1. Gao P, Rivera M, Lin X, Holmes TC, Zhao H, Xu X. Immunolabeling-compatible PEGASOS tissue clearing for high-resolution whole mouse brain imaging. Front Neural Circuits. 2024 Apr 17;18:1345692.

2. Prince MNH, Garcia B, Henn C, Yi Y, Susaki EA, Watakabe Y, Nemoto T, Lidke KA, Zhao H, Remiro IS, Liu S, Chakraborty T. Signal Improved ultra-Fast Light-sheet Microscope (SIFT) for large tissue imaging.Res Sq [Preprint]. 2023 Jun 28:rs.3.rs-2990328.

3. Yi Y, Li Y, Zhang S, Men Y, Wang Y, Jing D, Ding J, Zhu Q, Chen Z, Chen X, Li JL, Wang Y, Wang J, Peng H, Zhang L, Luo W, Feng JQ, He Y, Ge WP, Zhao H. Mapping of individual sensory nerve axons from digits to spinal cord with the transparent embedding solvent system.Cell Res. 2024 Feb;34(2):124-139.   Download

4. Zhang H, Zhu L, Zhao H, Li Z. Plant Accessible Tissue Clearing Solvent System (PATCSOS) for 3-D Imaging of Whole Plants. bioRxiv, 2024: 2024.04. 20.590386.    Download

5. Lin S, Li M, Zhou Y, Chen L, Wang Y, Zhuang Z, Zhao H, Yang R. Annexin A3 accelerates osteoclast differentiation by promoting the level of RANK and TRAF6. Bone. 2023 Jul;172:116758.   Download

6. Prince MNH, Garcia B, Henn C, Yi Y, Susaki EA, Watakabe Y, Nemoto T, Lidke KA, Zhao H, Remiro IS, Liu S, Chakraborty T. Signal Improved ultra-Fast Light-sheet Microscope (SIFT) for large tissue imaging. Res Sq [Preprint]. 2023 Jun 28:rs.3.rs-2990328.

7. Dibaji H, Prince MNH, Yi Y, Zhao H, Chakraborty T. Axial scanning of dual focus to improve light sheet microscopy. Biomed Opt Express. 2022 Aug 30;13(9):4990-5003.

8. Yi Y, Liu Y, Men Y, Wang J, Zhao H. Advances in periodontal stem cells and the regulating niche: From in vitro to in vivo. Genesis. 2022 Sep;60(8-9):e23494. Download

9. Stenberg W, Yi Y, Zhao H. Zirconia vs Titanium Dental Implants Demonstrate Superior Early Healing in Mice Assessed with PEGASOS Tissue Clearing and Two-Photon Microscopy. Microscopy and Microanalysis, 2022, 28(S1): 1428-1429.

10. Li X, Yang S, Yuan G, Jing D, Qin L, Zhao H, Yang S. Type II collagen-positive progenitors are important stem cells in controlling skeletal development and vascular formation.Bone Res. 2022 Jun 23;10(1):46.

11. Glaser AK, Bishop KW, Barner LA, Susaki EA, Kubota SI, Gao G, Serafin RB, Balaram P, Turschak E, Nicovich PR, Lai H, Lucas LAG, Yi Y, Nichols EK, Huang H, Reder NP, Wilson JJ, Sivakumar R, Shamskhou E, Stoltzfus CR, Wei X, Hempton AK, Pende M, Murawala P, Dodt HU, Imaizumi T, Shendure J, Beliveau BJ, Gerner MY, Xin L, Zhao H, True LD, Reid RC, Chandrashekar J, Ueda HR, Svoboda K, Liu JTC. A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues. Nat Methods. 2022 May;19(5):613-619.

12. Yi Y, Stenberg W, Luo W, Feng JQ, Zhao H. Alveolar Bone Marrow Gli1+ Stem Cells Support Implant Osseointegration. J Dent Res. 2022 Jan;101(1):73-82.   Download

13. Xie X, Xu C, Zhao H, Wang J, Feng JQ. A Biphasic Feature of Gli1+-Mesenchymal Progenitors during Cementogenesis That Is Positively Controlled by Wnt/β-Catenin Signaling. J Dent Res. 2021 Oct;100(11):1289-1298.

14. Xu C, Xie X, Zhao H, Wu Y, Wang J, Feng JQ. TGF-Beta Receptor II Is Critical for Osteogenic Progenitor Cell Proliferation and Differentiation During Postnatal Alveolar Bone Formation. Front Physiol. 2021 Sep 24;12:721775.

15. Jing D, Li C, Yao K, Xie X, Wang P, Zhao H, Feng JQ, Zhao Z, Wu Y, Wang J. The vital role of Gli1+ mesenchymal stem cells in tissue development and homeostasis. J Cell Physiol. 2021 Sep;236(9):6077-6089.

16. Shen B, Tasdogan A, Ubellacker JM, Zhang J, Nosyreva ED, Du L, Murphy MM, Hu S, Yi Y, Kara N, Liu X, Guela S, Jia Y, Ramesh V, Embree C, Mitchell EC, Zhao YC, Ju LA, Hu Z, Crane GM, Zhao Z, Syeda R, Morrison SJ. A mechanosensitive peri-arteriolar niche for osteogenesis and lymphopoiesis. Nature. 2021 Mar;591(7850):438-444.

17. Wang L, Yang H, Huang J, Pei S, Wang L, Feng JQ, Jing D, Zhao H, Kronenberg HM, Moore DC, Yang W. Targeted Ptpn11 deletion in mice reveals the essential role of SHP2 in osteoblast differentiation and skeletal homeostasis. Bone Res. 2021 Jan 27;9(1):6.

18. Jing J, Feng J, Li J, Zhao H, Ho TV, He J, Yuan Y, Guo T, Du J, Urata M, Sharpe P, Chai Y. Reciprocal interaction between mesenchymal stem cells and transit amplifying cells regulates tissue homeostasis. Elife. 2021 Jan 22;10:e59459.

19. Wang L, Moore DC, Huang J, Wang Y, Zhao H, D-H Yue J, Jackson CL, Quesenberry PJ, Cao W, Yang W. SHP2 regulates the development of intestinal epithelium by modifying OSTERIX+ crypt stem cell self-renewal and proliferation. FASEB J. 2021 Jan;35(1):e21106.

20. Jing D, Men Y, Zhao H. Tissue Clearing and 3-D Visualization of Vasculature with the PEGASOS Method. Methods Mol Biol. 2021;2319:1-13.   Download

21. Wang K, Ren Y, Lin S, Jing Y, Ma C, Wang J, Yuan XB, Han X, Zhao H, Wang Z, Zheng M, Xiao Y, Chen L, Olsen BR, Feng JQ. Osteocytes but not osteoblasts directly build mineralized bone structures. Int J Biol Sci. 2021 Jun 11;17(10):2430-2448.

22. Jing D, Chen Z, Men Y, Yi Y, Wang Y, Wang J, Yi J, Wan L, Shen B, Feng JQ, Zhao Z, Zhao H, Li C. Response of Gli1+ Suture Stem Cells to Mechanical Force Upon Suture Expansion.J Bone Miner Res. 2022 Jul;37(7):1307-1320.   Download

23. Gao X, Li JL, Chen X, Ci B, Chen F, Lu NN, Shen B, Zheng L, Jia JM, Yi Y, Zhang S, Shi Y, Shi K, Propson NE, Huang Y, Poinsatte K, Zhang Z , Yue Y, Bosco DB, Lu YM, Yang SB, Adams RH, Lindner V, Huang F, Wu LJ, Zheng H, Han F, Hippenmeyer S, Stowe AM, Peng B, Margeta M, Wang X, Liu Q, Körbelin J, Trepel M, Lu H, Zhou BO, Zhao H, Su W, Bachoo RM, Ge WP. Reduction of neuronal activity mediated by blood-vessel regression in the brain. bioRxiv, 2020: 2020.09. 15.262782.

24. Men Y, Wang Y, Yi Y, Jing D, Luo W, Shen B, Stenberg W, Chai Y, Ge WP, Feng JQ, Zhao H. Gli1+ Periodontium Stem Cells Are Regulated by Osteocytes and Occlusal Force. Dev Cell. 2020 Sep 14;54(5):639-654.e6.   Download

25. Li X, Yang S, Jing D, Qin L, Zhao H, Yang S. Type II collagen-positive progenitors are major stem cells to control skeleton development and vascular formation. bioRxiv, 2020: 2020.09. 06.284588.

26. Song A, Dai W, Jang MJ, Medrano L, Li Z, Zhao H, Shao M, Tan J, Li A, Ning T, Miller MM, Armstrong B, Huss JM, Zhu Y, Liu Y, Gradinaru V, Wu X, Jiang L, Scherer PE, Wang QA. Low- and high-thermogenic brown adipocyte subpopulations coexist in murine adipose tissue. J Clin Invest. 2020 Jan 2;130(1):247-257.   Download

27. Li S, Sun Y, Tian T, Qin X, Lin S, Zhang T, Zhang Q, Zhou M, Zhang X, Zhou Y, Zhao H, Zhu B, Cai X. MicroRNA-214-3p modified tetrahedral framework nucleic acids target survivin to induce tumour cell apoptosis. Cell Prolif. 2020 Jan;53(1):e12708.

28. Wang K, Wang J, Jing Y, Xie X, Liu X, Zhao H, Feng JQ, Ren Y, Ma C, Kim H. From Osteon Formation/Remodeling of Dog Bones to Loss of Cortical Bone in Human Bones. JOURNAL OF BONE AND MINERAL RESEARCH. 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY, 2019, 34: 239-240.

29. Jing, D. and Zhao, H. Tissue clearing of both hard and soft tissue organs with the PEGASOS method. JOURNAL OF BONE AND MINERAL RESEARCH. 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY, 2019, 34: 132-132.

30. Men, Y. and Zhao, H. Physiological occlusal force regulates periodontium mesenchymal stem cells activation by modulating Wnt inhibitor level within the niche. JOURNAL OF BONE AND MINERAL RESEARCH. 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY, 2019, 34: 225-225.

31. Chakraborty T, Driscoll MK, Jeffery E, Murphy MM, Roudot P, Chang BJ, Vora S, Wong WM, Nielson CD, Zhang H, Zhemkov V, Hiremath C, De La Cruz ED, Yi Y, Bezprozvanny I, Zhao H, Tomer R, Heintzmann R, Meeks JP, Marciano DK, Morrison SJ, Danuser G, Dean KM, Fiolka R. Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution. Nat Methods. 2019 Nov;16(11):1109-1113.

32. Xie X, Wang J, Wang K, Li C, Zhang S, Jing D, Xu C, Wang X, Zhao H, Feng JQ. Axin2+-Mesenchymal PDL Cells, Instead of K14+ Epithelial Cells, Play a Key Role in Rapid Cementum Growth. J Dent Res. 2019 Oct;98(11):1262-1270.

33. Luo W, Yi Y, Jing D, Zhang S, Men Y, Ge WP, Zhao H. Investigation of Postnatal Craniofacial Bone Development with Tissue Clearing-Based Three-Dimensional Imaging. Stem Cells Dev. 2019 Oct 1;28(19):1310-1321. doi: 10.1089/scd.2019.0104. Epub 2019 Sep 9. PMID: 31392933; PMCID: PMC6767869.  Download

34. Jing D, Yi Y, Luo W, Zhang S, Yuan Q, Wang J, Lachika E, Zhao Z, Zhao H. Tissue Clearing and Its Application to Bone and Dental Tissues. J Dent Res. 2019 Jun;98(6):621-631.   Download

35. Jing D, Zhang S, Luo W, Gao X, Men Y, Ma C, Liu X, Yi Y, Bugde A, Zhou BO, Zhao Z, Yuan Q, Feng JQ, Gao L, Ge WP, Zhao H. Author Correction: Tissue clearing of both hard and soft tissue organs with the PEGASOS method. Cell Res. 2019 Jun;29(6):506.  Download

36. Liu T, Wang J, Xie X, Wang K, Sui T, Liu D, Lai L, Zhao H, Li Z, Feng JQ. DMP1 Ablation in the Rabbit Results in Mineralization Defects and Abnormalities in Haversian Canal/Osteon Microarchitecture.J Bone Miner Res. 2019 Jun;34(6):1115-1128. doi: 10.1002/jbmr.3683. Epub 2019 Mar 3. PMID: 30827034.

37. Yi Y, Men Y, Jing D, Luo W, Zhang S, Feng JQ, Liu J, Ge WP, Wang J, Zhao H. 3-dimensional visualization of implant-tissue interface with the polyethylene glycol associated solvent system tissue clearing method. Cell Prolif. 2019 May;52(3):e12578.  Download

38. Chakraborty T, Dean KM, Zhao H, Fiolka R. A multimodal light-sheet microscope that is compatible with all clearing techniques. Novel Techniques in Microscopy. Optica Publishing Group, 2019: NW5C. 6.

39. Chakraborty T, Driscoll M, Murphy M, Roudot P, Chang BJ, Vora S, Wen Mai Wong, Nielson C, Zhang H, Zhemkov V, Hiremath C, De La Cruz ED, Bezprozvanny I, Zhao H, Tomer R, Heintzmann R, Meeks J, Marciano D, Morrison S, Danuser G, Dean KM, Fiolka R. Light-sheet microscopy with isotropic, sub-micron resolution and solvent-independent large-scale imaging. BioRxiv, 2019: 605493.

40. Jiang Y, Zhang S, Mao C, Lai Y, Wu D, Zhao H, Liao C, Chen W. Defining a critical period in calvarial development for Hedgehog pathway antagonist-induced frontal bone dysplasia in mice. Int J Oral Sci. 2019 Feb 20;11(1):3.

41. Ma C, Liu C, Zhang L, Zhao H, Liu X, Jing Y, Feng JQ. Autograft ligament-tendon tissues formed a “new knee" in the damaged knee surface. JOURNAL OF BONE AND MINERAL RESEARCH. 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY, 2018, 33: 243-244.

42. Jing D, Zhang S, Luo W, Gao X, Men Y, Ma C, Liu X, Yi Y, Bugde A, Zhou BO, Zhao Z, Yuan Q, Feng JQ, Gao L, Ge WP, Zhao H. Tissue clearing of both hard and soft tissue organs with the PEGASOS method. Cell Res. 2018 Aug;28(8):803-818.   Download

43. Jing Y, Li C, Zhao H, Feng J. Critical Roles of Rostral-Process-Meckel's-Cartilage in Mandibular Formation and Repairing. The FASEB Journal, 2018, 32: 776.8-776.8.

44. Li C, Jing Y, Wang K, Ren Y, Liu X, Wang X, Wang Z, Zhao H, Feng JQ. Dentinal mineralization is not limited in the mineralization front but occurs along with the entire odontoblast process. Int J Biol Sci. 2018 Apr 30;14(7):693-704.

45. Zhang S, Luo W, Jing D, Men Y, Yuan Q, Zhao Z, Zhao H. The PEG Associated Solvent System (PEGASOS) Method Enables 3-Dimentional Visualization of Hard Tissue. JOURNAL OF BONE AND MINERAL RESEARCH. 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY, 2017, 32: S310-S311.

46. Feng J, Jing J, Li J, Zhao H, Punj V, Zhang T, Xu J, Chai Y. BMP signaling orchestrates a transcriptional network to control the fate of mesenchymal stem cells in mice. Development. 2017 Jul 15;144(14):2560-2569.

47. Park S, Zhao H, Urata M, Chai Y. Sutures Possess Strong Regenerative Capacity for Calvarial Bone Injury. Stem Cells Dev. 2016 Dec 1;25(23):1801-1807.

48. Liu W, Zhou L, Zhou C, Zhang S, Jing J, Xie L, Sun N, Duan X, Jing W, Liang X, Zhao H, Ye L, Chen Q, Yuan Q. GDF11 decreases bone mass by stimulating osteoclastogenesis and inhibiting osteoblast differentiation. Nat Commun. 2016 Sep 22;7:12794.

49. Zhao H, Chai Y. Stem Cells in Teeth and Craniofacial Bones. J Dent Res. 2015 Nov;94(11):1495-501.   Download

50. Liu Y, Feng J, Li J, Zhao H, Ho TV, Chai Y. An Nfic-hedgehog signaling cascade regulates tooth root development. Development. 2015 Oct 1;142(19):3374-82.

51. Zhao H, Feng J, Ho TV, Grimes W, Urata M, Chai Y. The suture provides a niche for mesenchymal stem cells of craniofacial bones. Nat Cell Biol. 2015 Apr;17(4):386-96. doi: 10.1038/ncb3139. Epub 2015 Mar 23. PMID: 25799059; PMCID: PMC4380556.

52. Zhong Z, Zhao H, Mayo J, Chai Y. Different requirements for Wnt signaling in tongue myogenic subpopulations. J Dent Res. 2015 Mar;94(3):421-9.

53. Han A, Zhao H, Li J, Pelikan R, Chai Y. ALK5-mediated transforming growth factor β signaling in neural crest cells controls craniofacial muscle development via tissue-tissue interactions. Mol Cell Biol. 2014 Aug;34(16):3120-31.

54. Zhao H, Feng J, Seidel K, Shi S, Klein O, Sharpe P, Chai Y. Secretion of shh by a neurovascular bundle niche supports mesenchymal stem cell homeostasis in the adult mouse incisor. Cell Stem Cell. 2014 Feb 6;14(2):160-73.

55. Sanchez-Lara PA, and Zhao H. Neural Crest Stem Cell: Tissue Regeneration and Repair. Neural Crest Cells. Academic Press, 2014: 413-421.

56. Han A, Zhao H, Li J, Pelikan R, Chai Y. ALK5-mediated transforming growth factor β signaling in neural crest cells controls craniofacial muscle development via tissue-tissue interactions. Mol Cell Biol. 2014 Aug;34(16):3120-31.

57. Sanchez-Lara PA, Zhao H, Bajpai R, Abdelhamid AI, Warburton D. Impact of stem cells in craniofacial regenerative medicine. Front Physiol. 2012 Jun 21;3:188.

58. Han D, Zhao H, Parada C, Hacia JG, Bringas P Jr, Chai Y. A TGFβ-Smad4-Fgf6 signaling cascade controls myogenic differentiation and myoblast fusion during tongue development. Development. 2012 May;139(9):1640-50.

59. Zhao H, Li S, Han D, Kaartinen V, Chai Y. Alk5-mediated transforming growth factor β signaling acts upstream of fibroblast growth factor 10 to regulate the proliferation and maintenance of dental epithelial stem cells. Mol Cell Biol. 2011 May;31(10):2079-89.

60. Chung IH, Yamaza T, Zhao H, Choung PH, Shi S, Chai Y. Stem cell property of postmigratory cranial neural crest cells and their utility in alveolar bone regeneration and tooth development. Stem Cells. 2009 Apr;27(4):866-77.

61. Zhao H, Oka K, Bringas P, Kaartinen V, Chai Y. TGF-beta type I receptor Alk5 regulates tooth initiation and mandible patterning in a type II receptor-independent manner. Dev Biol. 2008 Aug 1;320(1):19-29.

62. Ko SO, Chung IH, Xu X, Oka S, Zhao H, Cho ES, Deng C, Chai Y. Smad4 is required to regulate the fate of cranial neural crest cells. Dev Biol. 2007 Dec 1;312(1):435-47.

63. Zhao H, Bringas P Jr, Chai Y. An in vitro model for characterizing the post-migratory cranial neural crest cells of the first branchial arch. Dev Dyn. 2006 May;235(5):1433-40.

64. Andrade J, Pearce ST, Zhao H, Barroso M. Interactions among p22, glyceraldehyde-3-phosphate dehydrogenase and microtubules. Biochem J. 2004 Dec 1;384(Pt 2):327-36.

65. Andrade J, Zhao H, Titus B, Timm Pearce S, Barroso M. The EF-hand Ca2+-binding protein p22 plays a role in microtubule and endoplasmic reticulum organization and dynamics with distinct Ca2+-binding requirements. Mol Biol Cell. 2004 Feb;15(2):481-96.

66. Andrade J, Zhao H, Titus B, Timm Pearce S, Barroso M. The EF-hand Ca2+-binding protein p22 plays a role in microtubule and ER organization and dynamics with distinct Ca2+-binding requirements. Mol Biol Cell. 2003.