4. Seyedhassantehrani N, Burns CS, Verrinder R, Okafor V, Abbasizadeh N, Spencer JA. Intravital Two-Photon Microscopy of the Native Thymus. bioRxiv; 2023. p. 2023.04.10.536267.

3. Itkin T, Houghton S, Schreiner R, Lin Y, Badwe CR, Voisin V, Murison A, Seyedhassantehrani N, Kaufmann KB, Garcia-Prat L, Booth GT, Geng F, Liu Y, Gomez-Salinero JM, Shieh J-H, Redmond D, Xiang JZ, Josefowicz SZ, Trapnell C, Spencer JA, Zangi L, Hadland B, Dick JE, Xie SZ, Rafii S. Transcriptional Activation of Regenerative Hematopoiesis via Vascular Niche Sensing. bioRxiv; 2023. p. 2023.03.27.534417.

2. Gustafsson K, Isaev S, Kooshesh KA, Baryawno N, Kokkaliaris KD, Severe N, Zhao T, Scadden EW, Spencer JA, Burns C, Akilan K, Barkas N, Gessessew H, Lin CP, Kharchenko PV, Scadden DT. Thymic mesenchymal niche cells drive T cell immune regeneration. bioRxiv; 2022. p. 2022.10.12.511184.

1. Toghani D, Zeng S, Mahammadov E, Crosse EI, Seyedhassantehrani N, Burns C, Gravano D, Radtke S, Kiem H, Rodriguez S, Carlesso N, Pradeep A, Wilson NK, Kinston SJ, Göttgens B, Nerlov C, Pietras E, Mesnieres M, Maes C, Kumanogoh A, Worzfeld T, Kharchenko P, Scadden DT, Scialdone A, Spencer JA, Silberstein L. Myeloid-biased HSC require Semaphorin 4A from the bone marrow niche for self-renewal under stress and life-long persistence. bioRxiv; 2022. p. 2022.01.12.476097.

Peer-reviewed Articles:

31. Chicana B, Abbasizadeh N, Burns C, Taglinao H, Spencer JA,* Manilay JO.* Deletion of Vhl in Dmp1-Expressing Cells Causes Microenvironmental Impairment of B Cell Lymphopoiesis. Frontiers in Immunology. 2022;13.

* Spencer JA and Manilay JO are joint senior authors

30. Wu JW, Jung Y, Yeh S-CA, Seo Y, Runnels JM, Burns CS, Mizoguchi T, Ito K, Spencer JA,* Lin CP.* Intravital fluorescence microscopy with negative contrast. PLOS ONE. 2021;16: e0255204.

* Spencer JA and Lin CP are joint senior authors

29. Oki T, Mercier F, Kato H, Jung Y, McDonald TO, Spencer JA, et al. Imaging dynamic mTORC1 pathway activity in vivo reveals marked shifts that support time-specific inhibitor therapy in AML. Nature Communications. 2021;12: 245.

28. Christodoulou C,* Spencer JA,* Yeh S-CA,* Turcotte R, Kokkaliaris KD, Panero R, et al. Live-animal imaging of native haematopoietic stem and progenitor cells. Nature. 2020;578: 278–283.

* Spencer JA, Christodoulou C, and Yeh S-CA contributed equally

27. Lee J, Dykstra B, Spencer JA, Kenney LL, Greiner DL, Shultz LD, et al. mRNA-mediated glycoengineering ameliorates deficient homing of human stem cell–derived hematopoietic progenitors. J Clin Invest. 2017;127: 2433–2437.

26. Silberstein L, Goncalves KA, Kharchenko PV, Turcotte R, Kfoury Y, Mercier F, Baryawno N, Severe N, Bachand J, Spencer JA, Papazian A, Lee D, Chitteti BR, Srour EF, Hoggatt J, Tate T, Celso CL, Ono N, Nutt S, Heino J, Sipilä K, Shioda T, Osawa M, Lin CP, Hu G, Scadden DT. Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators. Cell Stem Cell. 2016;19: 530–543.

25. Itkin T, Gur-Cohen S, Spencer JA, Schajnovitz A, Ramasamy SK, Kusumbe AP, et al. Distinct bone marrow blood vessels differentially regulate haematopoiesis. Nature. 2016;532: 323–328.

24. Pang Y, Tsigkou O, Spencer JA, Lin CP, Neville C, Grottkau B. Analyzing Structure and Function of Vascularization in Engineered Bone Tissue by Video-Rate Intravital Microscopy and 3D Image Processing. Tissue Engineering Part C: Methods. 2015;21: 1025–1031.

23. Aceto N, Bardia A, Miyamoto DT, Donaldson MC, Wittner BS, Spencer JA, et al. Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis. Cell. 2014;158: 1110–1122.

22. Roussakis E, Spencer JA, Lin CP, Vinogradov SA. Two-Photon Antenna-Core Oxygen Probe with Enhanced Performance. Anal Chem. 2014;86: 5937–5945.

21. Park D, Spencer JA, Lin CP, Scadden DT. Sequential In vivo Imaging of Osteogenic Stem/Progenitor Cells During Fracture Repair. JoVE (Journal of Visualized Experiments). 2014; e51289.

20. Spencer JA, Ferraro F, Roussakis E, Klein A, Wu J, Runnels JM, et al. Direct measurement of local oxygen concentration in the bone marrow of live animals. Nature. 2014;508: 269–273.

19. Carlson AL, Fujisaki J, Wu J, Runnels JM, Turcotte R, Spencer JA, Celso CL, et al. Tracking Single Cells in Live Animals Using a Photoconvertible Near-Infrared Cell Membrane Label. PLOS ONE. 2013;8: e69257.

18. Park D, Spencer JA, Koh BI, Kobayashi T, Fujisaki J, Clemens TL, et al. Endogenous Bone Marrow MSCs Are Dynamic, Fate-Restricted Participants in Bone Maintenance and Regeneration. Cell Stem Cell. 2012;10: 259–272.

17. Sarkar D, Spencer JA, Phillips JA, Zhao W, Schafer S, Spelke DP, et al. Engineered cell homing. Blood. 2011;118: e184–e191.

16. Ferraro F, Lymperi S, Méndez-Ferrer S, Saez B, Spencer JA, Yeap BY, et al. Diabetes Impairs Hematopoietic Stem Cell Mobilization by Altering Niche Function. Science Translational Medicine. 2011;3: 104ra101-104ra101.

15. Pitsillides CM, Runnels JM, Spencer JA, Zhi L, Wu MX, Lin CP. Cell labeling approaches for fluorescence-based in vivo flow cytometry. Cytometry Part A. 2011;79A: 758–765.

14. Ashida N, SenBanerjee S, Kodama S, Foo SY, Coggins M, Spencer JA, et al. IKKβ regulates essential functions of the vascular endothelium through kinase-dependent and -independent pathways. Nature Communications. 2011;2: 318.

13. Runnels JM, Carlson AL, Pitsillides CM, Thompson B, Wu J, Spencer JA, et al. Optical techniques for tracking multiple myeloma engraftment, growth, and response to therapy. JBO. 2011;16: 011006.

12. Fan Z,* Spencer JA,* Lu Y, Pitsillides CM, Singh G, Kim P, et al. In vivo tracking of “color-coded” effector, natural and induced regulatory T cells in the allograft response. Nature Medicine. 2010;16: 718–722.

* Spencer JA and Fan Z contributed equally

11. Tsigkou O, Pomerantseva I, Spencer JA, Redondo PA, Hart AR, O’Doherty E, et al. Engineered vascularized bone grafts. PNAS. 2010;107: 3311–3316.

10. Horner BM, Ferguson KK, Randolph MA, Spencer JA, Carlson AL, Hirsh EL, et al. In vivo observations of cell trafficking in allotransplanted vascularized skin flaps and conventional skin grafts. Journal of Plastic, Reconstructive & Aesthetic Surgery. 2010;63: 711–719.

9. Sackstein R, Merzaban JS, Cain DW, Dagia NM, Spencer JA, Lin CP, et al. Ex vivo glycan engineering of CD44 programs human multipotent mesenchymal stromal cell trafficking to bone. Nature Medicine. 2008;14: 181–187.

8. Veilleux I, Spencer JA, Biss DP, Cote D, Lin CP. In Vivo Cell Tracking With Video Rate Multimodality Laser Scanning Microscopy. IEEE Journal of Selected Topics in Quantum Electronics. 2008;14: 10–18.

7. Xu X, Mannik J, Kudryavtseva E, Lin KK, Flanagan LA, Spencer J, et al. Co-factors of LIM domains (Clims/Ldb/Nli) regulate corneal homeostasis and maintenance of hair follicle stem cells. Developmental Biology. 2007;312: 484–500.

6. Leleu X, Jia X, Runnels J, Ngo HT, Moreau A-S, Farag M, Spencer JA, et al. The Akt pathway regulates survival and homing in Waldenstrom macroglobulinemia. Blood. 2007;110: 4417–4426.

5. Alsayed Y, Ngo H, Runnels J, Leleu X, Singha UK, Pitsillides CM, Spencer JA, et al. Mechanisms of regulation of CXCR4/SDF-1 (CXCL12)–dependent migration and homing in multiple myeloma. Blood. 2007;109: 2708–2717.

4. Dagia NM, Gadhoum SZ, Knoblauch CA, Spencer JA, Zamiri P, Lin CP, et al. G-CSF induces E-selectin ligand expression on human myeloid cells. Nature Medicine. 2006;12: 1185–1190.

3. Yu Z, Lin KK, Bhandari A, Spencer JA, Xu X, Wang N, et al. The Grainyhead-like epithelial transactivator Get-1/Grhl3 regulates epidermal terminal differentiation and interacts functionally with LMO4. Developmental Biology. 2006;299: 122–136.

2. Runnels JM, Zamiri P, Spencer JA, Veilleux I, Wei X, Bogdanov A, et al. Imaging Molecular Expression on Vascular Endothelial Cells by In Vivo Immunofluorescence Microscopy. Mol Imaging. 2006;5: 7290.2006.00004.

1. Lyubovitsky JG, Spencer JA, Krasieva TB, Andersen B, Tromberg BJ. Imaging corneal pathology in a transgenic mouse model using nonlinear microscopy. JBO. 2006;11: 014013.

Book Chapters:

2. Abbasizadeh N, Spencer JA. Two-Photon Phosphorescence Lifetime Microscopy. In: Wei X, Gu B, editors. Optical Imaging in Human Disease and Biological Research. Singapore: Springer; 2021. pp. 63–82.

1. Jung Y,* Spencer JA,* Raphael AP, Wu JW, Alt C, Runnels JR, et al. Intravital Imaging of Mouse Bone Marrow: Hemodynamics and Vascular Permeability. In: Ishii M, editor. Intravital Imaging of Dynamic Bone and Immune Systems : Methods and Protocols. New York, NY: Springer; 2018. pp. 11–22.

* Spencer JA and Jung Y contributed equally

Publications can be found online at: