Human Models for Analysis of Pathways (HMAPs) Center
Roy S and Sridharan R. (2017) “Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes”. Genome Research. In press.
Chasman D., Roy S (2017). Inference of cell type specific regulatory networks on mammalian lineages. Current Opinion in Systems Biology. In Press.
Marti-Figueroa CR., Ashton RS (2017). The case for applying tissue engineering methodologies to instruct human organoid morphogenesis. Acta Biomaterialia.In Press.
D.G. Belair, N.N. Le, W.L. Murphy. (2016) Regulating VEGF signaling in platelet concentrates via specific VEGF sequestering. Biomaterials Science, 2016, 4, 819-825
Morgan M. M., Johnson B. P., Livingston M. K., Schuler L. A., Alarid E. T., Sung K. E., & Beebe, D. J. (2016). Personalized in vitro cancer models to predict therapeutic response: challenges and a framework for improvement. Pharmacology & Therapeutics, 165, 79-92
M.R. Zanotelli, H. Ardalani, J. Zhang, Z. Hou, E.H. Nguyen, S. Swanson, B.K. Nguyen, J. Bolin, L. Bischel, A.W. Xie, R. Stewart, D.J. Beebe, J.A. Thomson, M.P. Schwartz, W.L. Murphy. Stable engineered vascular networks from human induced pluripotent stem cell-derived endothelial cells cultured in synthetic hydrogels. Acta Biomaterialia, 2016, 35, 32-41
D.G. Belair, M.P. Schwartz, T. Knudsen, W.L. Murphy. Human iPSC-derived endothelial cell sprouting assay in synthetic hydrogel arrays. Acta Biomaterialia. 2016, In Press
D. Chasman, K.B. Walters, T.J.S. Lopes, D. Pozorski, A.J. Eisfeld, Y. Kawaoka, S. Roy. Integrating transcriptomic and proteomic data with predictive regulatory network models of host response to pathogens. PLOS Computational Biology, 2016, 12(7): e1005013. doi:10.1371/journal.pcbi.1005013
D. Chasman, A. Fotuhi Siahpirani, S. Roy. Network-based approaches for analysis of complex biological systems. Current Opinion in Biotechnology, 2016, 39, 157-166
S. Roy., S. Sridharan. CMINT: Chromatin Module inference on cellular trajectories identifies poised epigenetic states in reprogramming to induced pluripotent stem cells. Submitted.
D.G. Belair, M.J. Miller, S. Wang, N. Sheibani, W.L. Murphy. Differential regulation of angiogenesis using degradable VEGF-binding microspheres. Biomaterials, 2016, 93, 27-37
E.S. Lippmann, M.C. Estevez-Silva, R.S. Ashton (2015). Chemically defined differentiation of human pluripotent stem cells to hindbrain and spinal cord neural stem cells with defined regional identities. Protocol Exchange.
Knight GT, Sha J, Ashton RS (2015). Micropatterned, clickable culture substrates enable in situ spatiotemporal control of human PSC-derived neural tissue morphology. Chemical Communications 2015;51:5238-5241.
A.W. Xie, B.Y.K. Binder, S.K. Schmitt, A.S. Khalil, W.L. Murphy. Controlled self-assembly of stem cell aggregates on chemically defined substrates. Submitted.
J.D. McNulty, C. Marti-Figueroa, T. Ellingham, L.J.L. Huddleston, S. Goris, B.L. Cox, T.A. Osswald, L. Turng, R. Ashton. Free-form controlled fabrication of 3-D neural organoids. Submitted.
E.S. Lippmann, N. Sehgal, M.C. Estevez-Silva, M.A. Bakooshli, G.T. Knight, K. Lemke, J. Plantz, P.M. Gilbert, and R.S. Ashton. Wnt/β-catenin induction of Nkx6.1 enables high yield derivation of spinal motor neurons of diverse regional identities from human pluripotent stem cells. Submitted.
S.K. Schmitt, J. Krutty, P. Gopalan, W.L. Murphy. Modification of polymer substrates for defined stem cell culture. Submitted.
E.H. Nguyen, W.L. Murphy. Biomaterials for modeling complex effects of anti-angiogenesis treatments in vitro. Submitted.
M. Farnoodian, C. Schrieber, C. Slinger, B. Pattnaik, C.M. Sorenson, N. Sheibani. High glucose promotes the migration of retinal pigment epithelial cells through increased oxidative stress and PEDF expression. Submitted.
S. Park, J. Falero-Preze, C.M. Sorenson, N. Sheibani. PEDF Expression Modulates Retinal Endothelial Cell Pro-Angiogenic Properties through Alterations in Cell Adhesive Mechanisms. In Preparation.
M.M. Morgan, B.P. Johnson, K.E. Sung, L. Schuler,/E. Alarid, D.J. Beebe. Personalized in vitro models of cancer to predict therapeutic response: utilizing therapeutic outcome pathways to guide model development. In Preparation.
M.K. Livingston, M.M. Morgan, B.P. Johnson, K.E. Sung, L.A. Schuler, D.J. Beebe. Influence of extracellular matrix proteins on the behavior, viability and structure of normal breast ductal structures. In Preparation.
M.M. Morgan, M.K. Livingston, B.P. Johnson, K.E. Sung, L.A. Schuler, D.J. Beebe. Modeling the adverse outcome pathway of estrogen receptor driven breast cancer progression in an organotypic system. In Preparation.
N. Sehgal, E.S. Lippmann, B. Macintosh, P. Jiang, D. Chasman, S. Roy, R.S. Stewart, J.A. Thomson, and R.S. Ashton. Time-course RNA-seq analysis of human hindbrain development using hPSC-derived tissue models. In Preparation.
E.H. Nguyen, W.L. Murphy. Endothelial cell responses to TGF-β signaling in 2D and 3D cell culture environments with defined mechanical properties. In Preparation.
E.H. Nguyen, W.T. Daly, N. Sheibani, W.L. Murphy. A synthetic alternative to Matrigel for endothelial tubulogenesis screening. In Preparation.