction networks of angiogenesis, arteriogenesis, and inflammation in peripheral arterial disease.

Chu LH, Vijay CG, Annex BH, Bader JS, Popel AS.

Physiol Genomics. 2015 Aug;47(8):331-43. doi: 10.1152/physiolgenomics.00125.2014. Epub 2015 Jun 9.


Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

Chu LH, Lee E, Bader JS, Popel AS.

PLoS One. 2014 Oct 16;9(10):e110871. doi: 10.1371/journal.pone.0110871. eCollection 2014.


Predicting diabetes mellitus genes via protein-protein interaction and protein subcellular localization information.

Tang X, Hu X, Yang X, Fan Y, Li Y, Hu W, Liao Y, Zheng MC, Peng W, Gao L.

BMC Genomics. 2016 Aug 18;17 Suppl 4:433. doi: 10.1186/s12864-016-2795-y.


Bioinformatics Analysis of Protein Phosphorylation in Plant Systems Biology Using P3DB.

Yao Q, Xu D.

Methods Mol Biol. 2017;1558:127-138. doi: 10.1007/978-1-4939-6783-4_6.


Interaction networks: from protein functions to drug discovery. A review.

Chautard E, Thierry-Mieg N, Ricard-Blum S.

Pathol Biol (Paris). 2009 Jun;57(4):324-33. doi: 10.1016/j.patbio.2008.10.004. Epub 2008 Dec 13. Review.


A systems biology approach for miRNA-mRNA expression patterns analysis in non-small cell lung cancer.

Najafi A, Tavallaei M, Hosseini SM.

Cancer Biomark. 2016;16(1):31-45. doi: 10.3233/CBM-150538.


pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis.

Rahmati S, Abovsky M, Pastrello C, Jurisica I.

Nucleic Acids Res. 2017 Jan 4;45(D1):D419-D426. doi: 10.1093/nar/gkw1082. Epub 2016 Nov 28.


Computational gene network analysis reveals TNF-induced angiogenesis.

Ogami K, Yamaguchi R, Imoto S, Tamada Y, Araki H, Print C, Miyano S.

BMC Syst Biol. 2012;6 Suppl 2:S12. doi: 10.1186/1752-0509-6-S2-S12. Epub 2012 Dec 12.


Deciphering the pharmacological mechanism of the Chinese formula huanglian-jie-du decoction in the treatment of ischemic stroke using a systems biology-based strategy.

Zhang YQ, Wang SS, Zhu WL, Ma Y, Zhang FB, Liang RX, Xu HY, Yang HJ.

Acta Pharmacol Sin. 2015 Jun;36(6):724-33. doi: 10.1038/aps.2014.124. Epub 2015 May 4.


Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases.

Gorenshteyn D, Zaslavsky E, Fribourg M, Park CY, Wong AK, Tadych A, Hartmann BM, Albrecht RA, García-Sastre A, Kleinstein SH, Troyanskaya OG, Sealfon SC.

Immunity. 2015 Sep 15;43(3):605-14. doi: 10.1016/j.immuni.2015.08.014. Epub 2015 Sep 8.


Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.

Kirouac DC, Saez-Rodriguez J, Swantek J, Burke JM, Lauffenburger DA, Sorger PK.

BMC Syst Biol. 2012 May 1;6:29. doi: 10.1186/1752-0509-6-29.


Integrated systems approach identifies risk regulatory pathways and key regulators in coronary artery disease.

Zhang Y, Liu D, Wang L, Wang S, Yu X, Dai E, Liu X, Luo S, Jiang W.

J Mol Med (Berl). 2015 Dec;93(12):1381-90. doi: 10.1007/s00109-015-1315-x. Epub 2015 Jul 26.


Constructing a gene semantic similarity network for the inference of disease genes.

Jiang R, Gan M, He P.

BMC Syst Biol. 2011;5 Suppl 2:S2. doi: 10.1186/1752-0509-5-S2-S2. Epub 2011 Dec 14.


Computational Systems Biology of Psoriasis: Are We Ready for the Age of Omics and Systems Biomarkers?

Sevimoglu T, Arga KY.

OMICS. 2015 Nov;19(11):669-87. doi: 10.1089/omi.2015.0096. Epub 2015 Oct 19.


Essential protein discovery based on a combination of modularity and conservatism.

Zhao B, Wang J, Li X, Wu FX.

Methods. 2016 Nov 1;110:54-63. doi: 10.1016/j.ymeth.2016.07.005. Epub 2016 Jul 9.


A directed protein interaction network for investigating intracellular signal transduction.

Vinayagam A, Stelzl U, Foulle R, Plassmann S, Zenkner M, Timm J, Assmus HE, Andrade-Navarro MA, Wanker EE.

Sci Signal. 2011 Sep 6;4(189):rs8. doi: 10.1126/scisignal.2001699.


Visualization and analysis of biological networks.

Millán PP.

Methods Mol Biol. 2013;1021:63-88. doi: 10.1007/978-1-62703-450-0_4.


Integrative analysis of human protein, function and disease networks.

Liu W, Wu A, Pellegrini M, Wang X.

Sci Rep. 2015 Sep 24;5:14344. doi: 10.1038/srep14344.

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