Publications

P69.    S. Sarabipour, F. Mac Gabhann. Tumor and endothelial cells collaborate via transcellular receptor complexes.  J Pathol (2019) 247:155-157. doi: 10.1002/path.5185.

P68.    I. Lam, C.M. Pickering, F. Mac Gabhann. Context-dependent regulation of receptor tyrosine kinases: Insights from systems biology approaches.  Wiley Interdiscip Rev Syst Biol Med (2018) 26:e1437. doi: 10.1002/wsbm.1437. 

P67.    L.E. Clegg, F. Mac Gabhann. A computational analysis of pro-angiogenic therapies for peripheral artery disease.  Integrative Biology (2018) doi: 10.1039/c7ib00218a.

P66.    K.H. Gouin 3rd, S.K. Hellstrom, L.E. Clegg, J. Cutts, F. Mac Gabhann, T.R. Cardinal. Arterialized collateral capillaries progress from non‐reactive to capable of increasing perfusion in an ischemic tree. Microcirculation (2017) doi: 10.1111/micc.12438.

P65.    S. Sarabipour, F. Mac Gabhann. Computational Systems Biochemistry: Beyond the Static Interactome.  Biochemistry (2017) 57:9-10.

P64.    L. Clegg, V.C. Ganta, B.H. Annex, F. Mac Gabhann. Systems Pharmacology of VEGF165b in Peripheral Artery Disease.  CPT:PSP (Pharmacometrics & Systems Pharmacology) (2017) 6:833-844.

P63.    J. Walpole, F. Mac Gabhann, S.M. Peirce, J.C. Chappell. Agent-based Computational Model of Retinal Angiogenesis Simulates Microvascular Network Morphology as a Function of Pericyte Coverage. Microcirculation (2017) 24: e12393.

P62.    S. Sarabipour and F. Mac Gabhann. VEGF-A121a binding to Neuropilins – a concept revisited. Cell Adhesion & Migration (2017) 2:1-11.

P61.    C. Avalos, C. Abreu, S. Queen, M. Li, S. Price, E. Shirk, E. Engle, B. Bullock, F. Mac Gabhann, S. Wietgrefe, A. Haase, M.C. Zink, J. Mankowski, J. Clements, L. Gama. Brain macrophages in SIV-infected, antiretroviral-suppressed macaques: a functional latent reservoir.  mBio (2017) 8: e01186-17.

P60.    F. Mac Gabhann. TILRR steers IL-1 signaling. JACC: Basic To Translational Science (2017) 2:415-7.

P59.    L. Clegg and F. Mac Gabhann. A computational analysis of in vivo VEGFR activation by multiple co-expressed ligands.  PLOS Comput Biol (2017) 13:e1005445.

P58.    L. Clegg and F. Mac Gabhann. Further support for ECM control of receptor trafficking and signaling. J Cell Physiol (2017) 232:36.

P57.    J.C. Chappell, J.G. Cluceru, J. Nesmith, J. Walpole, S.M. Peirce, F. Mac Gabhann, V.L. Bautch. Flt-1 (VEGFR-1) Coordinates Discrete Stages of Blood Vessel Branching and Coalescence. Cardiovasc Res (2016) 111:84.

P56.    I. Hosseini & F. Mac Gabhann. Mechanistic Models Predict Efficacy of CCR5-Deficient Stem Cell Transplants in HIV Patient Populations. CPT:Pharmacometrics & Systems Pharmacology (2016) 5:82.

P55.    P.S. Briquez, L.E. Clegg, M.M. Martino, F. Mac Gabhann, J.A. Hubbell. An Integrated Materials-Centric View of Therapeutic Angiogenesis. Nature Reviews Materials (2016) 1:15006.

P54.    R.J. Bender & F. Mac Gabhann. Dysregulation of the Vascular Endothelial Growth Factor and Semaphorin ligand-receptor families in prostate cancer metastasis. BMC Systems Biology (2015) 9:55.

P53.    J. Walpole, J.C. Chappell, J.G. Cluceru, F. Mac Gabhann, V.L. Bautch, and S.M. Peirce. Agent-based model of angiogenesis predicts capillary sprout initiation in multicellular networks. Integrative Biology (2015) 7:987-97. **Cover image article

P52.    L.E. Clegg and F. Mac Gabhann. Molecular Mechanism Matters: Benefits of mechanistic computational models for drug development. Pharmacol Res (2015) 99:149-154.

P51.    I. Hosseini, L. Gama and F. Mac Gabhann. Multiplexed Component Analysis to Identify Genes Contributing to the Inflammatory Response During Acute SIV Infection. PLoS ONE (2015) 10:e0126843.

P50.    L.E. Clegg and F. Mac Gabhann. Site-specific Phosphorylation of VEGFR2 is Mediated by Receptor Trafficking: Insights from a Computational Model. PLoS Comput Biol (2015) 11:e1004158.

P49.    L.E. Clegg and F. Mac Gabhann. Systems Biology of Vascular Remodeling and Vascular Diseases. Integrative Biology (2015) 7:498-512.

P48.    F. Mac Gabhann. Divide and conquer, faster: speeding up molecular simulations. Biophys J (2015) 108:455-6 (invited commentary).

P47.    W.L. Murfee, R.S. Sweat, K. Tsubota, F. Mac Gabhann, D. Khismatullin, S.M. Peirce. Applications of Computational Models to Better Understand Microvascular Remodeling. J Roy Soc Interface Focus (2015) 5:20140077.

P46.    AA Khan, VK Sandhya, P Singh, D Parthasarathy, A Kumar, J Advani, R Gattu, DV Ranjit, R Vaidyanathan, TSK Prasad, F Mac Gabhann, A Pandey, R Raju, H Gowda and PP Mathur. Signaling network map of endothelial TEK tyrosine kinase. J Sig Trans (2014) 2014:173026.

P45.    P. Vempati, A.S. Popel & F. Mac Gabhann. Extracellular regulation of VEGF: isoforms, proteolysis, and vascular patterning. Cytokines and Growth Factor Reviews (2014) 25:1-19.

P44.    E.A. Logsdon, S.D. Finley, A.S. Popel & F. Mac Gabhann. A systems biology view of blood vessel growth and remodeling. J Cell Mol Med (2013) 18:1491-1508.

P43.    W.-H. Tan, A.S. Popel & F. Mac Gabhann. Computational Model of VEGFR2 pathway to ERK activation and modulation through receptor trafficking. Cellular Signaling (2013) 25:2496-510.

P42.    F. Moraes, J. Paye, F. Mac Gabhann, Z.W. Zhuang, J. Zhang, A. Lanahan & M. Simons. Endothelial cell-dependent regulation of arteriogenesis. Circ Res (2013) 113:1076-86. **Cover image article  **Most viewed Circ Res article of 2013

P41.    W.-H. Tan, A.S. Popel & F. Mac Gabhann. Computational Model of Gab1/2-dependent VEGFR2 pathway to Akt activation. PLoS ONE (2013) 8:e67438.

P40.    I. Hosseini & F. Mac Gabhann. APOBEC3G-Enhanced Stem Cell Therapy to Modulate HIV Replication: a Computational Study. PLoS ONE (2013) 8:e63984.

P39.    R.J. Bender & F. Mac Gabhann. Expression of VEGF and Semaphorin genes define subgroups of triple negative breast cancer. PLoS ONE (2013) 8:e61788.

P38.    A. Guendel, J. Cutts, K. Martin, F. Mac Gabhann, T.R. Cardinal & S. M. Peirce. Surgical ligation of artery supplying spinotrapezius muscle in mice. J. Vis. Exp. (2013) 73:e50218.

P37.    G. Liu, F. Mac Gabhann & A.S. Popel. Effects of fiber type 1 and size on the heterogeneity of oxygen distribution in exercising skeletal muscle. PLoS ONE (2012) 7:e44375.

P36.    D.L. Hutton, E.A. Logsdon, E.M. Moore, F. Mac Gabhann, J.M. Gimble & W.L. Grayson. Vascular Morphogenesis of Adipose-Derived Stem Cells is Mediated by Heterotypic Cell-Cell Interactions. Tissue Eng Part A (2012) 18:1729.

P35.    S.M. Peirce, F. Mac Gabhann & V.L. Bautch. Integration of Experimental and Computational Approaches to Sprouting Angiogenesis. Curr Opin Hematol (2012) 19:184-91.

P34.    I. Hosseini and F. Mac Gabhann. Multi-Scale Modeling of HIV Infection in vitro and APOBEC3G-Based Anti-Retroviral Therapy. PLoS Comput Biol (2012) 8:e1002371.

P33.    Y. Hashambhoy, J.C. Chappell, S.M. Peirce, V.L Bautch. and F. Mac Gabhann. Computational modeling of interacting VEGF and soluble VEGF receptor concentration gradients. Front Physiol (2011) 2:62.

P32.    P. Vempati, A.S. Popel & F. Mac Gabhann. Formation of VEGF isoform-specific spatial distributions governing angiogenesis: computational analysis. BMC Syst Biol (2011) 5:59.

P31.    G. Liu, A.A. Qutub, P. Vempati, F. Mac Gabhann & A.S. Popel. Module-based multiscale simulation of angiogenesis in skeletal muscle. Theor Biol Med Model (2011) 8:6.

P30.    M.O. Stefanini, A.A. Qutub, F. Mac Gabhann & A.S. Popel. Computational models of VEGF-associated angiogenic processes in cancer. Math Med Biol (2011) 29:85-94

P29.    K.F. Benedict, F. Mac Gabhann, R.K. Amanfu, A.K. Chavali, E.P. Gianchandani, L.S. Glaw, M.A. Oberhardt, B.C. Thorne, J.H. Yang, J.A. Papin, S.M. Peirce, J.J. Saucerman & T.C. Skalak. Systems analysis of small signaling modules relevant to eight human diseases. Ann Biomed Eng (2011) 39:621-35.

P28.    L.S. Sefcik, C. Petrie Aronin, A Awojoodu, S.J. Shin, F. Mac Gabhann, T.L. MacDonald, B.R. Wamhoff, K.R. Lynch, S.M. Peirce and E. Botchwey. Selective Activation of Sphingosine 1-Phosphate Receptors 1 and 3 Promotes Local Microvascular Network Growth. Tissue Eng Part A (2011) 17:617-29.

P27.    F. Mac Gabhann, B.H. Annex & A.S. Popel. Gene therapy from the perspective of systems biology. Current Opinion in Molecular Therapeutics (2010) 12:570.

P26.    M.O. Stefanini, F.T. Wu, F. Mac Gabhann & A.S. Popel. Increase of plasma VEGF after intravenous administration of bevacizumab is predicted by a pharmacokinetic model. Cancer Res (2010) 70:9886.

P25.    F.T. Wu, M.O. Stefanini, F. Mac Gabhann, B.H. Annex & A.S. Popel. VEGF and soluble VEGF receptor-1 (sFlt-1) distributions in peripheral arterial disease: an in silico model. American Journal of Physiology: Heart and Circulatory Physiology (2010) 298:H2174-2191

P24.    P. Vempati, F. Mac Gabhann and A.S. Popel. Quantifying the proteolytic release of extracellular matrix-sequestered VEGF with a computational model. PLoS One (2010) 5:e11860.

P23.    F. Mac Gabhann and S.M. Peirce. Collateral capillary arterialization following arteriolar ligation in murine skeletal muscle. Microcirculation (2010) 17:333.

P22.    F. Mac Gabhann, A.A. Qutub, B.H. Annex and A.S. Popel. Systems biology of pro-angiogenic therapies targeting the VEGF system. (Review) Wiley Interdisciplinary Reviews: Systems Biology & Medicine (2010) 2:694-707.

P21.    M.O. Stefanini, F.T. Wu, F. Mac Gabhann and A.S. Popel. The presence of VEGF receptors on the luminal surface of endothelial cells affects VEGF distribution and VEGF signaling in humans. PLoS Comput Biol (2009) 5:e1000622.

P20.    F.T.H. Wu, M.O. Stefanini, F. Mac Gabhann, C.D. Kontos, B.H. Annex and A.S. Popel. A systems biology perspective on sVEGFR1: its biological function, pathogenic role & therapeutic use. (Review) J Cell Mol Med (2009) 14:528.

P19.    F.T.H. Wu, M.O Stefanini, F. Mac Gabhann and A.S. Popel. Modeling of growth factor-receptor systems: from molecular-level protein interaction networks to whole-body compartment models. Methods in Enzymology (2009) 467:461.

P18.    F.T.H. Wu, M.O. Stefanini, F. Mac Gabhann, C.D. Kontos, B.H. Annex and A.S. Popel. Computational kinetic model of VEGF trapping by soluble VEGF receptor-1: Effects of transendothelial and lymphatic macromolecular transport. Physiol Genomics (2009) 38:29-41. **Cover image article

P17.    F.T.H. Wu, M.O. Stefanini, F. Mac Gabhann and A.S. Popel. A Compartment Model of VEGF Distribution in Humans in the Presence of Soluble VEGF Receptor-1 Acting as a Ligand Trap. PLoS ONE (2009) 4:e5108.

P16.    A.A. Qutub, F. Mac Gabhann, E.D. Karagiannis, P. Vempati and A.S. Popel. Multiscale Models of Angiogenesis: Integration of molecular mechanisms with cell- and organ-level models. (Review) IEEE Eng Med Biol Mag (2009) 28:14-31.

P15.    M.O. Stefanini, F.T.H. Wu, F. Mac Gabhann & A.S. Popel. A compartment model of VEGF distribution in blood, healthy and diseased tissues. BMC Syst Biol (2008) 2:77.

P14.    F. Mac Gabhann and A.S. Popel. Systems Biology of Vascular Endothelial Growth Factors. (Review) Microcirculation (2008) 15:715-38.

P13.    A.M. Demetriades, T. Deering, H. Liu, L. Lu, P. Gehlbach, J.D. Packer, F. Mac Gabhann, A. S. Popel, L. L. Wei and P. A. Campochiaro. Trans-scleral Delivery of Antiangiogenic Proteins. Journal of Ocular Pharmacology and Therapeutics (2008) 24:70-79.

P12.    J.W. Ji, F. Mac Gabhann, and A.S. Popel. Skeletal muscle VEGF gradients in Peripheral Arterial Disease: Simulations of rest and exercise. Am J Physiol: Heart Circ Physiol (2007) 293:H3740-9.

P11.    C. Kut, F. Mac Gabhann and A.S. Popel. Where is VEGF in the body? A meta-analysis of VEGF distribution in cancer. Br J Cancer (2007) 97:978-85.

P10.    F. Mac Gabhann, J.W. Ji, and A.S. Popel. Multi-scale computational models of pro-angiogenic treatments in peripheral arterial disease. Ann Biomed Eng (2007) 35:982-94.

P9.       F. Mac Gabhann and A.S. Popel. Dimerization of VEGF receptors and implications for signal transduction: a computational study. Biophys Chem (2007) 128:125-39.

P8.       F. Mac Gabhann and A.S. Popel. Interactions of VEGF isoforms with VEGFR1, VEGFR2 and Neuropilin in vivo: Applications to human skeletal muscle. Am J Physiol Heart Circ Physiol (2007) 292:H459-H474.

P7.       F. Mac Gabhann, J.W. Ji and A.S. Popel. VEGF gradients, receptor activation, and sprout guidance in resting and exercising skeletal muscle. J Appl Physiol (2007) 102:722-734.

P6.       F. Mac Gabhann, A.M. Demetriades, T. Deering, J.D. Packer, S.M. Shah, E. Duh, P.A. Campochiaro and A.S. Popel. Protein transport to choroid and retina following periocular injection: Theoretical and experimental study. Ann Biomed Eng (2007) 35(4):615-30.

P5.       F. Mac Gabhann and A.S. Popel. Targeting Neuropilin-1 to inhibit VEGF signaling in cancer: comparison of therapeutic approaches. PLoS Comput Biol (2006) 2(12):e180.

P4.       F. Mac Gabhann, J.W. Ji, and A.S. Popel. Computational model of VEGF spatial distribution in muscle and application to proangiogenic cell therapy. PLoS Comput Biol (2006) 2(9):e127.

P3.       F. Mac Gabhann, M.T. Yang and A.S. Popel. Monte Carlo simulations of VEGF binding to cell surface receptors in vitro. Biochim Biophys Acta-Mol Cell Res (2005) 1746:95-107.

P2.       F. Mac Gabhann and A.S. Popel. Differential binding of VEGF isoforms to VEGF Receptor 2 in the presence of Neuropilin-1: a computational model. Am J Physiol Heart Circ Physiol (2005) 288:H2851-60.

P1.       F. Mac Gabhann and A.S. Popel. Model of competitive binding of vascular endothelial growth factor and placental growth factor to VEGF receptors on endothelial cells. Am J Physiol Heart Circ Physiol (2004) 286: H153-H164.

Conference Paper

C1.      F. Mac Gabhann, E.D. Karagiannis and A.S. Popel. Building Blocks for Computational Models of Angiogenesis. 38^th Asilomar Conference on Signals, Systems, and Computers (2004), 739-745.

Book Chapters

B2.        F. Mac Gabhann, M.O. Stefanini, A.S. Popel. Simulating therapeutics using multiscale models of the VEGF receptor system in cancer. In: Modeling Tumor Vasculature:  Molecular, Cellular, and Tissue Level Aspects and Implications, edited by Trachette Jackson (2011)

B1.       A.A. Qutub, F. Mac Gabhann, E.D. Karagiannis & A.S. Popel. In silico modeling of angiogenesis at multiple scales: From nanoscale to organ system. In: Multiscale Modeling of Particle Interactions: Applications in Biology and Nanotechnology. M.R. King and D.J. Gee, editors, Wiley, pp. 287-320. (2009)