Publications

Sun AX, Lin H, Fritch MR, Shen H, Alexander PG, DeHart M, Tuan RS. Chondrogenesis of human bone marrow mesenchymal stem cells in 3-dimensional, photocrosslinked hydrogel constructs: Effect of cell seeding density and material stiffness. Acta Biomater. 2017 Aug;58:302-311. doi: 10.1016/j.actbio.2017.06.016. Epub 2017 Jun 10. PMID: 28611002; PMCID: PMC5813286.

Whitehead A, Zhang Y, McCabe Dunn J, Sherer EC, Lam YH, Stelmach J, Sun A, Shiroda M, Orr RK, Waddell ST, Raghavan S. 2017. Selective Formation of Functionalized α-Quaternary Malononitriles toward 5,5-Disubstituted Pyrrolopyrimidinones. Organic Letters. 4448-4451. PMID: 28812897.

Sun AX, Numpaisal P, Gottardi R, Shen H, Yang G, Tuan RS. 2016. Cell and Biomimetic Scaffold-Based Approaches for Cartilage Regeneration. Operative Techniques in orthopaedics. 135-146. PMID:

Londono R, Sun AX, Tuan RS, Lozito TP. TISSUE REPAIR AND EPIMORPHIC REGENERATION: AN OVERVIEW. Curr Pathobiol Rep. 2018 Mar;6(1):61-69. doi: 10.1007/s40139-018-0161-2. Epub 2018 Feb 4. PMID: 29967714; PMCID: PMC6025457.

Deng Y, Sun AX, Overholt KJ, Yu GZ, Fritch MR, Alexander PG, Shen H, Tuan RS, Lin H. Enhancing chondrogenesis and mechanical strength retention in physiologically relevant hydrogels with incorporation of hyaluronic acid and direct loading of TGF-β. Acta Biomater. 2019 Jan 1;83:167-176. doi: 10.1016/j.actbio.2018.11.022. Epub 2018 Nov 17. PMID: 30458242; PMCID: PMC6733255.

Shen H , Lin H , Sun AX, Song S , Zhang Z , Dai J , Tuan RS . Chondroinductive factor-free chondrogenic differentiation of human mesenchymal stem cells in graphene oxide-incorporated hydrogels. J Mater Chem B. 2018 Feb 14;6(6):908-917. doi: 10.1039/c7tb02172k. Epub 2018 Jan 23.

Sun AX, Londono R, Hudnall ML, Tuan RS, Lozito TP. Differences in neural stem cell identity and differentiation capacity drive divergent regenerative outcomes in lizards and salamanders. Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8256-E8265. doi: 10.1073/pnas.1803780115. Epub 2018 Aug 13. PMID: 30104374; PMCID: PMC6126763.

Sun AX, Prest TA, Fowler JR, Brick RM, Gloss KM, Li X, DeHart M, Shen H, Yang G, Brown BN, Alexander PG, Tuan RS. Conduits harnessing spatially controlled cell-secreted neurotrophic factors improve peripheral nerve regeneration. Biomaterials. 2019 May;203:86-95. doi: 10.1016/j.biomaterials.2019.01.038. Epub 2019 Feb 19.

Brick RM, Sun AX, Tuan RS. Neurotrophically Induced Mesenchymal Progenitor Cells Derived from Induced Pluripotent Stem Cells Enhance Neuritogenesis via Neurotrophin and Cytokine Production. Stem Cells Transl Med. 2018 Jan;7(1):45-58. doi: 10.1002/sctm.17-0108. Epub 2017 Dec 7. PMID: 29215199; PMCID: PMC5746147.

Sun AX, Lin H, Fritch MR, Shen H, Alexander PG, DeHart M, Tuan RS. Chondrogenesis of human bone marrow mesenchymal stem cells in 3-dimensional, photocrosslinked hydrogel constructs: Effect of cell seeding density and material stiffness. Acta Biomater. 2017 Aug;58:302-311. doi: 10.1016/j.actbio.2017.06.016. Epub 2017 Jun 10.

Shen H, Lin H, Sun AX, Song S, Wang B, Yang Y, Dai J, Tuan RS. Acceleration of chondrogenic differentiation of human mesenchymal stem cells by sustained growth factor release in 3D graphene oxide incorporated hydrogels. Acta Biomater. 2020 Mar 15;105:44-55. doi: 10.1016/j.actbio.2020.01.048. Epub 2020 Feb 5.

Sun AX, Lin H, Beck AM, Kilroy EJ, Tuan RS. Projection Stereolithographic Fabrication of Human Adipose Stem Cell-Incorporated Biodegradable Scaffolds for Cartilage Tissue Engineering. Front Bioeng Biotechnol. 2015 Aug 18;3:115. doi: 10.3389/fbioe.2015.00115. PMID: 26347860; PMCID: PMC4539543.

3D printing of collagen to rebuild components of the heart. - A. Lee*, A. R. Hudson*, D. J. Shiwarski, J. W. Tashman, T. J. Hinton, S. Yerneni, J. Bliley, and Adam W. Feinberg. Science. 365, 6452 (2019); doi: 10.1126/science.aav9051.

Organ-on-e-chip: Three-dimensional self-rolled biosensor array for electrical interrogations of human electrogenic spheroids. - A. Kalmykov, C. Huang, J. Bliley,1 D. J. Shiwarski, J. W. Tashman, A. Abdullah, S. Rastogi, E. Mataev, A. W. Feinberg, K. J. Hsia, T. Cohen-Karni. Science Advances. 5, 8 (2019); doi: 10.1126/sciadv.aax0729.

3D Printed Biaxial Stretcher Compatible with Live Fluorescence Microscopy -  D. J. Shiwarski*, J. W. Tashman *, A. Eaton, G. Apodaca, A. W. Feinberg. HardwareX. 7, e00095 (2020).

Fibronectin-Based Nanomechanical Biosensors to Map 3D Mechanical Strain in Live Cells and Tissues - D. J. Shiwarski*, J. W. Tashman*, A. Tsamis, Malachi Blundon, E. A. Michel, B. McCartney, L. Davidson, and A. W. Feinberg. Nat. Commun. 11 (2020), doi:10.1038/s41467-020-19659-z.

FRESH 3D Bioprinting a Full-Size Model of the Human Heart - E. Mirdamadi, J. W. Tashman, D. J. Shiwarski, R. N. Palchesko, A. W. Feinberg, ACS Biomater. Sci. Eng. 6, 6453–6459 (2020).

3D Bioprinting using UNIversal Orthogonal Network (UNION) Bioinks - S. M. Hull, C. D. Lindsay, L. G. Brunel, D. J. Shiwarski, J. W. Tashman, J. G. Roth, D. Myung, A. W. Feinberg, S. C. Heilshorn. Adv. Funct. Mater. n/a, 2007983.

Transparent Support Bath for Embedded 3D Printing and System for In Process Monitoring.- J.W. Tashman, D. J. Shiwarski, F. Lanni, A. W. Feinberg. U.S. Provisional Patent 63/082621

Emergence of FRESH 3D Printing as a Platform for Advanced Tissue Biofabrication - D. J. Shiwarski, A. R. Hudson, J. W. Tashman, A. W. Feinberg. APL Bioeng. 5, 010904 (2021).

Dynamic Loading of Human Engineered Heart Tissue Improves Contractility and Provokes Cardiac Disease - J. M. Bliley*, M. Vermeer*, R. Duffy, I. Batalov, D. Kramer, J. W. Tashman, D. J. Shiwarski, A. Lee, A. S. Teplenin, L. Volkers, B. Coffin, M. F. Hoes, A. Kalmykov, R. Palchesko, Y. Sun, J. D. H. Jongbloed, N. Bomer, R.. A. de Boer, A. J. H. Suurmeijer, D. A. Pijnappels, M. C. Bolling, P. van der Meer, A. W. Feinberg. Science Translational Medicine. Accepted

A High Performance Open-source Syringe Extruder Optimized for Extrusion and Retraction during FRESH 3D Bioprinting - J. W. Tashman*, D. J. Shiwarski*, A. W. Feinberg. HardwareX. 9, e00170 (2021).

FRESH 3D Bioprinting a Contractile Heart Tube Using Human Stem Cell-Derived Cardiomyocytes - J. M. Bliley, J. W. Tashman, D. J. Shiwarski, M. A. Stang, A. Lee, B. Coffin, A. Behre, A. R. Hudson, A. W. Feinberg. Biofabrication. In Revision

Long-fiber Embedded Hydrogel 3D Printing for Structural Reinforcement - W. Sun, J. W. Tashman, D. J. Shiwarski, A. W. Feinberg, and V. A. Webster-Wood. Submitted to ACS Biomater. Sci. Eng

In Situ Volumetric Imaging and Analysis of FRESH 3D Bioprinted Constructs Using Optical Coherence Tomography - J. W. Tashman*, D. J. Shiwarski*, A. Ruesch, F. Lanni, J. M. Kainerstorfer, A. W. Feinberg. Preprint on bioRxiv Prepared for submission to Science Advances.

A Low-Cost, Open-Source Bioprinter Conversion with the Replistruder 4 - J. W. Tashman*, D. J. Shiwarski*, A.W.Feinberg. Prepared for submission to Scientific Reports.

FRESH Printed Patient-Specific Extracellular Matrix Patches for Volumetric Muscle Loss - A. Behre1*, J. W. Tashman1*, D. J. Shiwarski1, R. Crum2, S. Johnson2, G. Hussey2, S. F. Badylak2, A. W. Feinberg1.3. In Preparation

Understanding the Role of Rheology, Deformability, and Pathing for the 3D Printing of Silicone Prepolymers using Freeform Reversible Embedding - M. A. Stang, J. W. Tashman, D. J.  Shiwarski, H. Yang, L. Yao, A. W. Feinberg. In Preparation

*  indicates co-first authorship

Vignali, P.D.A., DePeaux, K., Watson, M.J. et al. Hypoxia drives CD39-dependent suppressor function in exhausted T cells to limit antitumor immunity. Nat Immunol (2022). https://doi.org/10.1038/s41590-022-01379-9

Ford BR*, Vignali PDA*, Rittenhouse NL, Scharping NE, Peralta R, Lontos K, Frisch AT, Delgoffe GM, Poholek AC. Tumor microenvironmental signals reshape chromatin landscapes to limit the functional potential of exhausted T cells. Sci Immunol. 2022 Aug 5;7(74):eabj9123. doi: 10.1126/sciimmunol.abj9123. Epub 2022 Aug 5. PMID: 35930654. *co-first author https://doi.org/10.1126/sciimmunol.abj9123

Jayaprakash P*, Vignali PDA*, Delgoffe GM, Curran MA. Hypoxia Reduction Sensitizes Refractory Cancers to Immunotherapy. Annu Rev Med. 2022 Jan 27;73:251-265. doi: 10.1146/annurev-med-060619-022830. Epub 2021 Oct 26. PMID: 34699264. https://doi.org/10.1146/annurev-med-060619-022830 *co-first author

Watson MJ, Vignali PDA, Mullett SJ, Overacre-Delgoffe AE, Peralta R, Grebinowski S, Menk AV, Rittenhouse NL, DePeaux K, Whetstone RD, Vignali DAA, Hand TW, Poholek AC, Morrison BM, Rothstein JD, Wendell SG, Delgoffe GM. (2021). Regulatory T cell functional identity is sustained by a glucose:lactate axis that is exploited in the tumor microenvironment. Nature. doi: https://doi.org/10.1038/s41586-020-03045-2

Scharping NE, Rivadeneria DB*, Menk AV*, Vignali PDA, Rittenhouse NL, Ford RB, Ronal P, DePeaux K, Poholek AC, Delgoffe GM. (2021). Metabolic stress induced by continuous stimulation under hypoxia rapidly promotes a terminally exhausted T cell state. Nature Immunology. doi: https://doi.org/10.1038/s41590-020-00834-9.

Wang MB, Rahmani F, Benzinger TLS, Raji CA. Edge Density Imaging Identifies White Matter Biomarkers of Late-Life Obesity and Cognition. Aging Dis. 2024 Aug 1;15(4):1899-1912. doi: 10.14336/AD.2022.1210. PMID: 37196133; PMCID: PMC11272213.

Wang M, G'Sell M, Castellano JF, Richardson RM, Ghuman A. A week in the life of the human brain: stable states punctuated by chaotic transitions. Res Sq [Preprint]. 2024 Jan 15:rs.3.rs-2752903. doi: 10.21203/rs.3.rs-2752903/v1. PMID: 37034705; PMCID: PMC10081438.

Wang MB, Boring MJ, Ward MJ, Richardson RM, Ghuman AS. Deep brain stimulation for parkinson's disease induces spontaneous cortical hypersynchrony in extended motor and cognitive networks. Cereb Cortex. 2022 Oct 8;32(20):4480-4491. doi: 10.1093/cercor/bhab496. PMID: 35136991; PMCID: PMC9574237.

Payabvash S, Palacios EM, Owen JP, Wang MB, Tavassoli T, Gerdes M, Brandes-Aitken A, Mukherjee P, Marco EJ. White Matter Connectome Correlates of Auditory Over-Responsivity: Edge Density Imaging and Machine-Learning Classifiers. Front Integr Neurosci. 2019 Mar 29;13:10. doi: 10.3389/fnint.2019.00010. PMID: 30983979; PMCID: PMC6450221.

Payabvash S, Palacios EM, Owen JP, Wang MB, Tavassoli T, Gerdes M, Brandes-Aitken A, Cuneo D, Marco EJ, Mukherjee P. White Matter Connectome Edge Density in Children with Autism Spectrum Disorders: Potential Imaging Biomarkers Using Machine-Learning Models. Brain Connect. 2019 Mar;9(2):209-220. doi: 10.1089/brain.2018.0658. PMID: 30661372; PMCID: PMC6444925.

Brown W, Wesalo J, Tsang M, Deiters A. Engineering Small Molecule Switches of Protein Function in Zebrafish Embryos. J Am Chem Soc. 2023 Feb 1;145(4):2395-2403. doi: 10.1021/jacs.2c11366. Epub 2023 Jan 20. PMID: 36662675.

Brown, W., Wesalo, J., Samanta, S., Luo, J., Caldwell, S. E., Tsang, M., & Deiters, A. (2023). Genetically Encoded Aminocoumarin Lysine for Optical Control of Protein–Nucleotide Interactions in Zebrafish Embryos. ACS Chemical Biology.

Joest, E. F.; Winter, C.; Wesalo, J. S.; Deiters, A.; Tampé, R. “Efficient Amber Suppression by Ribosomal Skipping for In Situ Synthesis of Photoconditional Nanobodies.” Angewandte Chemie.

Joest, E. F.; Winter, C.; Wesalo, J. S.; Deiters, A.; Tampé, R. “Light-guided intrabodies for on-demand in situ target recognition in human cells.” Chem. Sci. 2021, 12, 5787–5795.

Zhou, W.; Wesalo, J. S.; Liu, J.; Deiters, A. “Genetic code expansion in mammalian cells: A plasmid system comparison.” Bioorg. Med. Chem. 2020, 28, 115772.

Wesalo, J. S.; Deiters, A. “Fast phosphine-activated control of protein function using unnatural lysine analogues.” Methods Enzymol. 2020, 638, 191–217.

Wesalo, J. S.; Luo, J.; Morihiro, K.; Liu, J.; Deiters, A. “Phosphine-Activated Lysine Analogues for Fast Chemical Control of Protein Subcellular Localization and Protein SUMOylation.” ChemBioChem 2020, 21, 141–148

Williamson RC, Cowley BR, Litwin-Kumar A, Doiron B, Kohn A, Smith MA, Yu BM. 2016. Scaling Properties of Dimensionality Reduction for Neural Populations and Network Models. PLoS Comput Biol. PMID: 27926936.

Bittner SR, Williamson RC, Snyder AC, Litwin-Kumar A, Doiron B, Chase SM, Smith MA, Yu BM. 2017. Population activity structure of excitatory and inhibitory neurons. PLoS One. PMID: 28817581.

Cowley B, Williamson R, Clemens K, Smith M, Yu B. (2017) Adaptive Sampling for a Population of Neurons. Neural Information Processing Systems Conference. Accepted.

Williamson RC, Doiron B, Smith MA, Yu BM. Bridging large-scale neuronal recordings and large-scale network models using dimensionality reduction. Curr Opin Neurobiol. 2019 Apr;55:40-47. doi: 10.1016/j.conb.2018.12.009. Epub 2019 Jan 22. PMID: 30677702; PMCID: PMC6548625.

Issar D, Williamson RC, Khanna SB, Smith MA. A neural network for online spike classification that improves decoding accuracy. J Neurophysiol. 2020 Apr 1;123(4):1472-1485. doi: 10.1152/jn.00641.2019. Epub 2020 Feb 26. PMID: 32101491; PMCID: PMC7191521.

Cowley BR, Snyder AC, Acar K, Williamson RC, Yu BM, Smith MA. Slow Drift of Neural Activity as a Signature of Impulsivity in Macaque Visual and Prefrontal Cortex. Neuron. 2020 Nov 11;108(3):551-567.e8. doi: 10.1016/j.neuron.2020.07.021. Epub 2020 Aug 17. PMID: 32810433.

Mortensen, P., Enzor, R., Keppel, K., Williamson, R., Jones, P., Nkrumah, G., Safiullah, Z., Michelson, S., Nadimpalli, S., Shue, A., Waxman, E. The Ophthalmology Mini-Elective Gives Vision to Preclinical Medical Students. MedEdPortal. 2020. https://doi.org/10.15766/mep_2374-8265.11024

u GZ, Istvanic F, Chen X, Nouraie M, Shiva S, Straub AC, Pacella JJ. Ultrasound-Targeted Microbubble Cavitation with Sodium Nitrite Synergistically Enhances Nitric Oxide Production and Microvascular Perfusion. Ultrasound Med Biol. 2020 Mar;46(3):667-678. doi: 10.1016/j.ultrasmedbio.2019.10.012. Epub 2019 Dec 3. PMID: 31810801; PMCID: PMC7010556.

Istvanic F, Yu GZ, Yu FTH, Powers J, Chen X, Pacella JJ. Sonoreperfusion therapy for microvascular obstruction: A step toward clinical translation. Ultrasound Med Biol. 2020 Mar;46(3):712-720. doi: 10.1016/j.ultrasmedbio.2019.11.011. Epub 2020 Jan 7. PMID: 31924423; PMCID: PMC7010545.

Deng Y, Sun AX, Overholt KJ, Yu GZ, Fritch MR, Alexander PG, Shen H, Tuan RS, Lin H. Enhancing chondrogenesis and mechanical strength retention in physiologically relevant hydrogels with incorporation of hyaluronic acid and direct loading of TGF-β. Acta Biomater. 2019 Jan 1;83:167-176. doi: 10.1016/j.actbio.2018.11.022. Epub 2018 Nov 17. PMID: 30458242; PMCID: PMC6733255.