Web server


GeneHits: a graph diffusion-based algorithm to expand on known molecules to construct the protein-protein interaction network.

Chu LH, Rivera CG, Popel AS, Bader JS. Constructing the angiome: a global angiogenesis protein interaction network. Physiol Genomics. 2012 Oct 2;44(19):915-24. PMID: 22911453



The codes are freely provided for researchers and educators in the non-profit sector. Please send an email to lchu5@jhmi.edu for the request of password.



Chu LH, Lee E, Bader JS, Popel AS. Angiogenesis Interactome and Time Course Microarray Data Reveal the Distinct Activation Patterns in Endothelial Cells. PLoS ONE (In Revision)

SBML code download: Chu_PLoSONE2014 (password required)



Finley SD, Dhar M, Popel AS. Compartment model predicts VEGF secretion and investigates the effects of VEGF trap in tumor-bearing mice. Front Oncol. 2013 Jul 30;3:196. PMID:23908970

SBML code download: Finley_FrontOncol2013 (password required)

Finley SD, Popel AS. Effect of tumor microenvironment on tumor VEGF during anti-VEGF treatment: systems biology predictions. J Natl Cancer Inst. 2013 Jun 5;105(11):802-11. PMID: 23670728

SBML code download: Finley_JNCI 2013 (password required)



Finley SD, Popel AS. Predicting the Effects of Anti-angiogenic Agents Targeting Specific VEGF Isoforms. The AAPS Journal. 14(3), 500-509. PMID: 22547351

SBML code download: Isoform-specific Anti-VEGF Human Model_May2012_Finley AAPS J (password required)


Liu G, Mac Gabhann F, Popel AS. Effects of fiber type and size on the heterogeneity of oxygen distribution in exercising skeletal muscle. PLoS One. 2012;7(9):e44375. PMID: 23028531

C++ code download: AngioFiberTypeSize_Gang2011 (password required)



BMC sys bio 2011

Finley SD, Engel-Stefanini MO, Imoukhuede PI, Popel AS. Pharmacokinetics and pharmacodynamics of VEGF-neutralizing antibodies. BMC Syst Biol. 2011 Nov 21;5:193. PMID: 22104283

SBML code download: Finley et al_BMC Syst Biol_2011 (password required)


Yen P, Finley SD, Engel-Stefanini MO, Popel AS. A two-compartment model of VEGF distribution in the mouse. PLoS One. 2011;6(11):e27514. PMID: 22087332

SBML code download: Yen et al_PLoS ONE_2011 (password required)


Vempati et al. Formation of VEGF isoform-specific spatial distributions governing angiogenesis: computational analysis. BMC Syst Biol. 2011 May 2;5:59.PMID: 21535871
Vempati et al. Quantifying the proteolytic release of extracellular matrix-sequestered VEGF with a computational model. PLoS One. 2010 Jul 29;5(7):e11860. PMID: 20686621

Matlab code download: Vempati_solver (password required)








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