Journal Publications

1. "Human Organ-specific Endothelial Cell Heterogeneity ", Marcu R, Choi YJ, Xue J, Fortin CL, Wang Y, Nagao R, Xu J, MacDonald J, Bammler T, Murry CE, Muczynski K, Stevens KR, Himmelfarb J, Schwartz SM, Zheng Y, iScience, 2018 , Volume 4 , 20 – 35.

2. "A 3D Human Renal Cell Carcinoma-on-a-Chip for the Study of Tumor Angiogenesis", Neoplasia, Miller C, Tsuchida C, Zheng Y*, Himmelfarb J*, Akilesh S*, 20(6), 610-620, 2018. *: corresponding authors. .

3. “Microvasculature Directed Hematopoietic Trafficking and Thrombopoiesis in a 3D in vitro Marrow Niche”, Kotha S, Sun S, Adams A, Hayes B, Nagao R, Reems J-A, Gao, D, Torok-Storb B, Lopez, JA, Zheng, Y, PLoS One, 13(4), e0195082, 2018.

4. "Engineering a multicellular vascular niche to model hematopoietic cell trafficking", Kotha S, Hayes BJ, Phong KT, Redd MA, Bomsztyk K, Ramakrishnan A, Torok-Storb B, Zheng Y, Stem Cell Research & Therapy, 9:77 2018

5. "Multicellular Vascularized Engineered Tissues through User-Programmable Biomaterial Photodegradation ", Arakawa CK, Badeau BA, Zheng Y, DeForest CA, Adv Mater, 29(37), 2017.

6. "Tissue engineering toward organ-specific regeneration and disease modeling ", Mandrycky C, Phong KT, Zheng Y, MRS Communications, 7(3), 332-347, 2017.

7. “Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis”, Palpant N, Wang Y, Hadland B, Zaunbrecher R, Redd M, Jones D, Pabon L, Jain R, Epstein J, Ruzzo WL, Zheng Y, Bernstein I, Margolin AA, Murry CE, Cell Reports, 2017

8. “Epigenetic and transcriptional analysis of mesoderm progenitor cells identifies HOPX as a novel regulator of hemogenic endothelium”, Palpant N, Wang Y, Hadland B, Zaunbrecher R, Redd M, Pabon L, Jain R, Epstein J, Zheng Y, Bernstein I, Margolin AA, Murry CE, Mechanisms of Development, 2017

9. "miR-155 Modifies Inflammation, Endothelial Activation and Blood-Brain Barrier Dysfunction in Cerebral Malaria", Barker KR, Lu Z, Kim H, Zheng Y, Chen J, Conroy AL, Hawkes M, Cheng HS, Njock MS, Fish JE, Harlan JM, López JA, Liles WC, and Kain KC, Molecular Medicine, 23: 24-33, 2017.

10. "Generating high-purity cardiac and endothelial derivatives from patterned mesoderm using human pluripotent stem cells", Palpant, N.J., Pabon, L., Friedman C.E., Roberts, M., Hadland, B., Zaunbrecker, B., Bernstein, I., Zheng, Y., Murry, C.E.,Nature Protocol, 12, 15–31, 2017.

11. "Depth-resolved 3D visualization of coronary microvasculature with optical microangiography", Qin, W., Roberts, M., Qi, X., Murry, C.E.,Zheng, Y., Wang, R., Physics in Medicine and Biology, 61(21):7536-7550, 2016.

12. "Polarization of mesoderm to generate high-purity cardiomyocytes, endocardial-like endothelium, and hemogenic endothelium from human pluripotent stem cells", Palpant, N.J., Pabon, L., Friedman C.E., Roberts, M., Hadland, B., Zaunbrecker, B., Bernstein, I., Zheng, Y., Murry, C.E., Nature Protocol, in press.

13. "Decellularized human kidney cortex hydrogels enhance kidney microvascular endothelial cell maturation and quiescence", Nagao, R.J., Xu, J., Luo, P., Xue, J., Wang, Y., Kotha, S., Zeng, W., Fu, X., Himmelfarb, J., Zheng, Y., 2016, Tissue Engineering Part A, ahead of print.

14. "Engineered microvessels for the study of human disease", Rayner, S.G., Zheng, Y., 2016, Journal of Biomechanical Engineering, in press.

15. "Micropatterning and Assembly of 3D Microvessels", Roberts M.A., Kotha S.S., Phong K.T., Zheng Y., 2016, JoVE, in press

16. "Scalable vascularized implants", Zheng, Y., Roberts, M.A., 2016, Nature Materials, 15: 597-599.

17. "Stromal cells in dense collagen promote cardiomyocyte and microvascular patterning in engineered human heart tissue", Roberts, M.A., Tran, D., Coulombe, K.L.K., Razumova, M., Regnier, M., Murry, C.E., Zheng, Y., Tissue Engineering, 2016, 22(7-8):633-44.

18. "High density lipoprotein and apolipoprotein A-I prevent von Willebrand factor self-association and fiber formation ", Chung, D.W., Chen, J., Ling, M., Fu, X., Parsons, S., Le, J., Harris, J., Martin, T.R., Konkle, B.A., Zheng, Y., Lopez, J.A., Blood 2016;127:637-45.

19. “A Novel Three–Dimensional Human Peritubular Microvascular System” Ligresti, G., Nagao, R.J., Xue, J., Choi, Y.J., Xu, J., Ren, S., Aburatani., T., Anderson, S.K., MacDonald, J.W., Bammler, T.K., Schwartz, S. W., Muczynski, K. A., Duffield, D. S., Himmelfarb, J and Zheng, Y., JASN, 2015, doi: 10.1681/ASN.2015070747.

20. "Flow Driven assembly of VWF fibers and webs in in vitro microvessels", Zheng, Y.*, Chen, J., Lopez, J.A.*, Nature Communications, 2015, 6:7858. doi: 10.1038/ncomms8858. PMID: 26223854 (* corresponding author)

21. "Inhibition of β-catenin signaling re-specifies anterior-like endothelium into beating cardiomyocytes", Palpant, N.J., Pabon, L., Roberts, M., Hadland, B., Jones, D., Jones, C., Moon, R., Ruzzo, W.L, Bernstein, I., Zheng, Y., Murry, C.E., Development, 2015, 142(18):3198-209. PMID: 26153229

22. "Mitochondrial Permeability Transition Pore Regulates Endothelial Bioenergetics and Angiogenesis", Marcu, R., Kotha, S., Zhi, Z., Qin, W., Neeley, C.K., Wang, R., Zheng, Y., Hawkins, B.J.,  Circ Res., 2015; 116(8):1336-45. PMID: 25722455

23. "Microvascular platforms for the study of platelet-vessel wall interactions.", Zheng, Y. *, Chen, J., Lopez, J.A., Thromb Res. 2014 133(4):525-31. PMID: 24438943.

24. "Restraint of the differentiation of mesenchymal stem cells by a nonfouling zwitterionic hydrogel." Bai, T., Sun, F., Zhang, L., Sinclair, A., Liu, S., Ella-Menye, J.R., Zheng, Y., Jiang, S., Angew Chem Int Ed Engl. 2014;53(47):12729-34. doi: 10.1002/anie.201405930. PubMed PMID: 25243389.

25."Formation of microvascular networks in vitro", Morgan, J, DelNero, P, Zheng, Y., Verbridge, S , Chen, J , Craven, M, Choi, NW, Diaz-Santana, A, Kermani, P, Hempstead, B, López, J, Corso, T , Fischbach C, Stroock, A, 2013, Nature Protocols, Sep;8(9):1820-36. PMID: 23989676.

26. "Synthetic microvessels", Lopez, J., Zheng, Y., Journal ofThrombosis and Haemostasis. 2013 Jun;11 Suppl 1:67-74. doi: 10.1111/jth.12245.

27. "Innovations in preclinical biology: ex vivo engineering of a human kidney tissue microperfusion system." Kelly, EJ, Wang, Z, Voellinger, JL, Yeung, CK, Shen, DD, Thummel, KE, Zheng, Y., Ligresti, G, Eaton, DL, Muczynski, KA, Duffield, JS, Neumann, T, Tourovskaia, A, Fauver, M, Kramer, G, Asp, E, Himmelfarb J.  Stem Cell Res Ther. 2013;4 Suppl 1:S17. doi: 10.1186/scrt378.

28. "Tracking Dynamic Microvascular Changes during Healing after Complete Biopsy Punch on the Mouse Pinna Using Optical Microangiography", Jung, Y., Dziennis, S., Zhi, Z., Reif, R., Zheng, Y., Wang, R, PLOS ONE. 2013, 8(2), e57976,10.1371/journal.pone.0057976.

29. “In vitro microvessels for the study of angiogenesis and thrombosis.”, Zheng,Y., Chen, J., Craven, M., Choi, N.W., Totorica, S., Diaz-Santana, A., Kermanie, P., Hempsteade, B., Fischbach-Teschl, C., Lopez, J.A., Stroock, A.D., 2012, Proceedings of the National Academy of Science, 109(24), 9342-9347.

30. “Mathematical Modeling and Frequency Gradient Analysis of Cellular and Vascular Invasion into Integra and Strattice: Toward Optimal Design of Tissue Regeneration Scaffolds”, Reiffel, A.J., Henderson, P.W., Krijgh, D.D., Belkin, D.A., Zheng, Y., Bonassar, L.J., Stroock, A.D., Spector, J.A., 2012, Plastic and Reconstructive Surgery, 129(1), 89-99.

31. “Shear stress-induced unfolding of von Willebrand factor accelerates oxidation of key methionine residues in the A1A2A3 region”, Fu X, Chen J, Gallagher R, Zheng Y, Chung DW, Lopez JA, Blood, doi: 10.1182/blood-2011-01-331074, (2011)

32.“Microstructured templates for directed growth and vascularization of soft tissue in vivo”, Zheng Y, Henderson PW, Choi NW, Bonassar LJ, Spector JA, Stroock AD, Biomaterials, 32 (23), 5391 – 401, (2011)

33.“Numerical study of flow fields in an airway closure model”, Tai CF, Bian S, Halpern D, Zheng Y, Filoche M, Grotberg JB, Journal of Fluid Mechanics 677, 483 (2011)

34.“Dense collagen matrices with microstructure and cellular remodeling for three-dimensional cell culture”, Cross V, Zheng, Y., Choi, N.W., Verbridge., S.S., Sutermaster, B.A., Bonassar, L.J., Fischbach-Teschl, C., Stroock, A.D., 31 (33), 8596 – 607, (2010)

35.“Oxygen-controlled 3-D cultures to analyze tumor angiogenesis”, Verbridge SS., Choi NW, Zheng Y, Brooks D, Stroock AD, Fischbach-Teschl C, Tissue Engineering, 16(7), 2133 – 3141, (2010)

36.“Patterning alginate hydrogels using light-directed release of caged calcium in a microfluidic device”, Chueh BH, Zheng Y, Torisawa Y, Hsiao A, Ge C, Hsiong S, Huebsch N, Franceschi R, Mooney DJ,Takayama S, Biomed Microdevices, 12, 145-151, (2010)

37.“Experimental study of flow fields in an airway closure model”, Bian S, Tai CF, Halpern D, Zheng Y, Grotberg JB,  Journal of Fluid Mechanics 647, 391 (2010)

38.“Liquid Plug Propagation through Flexible Microchannels – a Small Airway Model”, Zheng Y, Fujioka H, Bian S, Torisawa S, Huh D, Takayama S, Grotberg JB, Physics of Fluids, 21, 071903, (2009)

39.“Effects of Gravity, Inertia and Surfactant on Steady Plug Propagation in a Two-Dimensional Channel”, Zheng Y, Fujiok H, Grotberg JB, Physics of Fluids, 19(7), (2007).

40.“Effects of Gravity and Inertia on Liquid Plug Splitting at a Bifurcation”, Zheng Y, Fujioka H, Grotberg JC, Grotberg JB, Journal of Biomechanical Engineering-Transaction of ASME, 128(5), 707-716, (2006)

41.“Feasibility of Extracting Velocity Distribution in Choriocapillaris in Human Eyes from ICG Dye Angiograms”, Zhu L, Zheng Y, von Kerczek CH, Topoleski LDT, Flower RW, Journal of Biomechanical Engineering- Transaction of ASME, 128(2), 203-209, (2006)

42. “Vascular Dynamics and BOLD fMRI: CBF Level Effects and Analysis Considerations”, Vazquez, A., Cohen, E., Gulani, V., Hernandez-Garcia, L., Zheng, Y., Lee, G., Kim, S., Grotberg, J.B. and Noll, D.. 2006, NeuroImage, 32(4), pp1642-1655.

43.“Effects of Gravity on Liquid Plug transport through an airway bifurcation model ”, Zheng Y, Anderson JC, Suresh V, Grotberg JB, Journal of Biomechanical Engineering-Transaction of ASME, 127(5), 798-806, (2005)

44. “Determination of Thermal Conductivity of Biomaterials in the Temperature Range 233–313K Using a Tiny Detector Made of a Self-Heated Thermistor”, Zhang, H., Cheng, S., He, L., Zhang, A., Zheng, Y., and Gao, D., 2002,  Cell Preservation Technology, 1(2), 141-147.