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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.


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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