Publications

2025

• Mandrycky CJ, Ishida T, Rayner SG, Heck A, Hadland B, Zheng Y, Under pressure: integrated endothelial cell response to hydrostatic and shear stresses, bioRxiv, 2024.05. 30.596749.

• Kim DA, Armenta A, Vaughan JC, Terasaki M, Himmelfarb J, Zheng Y, Hemodynamic Simulation and in vitro Modeling of Three-Dimensional Glomeruli at Anatomical Scale, Physics of Fluids, 2025; 37 (5): 051907. https://doi.org/10.1063/5.0264128. 

• Shin YJ, Safina D, Zheng Y, Levenberg S, Microvascularization in 3D Human Engineered Tissue and Organoids, Ann Rev Biomed Eng, 2025;27:473-98. doi: https://doi.org/10.1146/annurev-bioeng-103023-115236..

• Nagao R, Lopez JA, Zheng Y, Platelets and endothelial permeability (book chapter), in Book “Platelets in Thrombotic and Non-Thrombotic Disorders”, 2025. 

2024

• Mandrycky CJ, Zheng Y. Macrophages: A missing key in cardiac tissue engineering for sustained vascularization. Cell Stem Cell. 2024, 31(8), P1093-1094.

• Joof F, Hu R, Saidi A, Seydel KB, Cohee LM, Zheng Y, Smith JD. Plasma from older children in Malawi inhibits Plasmodium falciparum binding in 3D brain microvessels. J Infect Dis. 2024 Jun 14:jiae315. doi: 10.1093/infdis/jiae315. 

• Barros G, Federico E, Fillingham P, Chanana P, Kaneko N, Zheng Y, Kim LJ, Levitt MR. Endothelial Cell Transcription Modulation in Cerebral Aneurysms After Endovascular Flow Diversion. Ann Biomed Eng. 2024 doi: 10.1007/s10439-024-03591-0. 

• Juliar BA, Stanaway IB, Sano F, Fu H, Smith KD, Akilesh S, Scales SJ, El Saghir J, Bhatraju PK, Liu E, Yang J, Lin J, Eddy S, Kretzler M, Zheng Y, Himmelfarb J, Harder JL, Freedman BS. Interferon-γ induces combined pyroptotic angiopathy and APOL1 expression in human kidney disease. Cell Rep. 2024 Jun 25;43(6):114310. 

• Xie Z, Zeinstra N, Kirby MA, Le NM, Murry CE, Zheng Y, Wang RK, Quantifying Microvascular Structure in Healthy and Infarcted Rat Hearts Using Optical Coherence Tomography Angiography, IEEE Transactions on Medical Imaging, 2024, doi: 10.1109/TMI.2024.3381934.

• Xu Y, Miller CP, Xue J, Zheng Y, Warren EH, Tykodi SS, Akilesh S, Single cell atlas of kidney cancer endothelial cells reveals distinct expression profiles and phenotypes, BJC Rep 2, 23 (2024).

• Whelan R, Lih D, Xue J, Himmelfarb J, Zheng Y. Modeling Shiga Toxin-induced Human Renal-specific Microvascular Injury. Integrative Biology, 16, 2024, zyae001.

2023

• Howard C, Joof F, Hu R, Smith JD, Zheng Y. Probing cerebral malaria inflammation in 3D human brain microvessels. Cell Reports, 2023, 42(10):113253. 

• Zeinstra N, Frey AL, Xie Z, Blakely LP, Wang RK, Murry CE, Zheng Y. Stacking thick perfusable human microvascular grafts enables dense vascularity and rapid integration into infarcted rat hearts, Biomaterials, 2023, 301:122250. 

• YJ Shin, KM Evitts, S Jin, CC Howard, M Sharp-Milgrom, JE Young, Zheng Y. Amyloid beta peptides (Aβ) from Alzheimer’s disease neuronal secretome induce endothelial activation in a human cerebral microvessel model. Neurobiology of Disease, 2023, 181:106125. 

• Mandrycky C, Abel A, Levy S, Marsh L, Chasagne F, Chivukula VK, Barczay S, Kelly C, Kim Louis, Aliseda A, Levitt M, Zheng Y, Endothelial responses to curvature-induced flow patterns in engineered cerebral aneurysms. J Biomech Eng. 2023 145(1). 

2022

• Sun S, Jin L, Zheng Y, Jia Zhu Modeling human HSV infection via a vascularized immune-competent skin-on-chip platform. Nat. Comm., 2022, 13, 5481. 

• Hirsch K, Nolley S, Ralph DD, Zheng Y, Altemeier WA, Rhodes CJ, Morrell NW, Wilkins MR, Leary PJ, Rayner SR, Circulating Markers of Inflammation and Angiogenesis and Clinical Outcomes Across Subtypes of Pulmonary Arterial Hypertension, The Journal of Heart and Lung Transplantation, 2023, 42 (2), 173-182.

• Rayner SG, Scholl Z, Mandrycky CJ, Chen J, LaValley KN, Leary PJ, Altemeier WA, Liles WC, Chung DW, Lopez JA, Fu H, Zheng Y., Endothelial-derived von Willebrand Factor Accelerates Fibrin Clotting within Engineered Microvessels, J Thromb Haemost., 2022，20(7):1627-1637. 

• O’Connor C, Brady E, Zheng Y, Moore E, Steven KR, Engineering the multiscale complexity of vascular networks, Nat. Rev. Mat., 2022, 7, 702-716.

• Nagao RJ, Marcu R, Shin YJ, Lih D, Xue J, Arang N, Wei L, Akilesh S, Kaushansky A, Himmelfarb J, Zheng Y, Cyclosporine Induces Fenestra-Associated Injury in Human Renal Microvessels In Vitro. ACS Biomater. Sci. Eng. 2022, 8, 1, 196–207.

• Ortolan LS, Avril M , Xue J, Seydel KB, Zheng Y, Smith JD, Plasmodium falciparum Parasite Lines Expressing DC8 and Group A PfEMP1 Bind to Brain, Intestinal, and Kidney Endothelial Cells. Front. Cell. Infect. Microbiol., 2022, 12,  doi: 10.3389/fcimb.2022.813011

• Piatti L, Howard CC, Zheng Y, Bernabeu M, Binding of-Infected Red Blood Cells to Engineered 3D Microvessels, 2022, 468, 557-585。

2021

• Tang P, Kirby MA, Le N, Li Y, Zeinstra N, Lu GN, Murry CE, Zheng Y, Wang R, Polarization sensitive optical coherence tomography with single input for imaging depth-resolved collagen organizations. Light Sci Appl, 2021, 10, 237. doi: 10.1038/s41377-021-00679-3.

• Mandrycky CJ, Howard CC, Rayner SG, Shin YJ, Zheng Y. Organ-on-a-chip systems for vascular biology. J Mol Cell Cardiol. 2021 Jun 9;159:1-13. doi: 10.1016/j.yjmcc.2021.06.002. [Epub ahead of print] Review. PubMed PMID: 34118217; NIHMSID:NIHMS1714844. 

• Bernabeu M, Howard C, Zheng Y, Smith JD. Bioengineered 3D Microvessels for Investigating Plasmodium falciparum Pathogenesis. Trends Parasitol. 2021 May;37(5):401-413. doi: 10.1016/j.pt.2020.12.008. Epub 2021 Jan 20. Review. PubMed PMID: 33485788; PubMed Central PMCID: PMC8049949. 

• Rayner SG, Howard CC, Mandrycky CJ, Stamenkovic S, Himmelfarb J, Shih AY, Zheng Y. Multiphoton-Guided Creation of Complex Organ-Specific Microvasculature. Adv Healthc Mater. 2021 May;10(10):e2100031. doi: 10.1002/adhm.202100031. Epub 2021 Feb 15. PubMed PMID: 33586357; PubMed Central PMCID: PMC8137585. 

• Choi YJ, Heck AM , Hayes BJ , Lih D, Rayner SG, Hadland B, Zheng Y. WNT5A from the fetal liver vascular niche supports human fetal liver hematopoiesis. Stem cell research & therapy, 2021, 12 (1), 1-10

2020

• Wei W, Zhang Q, Rayner SG, Qin W, Cheng Y, Wang F, Zheng Y, Wang RK. Automated vessel diameter quantification and vessel tracing for OCT angiography. J Biophotonics. 2020 Dec;13(12):e202000248. doi: 10.1002/jbio.202000248. Epub 2020 Sep 24. PubMed PMID: 32857462; PubMed Central PMCID: PMC7857721. 

• Mandrycky C, Hadland B, Zheng Y. 3D curvature-instructed endothelial flow response and tissue vascularization. Sci Adv. 2020 Sep;6(38). doi: 10.1126/sciadv.abb3629. Print 2020 Sep. PubMed PMID: 32938662; PubMed Central PMCID: PMC7494348. 

• Mandrycky CJ, Williams NP, Batalov I, El-Nachef D, de Bakker BS, Davis J, Kim DH, DeForest CA, Zheng Y, Stevens KR, Sniadecki NJ. Engineering Heart Morphogenesis. Trends Biotechnol. 2020 Aug;38(8):835-845. doi: 10.1016/j.tibtech.2020.01.006. Epub 2020 Mar 5. Review. PubMed PMID: 32673587; PubMed Central PMCID: PMC7368094. 

• Arakawa C, Gunnarsson C, Howard C, Bernabeu M, Phong K, Yang E, DeForest CA, Smith JD, Zheng Y. Biophysical and biomolecular interactions of malaria-infected erythrocytes in engineered human capillaries. Sci Adv. 2020 Jan;6(3):eaay7243. doi: 10.1126/sciadv.aay7243. eCollection 2020 Jan. PubMed PMID: 32010773; PubMed Central PMCID: PMC6968943. 

• Figueroa B, Hu R, Rayner SG , Zheng Y , Fu D., Real-time microscale temperature imaging by stimulated raman scattering . The Journal of Physical Chemistry Letters, 2020, 11 (17), 7083-7089

• Bhatraju PK, Cohen M, Nagao R J , Morrell ED , Kosamo S, Chai X, Nance R, Dmyterko V, Delaney J, Christie JD, Liu KD, Mikacenic C,  Gharib SA, Liles WC, Zheng Y, Christiani DC, Himmelfarb J, Wurfel MM, Genetic variation implicates plasma angiopoietin-2 in the development of acute kidney injury sub-phenotypes. BMC nephrology 21 (1), 1-12

• Zhang T, Lih D, Nagao RJ , Xue J ,Berthier E , Himmelfarb J, Zheng Y, Theberge AB, Open microfluidic coculture reveals paracrine signaling from human kidney epithelial cells promotes kidney specificity of endothelial cells. American Journal of Physiology-Renal Physiology, 2020, 319 (1), F41-F51

2019

• Nagao RJ, Marcu R, Wang Y, Wang L, Arakawa C, DeForest C, Chen J, López JA, Zheng Y. Transforming Endothelium with Platelet-Rich Plasma in Engineered Microvessels. Adv Sci (Weinh). 2019 Dec;6(24):1901725. doi: 10.1002/advs.201901725. eCollection 2019 Dec. PubMed PMID: 31871858; PubMed Central PMCID: PMC6918119. 

• Bernabeu M, Gunnarsson C, Vishnyakova M, Howard CC, Nagao RJ, Avril M, Taylor TE, Seydel KB, Zheng Y, Smith JD. Binding Heterogeneity of Plasmodium falciparum to Engineered 3D Brain Microvessels Is Mediated by EPCR and ICAM-1. mBio. 2019 May 28;10(3). doi: 10.1128/mBio.00420-19. PubMed PMID: 31138740; PubMed Central PMCID: PMC6538777. 

• Redd MA, Zeinstra N, Qin W, Wei W, Martinson A, Wang Y, Wang RK, Murry CE, Zheng Y. Patterned human microvascular grafts enable rapid vascularization and increase perfusion in infarcted rat hearts. Nat Commun. 2019 Feb 4;10(1):584. doi: 10.1038/s41467-019-08388-7. PubMed PMID: 30718840; PubMed Central PMCID: PMC6362250. 

2018

• Rayner SG, Phong KT, Xue J, Lih D, Shankland SJ, Kelly EJ, Himmelfarb J, Zheng Y. Reconstructing the Human Renal Vascular-Tubular Unit In Vitro. Adv Healthc Mater. 2018 Dec;7(23):e1801120. doi: 10.1002/adhm.201801120. Epub 2018 Oct 31. PubMed PMID: 30379416; PubMed Central PMCID: PMC6478624. 

• "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.

• "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. .

• “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.

• "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.

2017

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

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

• “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

• “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

• "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.

• "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.

2016

• "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.

• "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.

• "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.

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

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

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

• "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.

• "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.

2015

• “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.

• "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)

• "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

• "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

2014

• "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.

• "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.

2013

• "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.

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

• "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.

• "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.

2012

• “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.

• “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.

2011

• “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)

• “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)

• “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)

2010

• “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)

• “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)

• “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)

• “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)

2009 and before: Please check the Bibligraphy