Publications
Nguyen E, Smith KM, Cramer N, Holland RA, Bleimeister IH, Flores-Felix K, Silberberg H, Keller A, Le Pichon CE, Ross SE. Medullary kappa-opioid receptor neurons inhibit pain and itch through a descending circuit. Brain. 2022 Jul 29;145(7):2586-2601. doi: 10.1093/brain/awac189. PMID: 35598161.
Nguyen E, Lim G, Ross SE. Evaluation of Therapies for Peripheral and Neuraxial Opioid-induced Pruritus based on Molecular and Cellular Discoveries. Anesthesiology. 2021 Aug 1;135(2):350-365. doi: 10.1097/ALN.0000000000003844. PMID: 34237130.
Nguyen, E, Lim, G, Ding, H, Hachisuka, J, Ko, M.-C, and Ross, S.E. 2021. Morphine acts on spinal dynorphin neurons to cause itch through disinhibition. Science Translational Medicine.
Nguyen, E, Lim, G, and Ross, S.E. 2021. Mechanistic insights into spinal neurones involved in neuraxial opioid-induced pruritus. British Journal of Anaesthesia.
Chiang MC, Nguyen E, Bustos M, Papale A, and Ross SE. 2020. Divergent neural pathways emanating from the lateral parabrachial nucleus mediate distinct components of the pain response. Neuron.
Fuller A, Parmhans N, Nguyen E, et al. 2020. Identification of Retinal Ganglion Cell Types and Brain Nuclei expressing the transcription factor Brn3c/Pou4f3 using a Cre recombinase knock-in allele. Journal of Comparative Neurology.
Bain W, Li H, van der Geest R, Moore SR, Olonisakin TF, Ahn B, Papke E, Moghbeli K, DeSensi R, Rapport S, Saul M, Hulver M, Xiong Z, Mallampalli RK, Ray P, Morris A, Ma L, Doi Y, Zhang Y, Kitsios GD, Kulkarni HS, McVerry BJ, Ferreira VP, Nouraie M, Lee JS. Increased Alternative Complement Pathway Function and Improved Survival during Critical Illness. Am J Respir Crit Care Med. 2020;202(2):230-40. Epub 2020/05/07. doi: 10.1164/rccm.201910-2083OC. PubMed PMID: 32374177; PMCID: PMC7365364.
Bain W, Olonisakin T, Yu M, Qu Y, Hulver M, Xiong Z, Li H, Pilewski J, Mallampalli RK, Nouraie M, Ray A, Ray P, Cheng Z, Shanks RMQ, St Croix C, Silverstein RL, Lee JS. Platelets inhibit apoptotic lung epithelial cell death and protect mice against infection-induced lung injury. Blood Adv. 2019;3(3):432-45. Epub 2019/02/09. doi: 10.1182/bloodadvances.2018026286. PubMed PMID: 30733303; PMCID: PMC6373758.
Han S, Olonisakin TF, Pribis JP, Zupetic J, Yoon JH, Holleran KM, Jeong K, Shaikh N, Rubio DM, Lee JS. A checklist is associated with increased quality of reporting preclinical biomedical research: A systematic review. PLoS One. 2017;12(9):e0183591. Epub 2017/09/14. doi: 10.1371/journal.pone.0183591. PubMed PMID: 28902887; PMCID: PMC5597130.
Olonisakin TF, Lee JS. Fighting Bacterial Pathogens in the Lung: Platelets to the Rescue? Am J Respir Cell Mol Biol. 2018;58(3):282-3. Epub 2018/03/02. doi: 10.1165/rcmb.2017-0349ED. PubMed PMID: 29493323; PMCID: PMC5854961.
Olonisakin TF, Li H, Xiong Z, Kochman EJ, Yu M, Qu Y, Hulver M, Kolls JK, St Croix C, Doi Y, Nguyen MH, Shanks RM, Mallampalli RK, Kagan VE, Ray A, Silverstein RL, Ray P, Lee JS. CD36 Provides Host Protection Against Klebsiella pneumoniae Intrapulmonary Infection by Enhancing Lipopolysaccharide Responsiveness and Macrophage Phagocytosis. J Infect Dis. 2016;214(12):1865-75. Epub 2016/09/30. doi: 10.1093/infdis/jiw451. PubMed PMID: 27683817; PMCID: PMC5142085.
Olonisakin TF, Suber T, Gonzalez-Ferrer S, Xiong Z, Penaloza HF, van der Geest R, Xiong Y, Osei-Hwedieh DO, Tejero J, Rosengart MR, Mars WM, Van Tyne D, Perlegas A, Brashears S, Kim-Shapiro DB, Gladwin MT, Bachman MA, Hod EA, St Croix C, Tyurina YY, Kagan VE, Mallampalli RK, Ray A, Ray P, Lee JS. Stressed erythrophagocytosis induces immunosuppression during sepsis through heme-mediated STAT1 dysregulation. J Clin Invest. 2021;131(1). Epub 2020/09/18. doi: 10.1172/JCI137468. PubMed PMID: 32941182; PMCID: PMC7773401.
Qu Y, Olonisakin T, Bain W, Zupetic J, Brown R, Hulver M, Xiong Z, Tejero J, Shanks RM, Bomberger JM, Cooper VS, Zegans ME, Ryu H, Han J, Pilewski J, Ray A, Cheng Z, Ray P, Lee JS. Thrombospondin-1 protects against pathogen-induced lung injury by limiting extracellular matrix proteolysis. JCI Insight. 2018;3(3). Epub 2018/02/09. doi: 10.1172/jci.insight.96914. PubMed PMID: 29415890; PMCID: PMC5821195.
Zhao Y, Olonisakin TF, Xiong Z, Hulver M, Sayeed S, Yu MT, Gregory AD, Kochman EJ, Chen BB, Mallampalli RK, Sun M, Silverstein RL, Stolz DB, Shapiro SD, Ray A, Ray P, Lee JS. Thrombospondin-1 restrains neutrophil granule serine protease function and regulates the innate immune response during Klebsiella pneumoniae infection. Mucosal Immunol. 2015;8(4):896-905. Epub 2014/12/11. doi: 10.1038/mi.2014.120. PubMed PMID: 25492474; PMCID: PMC4465063.
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.
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.