1. Karagiannis E.D., and Popel A.S., A theoretical model of type I collagen proteolysis by matrix metalloproteinase (MMP) 2 and membrane type 1 MMP in the presence of tissue inhibitor of metalloproteinase 2. Journal of Biological Chemistry 279 (2004) 39105-14. [pdf]
2. Mac Gabhann F., Karagiannis E.D., and Popel A.S., Building blocks for computational models of angiogenesis. IEEE Volume on Signals, Systems and Computers (November 2004) 739-745. [pdf]
3. Karagiannis E.D., and Popel A.S., Distinct modes of collagen type I proteolysis by matrix metalloproteinase (MMP) 2 and membrane type I MMP during the migration of a tip endothelial cell: insights from a computational model. Journal of Theoretical Biology 238 (2006) 124-45. [pdf]
4. Karagiannis E.D., and Popel A.S., Peptides derived from type I thrombospondin repeat- containing proteins of the CCN family inhibit proliferation and migration of endothelial cells. International Journal of Biochemistry and Cell Biology 39 (2007) 2314-23. [pdf]
5. Karagiannis E.D., and Popel A.S., Anti-angiogenic peptides identified in thrombospondin type I domains. Biochemical and Biophysical Research Communications 359 (2007) 63-9. [pdf]
6. Karagiannis E.D., and Popel A.S., Identification of novel short peptides derived from the alpha 4, alpha 5, and alpha 6 fibrils of type IV collagen with anti-angiogenic properties. Biochemical and Biophysical Research Communications 354 (2007) 434-439. [pdf]
7. Vempati P., Karagiannis E.D., and Popel A.S., A biochemical model of the matrix metalloproteinase 9 activation and inhibition. Journal of Biological Chemistry 282 (2007) 37585-37596. [pdf]
8. Qutub A.A., Mac Gabhann F., Karagiannis E.D., Vempati P., and Popel A.S., Multiscale molecular-based models of angiogenesis. IEEE Engineering in Medicine and Biology Magazine (Special Issue on Multiscale Modeling) (2007) 14-31. [pdf]
9. Karagiannis E.D., and Popel A.S., Novel anti-angiogenic peptides derived from ELR-containing CXC chemokines. Journal of Cellular Biochemistry 104 (2008) 1356-1363. [pdf]
10. Karagiannis E.D., and Popel A.S., A systematic methodology for proteome-wide identification of peptides inhibiting the proliferation and migration of endothelial cells. Proceedings of the National Academy of Sciences USA 105 (2008) 13775-13780. [pdf]
11. Cano M.*, Karagiannis E.D.*, Zhuang W., Popel A.S., and Gehlbach P.L., A Peptide Derived from Type 1 Thrombospondin Repeat-containing Protein WISP-1 Inhibits Corneal and Choroidal Neovascularization. Investigative Ophthalmology and Visual Science 50 (2009) 3840-3845 (*Equal Contribution). [pdf]
12. Koskimaki J.E. *, Karagiannis E.D. *, Rosca E.V., Vesuna F., Winnard P.T., Jr., Raman V., Bhujwalla Z.M., Popel A.S., Peptides derived from type IV collagen, CXC chemokines, and thrombospondin-1 domain-containing proteins inhibit neovascularization and suppress tumor growth in MDA-MB-231 breast cancer xenografts, Neoplasia 11 (2009) 1285-1291 (*Equal Contribution). [pdf]
14. Koskimaki J.E., Karagiannis E.D., Tang B.C., Hammers H., Watkins D.N., Pili R., Popel A.S., Pentastatin-1, a collagen IV derived 20-mer peptide, suppresses tumor growth in a small cell lung cancer xenograft model, BMC Cancer (2010), 10-29. [pdf]
15. Zoldan J., Lytton-Jean A.K.R.*, Karagiannis E.D.*, Deiorio-Haggar K., Bellan L.M., Langer R., Anderson D.G., Directing human embryonic stem cell differentiation by non-viral delivery of siRNA In 3D culture, Biomaterials (2011), 7793-7800 (*Equal Contribution). [pdf]
16. Zoldan J., Karagiannis E.D., Lee C.Y., Anderson D.G., Langer R., Levenberg S., The influence of scaffold elasticity on germ layer specification of human embryonic stem cells, Biomaterials, (2011), 9612-9621. [pdf]
17. Urbanska A.M., Karagiannis E.D., Guajardo G., Langer R., Anderson D.G., Therapeutic effect of orally administered microencapsulated oxaliplatin for colorectal cancer, Biomaterials, (2012), 4752-4761. [pdf]
18. Lee H., Lytton-Jean A.K., Chen Y., Love K.T., Park A.I., Karagiannis E.D., Sehgal A., Querbes W., Zurenko C.S., Jayaraman M., Peng C.G., Charisse K., Borodovsky A., Manoharan M., Donahoe J.S., Truelove J., Nahrendorf M., Langer R., Anderson D.G., Molecularly self-assembled nucleic acid nanoparticles for targeted in vivo siRNA delivery, Nature Nanotechnology, (2012), 389-393. [pdf]
19. Karagiannis E.D., Alabi C.A., Anderson D.G., Rationally designed tumor-penetrating nanocomplexes, ACS Nano, (2012), 8484-8487. [pdf]
20. Sahay G., Querbes W., Alabi C., Eltoukhy A., Sarkar S., Zurenko C., Karagiannis E.D., Love K., Chen D., Zoncu R., Buganim Y., Schroeder A., Langer R., Anderson D.G.., Efficiency of siRNA delivery by lipid nanoparticles is limited by endocytic recycling., Nature Biotechnology, (2013), 31(7):653-658. [pdf]
21. Karagiannis E.D., Urbanska A.M., Sahay G., Pelet J.M., Jhunjhunwala S., Langer R., Anderson D.G., Rational Design of a Biomimetic Cell Penetrating Peptide Library for siRNA Delivery, ACS Nano, (2013), 7(10):8616-8626. [pdf]
22. Urbanska A.M., Karagiannis E.D., Au A.S., Dai S.Y., Mozafari M., Prakash S., What's Next for Gastrointestinal Disorders: No Needles?, Journal of Controlled Release, (2016), 221:48-61. [pdf]
23. Karagiannis E.D., Boyden E.S., Expansion Microscopy: Development and Neuroscience Applications, Current Opinion in Neurobiology, (2017), Accepted.
24. Karagiannis E.D., Kang J.S., Marblestone A., Boyden E.S., Optical Mapping of Neuronal Morphologies with Electron Microscopy Resolution, (2017) In Preparation.
Book Chapters 1. Qutub A.A., Mac Gabhann F., Karagiannis E.D. and Popel A.S., In Silico Modeling of Angiogenesis at Multiple Scales: From Nanoscale to Organ Systems, at Multiscale Modeling of Particle Interactions: Applications in Biology and Nanotechnology Chapter 10, 287-320,Wiley
Abstracts from Conference Proceedings 1. "A theoretical model of a collagen I matrix degradation by a moving cell expressing MMP2 and MT1-MMP." E.D. Karagiannis, and A.S. Popel. Experimental Biology/FASEB Conference, April 2004, Washington, DC, USA.
2. "Theoretical model of ECM proteolysis by a leading cell during sprouting angiogenesis." E.D. Karagiannis, and A.S. Popel. The Biomedical Engineering Society Meeting, October 2004, Philadelphia, PA, USA.
3. "Building blocks for computational models of angiogenesis." F. Mac Gabhann, E.D. Karagiannis, and A.S. Popel. Asilomar Conference on Signals, Systems and Computers, November 2004, Pacific Grove, CA, USA.
4. "The migrating endothelial tip cell regulates distinct protease activities during sprouting angiogenesis: Insights from a theoretical model." A.S. Popel and E.D. Karagiannis. 23rd Conference of the European Society for Microcirculation, September 2004, Lisbon, Portugal.
5. "Computational Modeling of Matrix Metalloproteinases in Angiogenesis." E.D. Karagiannis, and A.S. Popel. The Matrix Metalloproteinases Gordon Research Conference, August 2005 Big Sky, MT, USA.
6. "Dynamics Of Angiogenic Sprouting In Ischemia: Integrating Molecular, Cellular, And Tissue Responses." A.A. Qutub, J. Ji, F. Mac Gabhann, E.D. Karagiannis, M.O. Stefanini, and A.S. Popel. The Biomedical Engineering Society Meeting, October 2006, Chicago, IL, USA.
7. "Bioinformatic and experimental approaches for the identification of novel endogenous antiangiogenic peptides." E.D. Karagiannis, J. Koskimaki and A.S. Popel. Johns Hopkins Vascular Medicine Research Initiative, Inaugural Conference, September 2007, Baltimore, MD, USA.
8. "A Systematic Approach for the Identification of Novel Endogenous Antiangiogenic Peptides", E.D. Karagiannis, and A.S. Popel. The Biomedical Engineering Society Meeting, October 2007, Los Angeles, CA, USA.
9. "Towards a systematic design of novel endogenous peptide-based antiangiogenic approaches", E.D. Karagiannis, and A.S. Popel. Experimental Biology/FASEB Conference, April 2008, San Diego, CA, USA.
10. “Systematic methodologies for rational identification of peptide ligands for the delivery of small interfering RNAs”, E.D. Karagiannis, D.G. Anderson and R. Langer, The Biomedical Engineering Society Meeting, October 2011, Hartford, CT, USA.
11. “Rational Development of Cell Penetrating Peptides for siRNA Delivery”, E.D. Karagiannis, D.G. Anderson and R. Langer, Bioinspired Materials Gordon Research Conference, July 2012, Davidson College, Davidson, NC, USA.
12. “Rational Approaches to Direct human Embryonic Stem Cell Differentiation”, E.D. Karagiannis, D.G. Anderson and R. Langer, Qbio-2012 Conference on Quantitative Biology, Los Alamos Center for Nonlinear Studies, Santa Fe, NM, USA.
13. “Rational Development of a Bioinspired Cell Penetrating Peptide Library for siRNA Delivery”, E.D. Karagiannis, D.G. Anderson and R. Langer, Nano2012 International Conference on Nanostructured Materials, Rhodes, Greece.
14. "Lipidoid nanoparticle-containing alginate microparticles for small molecule oral delivery in colorectal cancer", A.M. Urbanska, E.D. Karagiannis, R. Langer and D.G. Anderson, The Biomedical Engineering Society Meeting, October 2012, Atlanta, GA, USA.
15. "Systems Biology Approaches to Direct human Embryonic Stem Cell Differentiation Using siRNAs", E.D. Karagiannis, J. Zoldan, R. Langer and D.G. Anderson, The Biomedical Engineering Society Meeting, October 2012, Atlanta, GA, USA.
16. "Rational Development of Cell Penetrating Peptides for in vivo siRNA Delivery", E.D. Karagiannis, A.M. Urbanska, R. Langer and D.G. Anderson, The Biomedical Engineering Society Meeting, October 2012, Atlanta, GA, USA
Patents (Approved) 1. "Compositions Having Antiangiogenic Activity and Uses Thereof", Popel A.S. and Karagiannis E.D. International Patent, No. WO2007033215. 2. "Peptide Modulators of Angiogenesis and Uses Thereof", Popel A.S. and Karagiannis E.D. US Patent No. US2011028395.
