Publications
Banerjee, H., Nieves-Rosado, HM, Kulkarni, A., Murter, B., McGrath, K. V., Chandran, U. R., . . . Kane, LP. Expression of Tim-3 drives phenotypic and functional changes in Treg cells in secondary lymphoid organs and the tumor microenvironment. Cell Rep; 2021. (PMID 34525351).
Nieves-Rosado HM., Jacobs JL., Naqvi A., Mellors JW., Macatangay BJC., Kane LP. TIM-3 signaling contributes to the suppressive capacity of Tregs from people with HIV on antiretroviral therapy. J Leukoc Biol; 2023. (PMID: 37350502).
Nieves-Rosado, HM., Banerjee, H., Gocher-Demske, A., Manandhar, P., Mehta, I., Ezenwa, O., Xie, B., Murter, B., Das, J., Vignali, DAA., Delgoffe, GM., Kane, LP. Tim-3 is required for Treg-mediated promotion of T cell exhaustion and viral persistence during chronic LCMV infection. Journal of Immunology; 2024.
Peralta, RM., Xie, B., Lontos, K., Nieves-Rosado, HM., Spahr, K., Ford, RB., Quann, K., Frisch, A., Dean, V., Philbin, M., Cillo, AR., Gingras, S., Poholek, AC., Kane, LP., Rivadeneira, DB., Delgoffe GM. Dysfunction of exhausted T cells is enforced by MCT11-mediated lactate metabolism. Nat. Immunol; 2024.
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.
Arokiaraj CM, Leone MJ, Kleyman M, Chamessian A, Noh MC, Phan BN, Lopes BC, Corrigan KA, Cherupally VK, Yeramosu D, Franusich ME, Podder R, Lele S, Shiers S, Kang B, Kennedy MM, Chen V, Chen Z, Mathys H, Dum RP, Lewis DA, Qadri Y, Price TJ, Pfenning AR, Seal RP. Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition. Cell Rep. 2024 Nov 26;43(11):114876. doi: 10.1016/j.celrep.2024.114876. Epub 2024 Oct 24. PMID: 39453813.
Ibarra AJ, Lopa SH, Phan BN, Himes K, Butters MA, Beck S, Catov JM. Novel Approach to Identify Severe Maternal Morbidity Clusters: A Latent Class Analysis. Am J Perinatol. 2024 Oct 8. doi: 10.1055/a-2418-9955. Epub ahead of print. PMID: 39379025.
Ibarra AJ, Lopa SH, Phan BN, Himes K, Butters MA, Beck S, Catov JM. Novel Approach to Identify Severe Maternal Morbidity Clusters: A Latent Class Analysis. Am J Perinatol. 2024 Oct 8. doi: 10.1055/a-2418-9955. Epub ahead of print. PMID: 39379025.
Ramamurthy E, Agarwal S, Toong N, Sestili H, Kaplow IM, Chen Z, Phan B, Pfenning AR. Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease. PLoS Comput Biol. 2024 Aug 26;20(8):e1012356. doi: 10.1371/journal.pcbi.1012356. PMID: 39186798; PMCID: PMC11389932.
Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E; Zoonomia Consortium; Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science. 2024 Mar 29;383(6690):eabn3263. doi: 10.1126/science.abn3263. Epub 2024 Mar 29. PMID: 38422184; PMCID: PMC11313673.
Phan BN, Ray MH, Xue X, Fu C, Fenster RJ, Kohut SJ, Bergman J, Haber SN, McCullough KM, Fish MK, Glausier JR, Su Q, Tipton AE, Lewis DA, Freyberg Z, Tseng GC, Russek SJ, Alekseyev Y, Ressler KJ, Seney ML, Pfenning AR, Logan RW. Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder. Nat Commun. 2024 Jan 31;15(1):878. doi: 10.1038/s41467-024-45165-7. PMID: 38296993; PMCID: PMC10831093.
Chen HY, Phan BN, Shim G, Hamersky GR, Sadowski N, O'Donnell TS, Sripathy SR, Bohlen JF, Pfenning AR, Maher BJ. Psychiatric risk gene Transcription Factor 4 (TCF4) regulates the density and connectivity of distinct inhibitory interneuron subtypes. Mol Psychiatry. 2023 Nov;28(11):4679-4692. doi: 10.1038/s41380-023-02248-z. Epub 2023 Sep 28. PMID: 37770578; PMCID: PMC11144438.
Gayden J, Puig S, Srinivasan C, Phan BN, Abdelhady G, Buck SA, Gamble MC, Tejeda HA, Dong Y, Pfenning AR, Logan RW, Freyberg Z. Integrative multi-dimensional characterization of striatal projection neuron heterogeneity in adult brain. bioRxiv [Preprint]. 2023 Oct 21:2023.05.04.539488. doi: 10.1101/2023.05.04.539488. PMID: 37205475; PMCID: PMC10187292.
Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP; Zoonomia Consortium**; Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science. 2023 Apr 28;380(6643):eabm7993. doi: 10.1126/science.abm7993. Epub 2023 Apr 28. PMID: 37104615; PMCID: PMC10322212.
Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler A, Keough KC, Zheng Z, Zeng J, Wray NR, Li Y, Johnson J, Chen J; Zoonomia Consortium§; Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science. 2023 Apr 28;380(6643):eabn2937. doi: 10.1126/science.abn2937. Epub 2023 Apr 28. PMID: 37104612; PMCID: PMC10259825.
Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR; Zoonomia Consortium§; Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Evolutionary constraint and innovation across hundreds of placental mammals. Science. 2023 Apr 28;380(6643):eabn3943. doi: 10.1126/science.abn3943. Epub 2023 Apr 28. PMID: 37104599; PMCID: PMC10250106.
Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wallerman O, Xue JR, Li Y, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler AJ, Keough KC, Zheng Z, Zeng J, Wray NR, Johnson J, Chen J; Zoonomia Consortium; Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease. bioRxiv [Preprint]. 2023 Mar 10:2023.03.10.531987. doi: 10.1101/2023.03.10.531987. Update in: Science. 2023 Apr 28;380(6643):eabn2937. doi: 10.1126/science.abn2937. PMID: 36945512; PMCID: PMC10028973.
Desai DD, Yu SE, Salvatore B, Goldberg Z, Bowers EMR, Moore JA, Phan B, Lee SE. Olfactory and neurological outcomes of SARS-CoV-2 from acute infection to recovery. Front Allergy. 2022 Oct 26;3:1019274. doi: 10.3389/falgy.2022.1019274. PMID: 36389036; PMCID: PMC9644087.
Morris J, Olonisakin TF, Moore JA, Phan B, Parker DM, Uribe BA, Barel SJ, Bowers EMR, Buchheit KM, Laidlaw TM, Lee SE. Inhibiting the type 2 inflammatory pathway with dupilumab is associated with an increase in interleukin-4 and interleukin-18 production. Int Forum Allergy Rhinol. 2022 Oct;12(10):1313-1316. doi: 10.1002/alr.23003. Epub 2022 Apr 29. PMID: 35394682.
Lawler AJ, Ramamurthy E, Brown AR, Shin N, Kim Y, Toong N, Kaplow IM, Wirthlin M, Zhang X, Phan BN, Fox GA, Wade K, He J, Ozturk BE, Byrne LC, Stauffer WR, Fish KN, Pfenning AR. Machine learning sequence prioritization for cell type-specific enhancer design. Elife. 2022 May 16;11:e69571. doi: 10.7554/eLife.69571. PMID: 35576146; PMCID: PMC9110026.
Xue X, Zong W, Glausier JR, Kim SM, Shelton MA, Phan BN, Srinivasan C, Pfenning AR, Tseng GC, Lewis DA, Seney ML, Logan RW. Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder. Transl Psychiatry. 2022 Mar 26;12(1):123. doi: 10.1038/s41398-022-01894-1. PMID: 35347109; PMCID: PMC8960783.
Ramnauth AD, Maynard KR, Kardian AS, Phan BN, Tippani M, Rajpurohit S, Hobbs JW, Page SC, Jaffe AE, Martinowich K. Induction of Bdnf from promoter I following electroconvulsive seizures contributes to structural plasticity in neurons of the piriform cortex. Brain Stimul. 2022 Mar-Apr;15(2):427-433. doi: 10.1016/j.brs.2022.02.003. Epub 2022 Feb 17. PMID: 35183789; PMCID: PMC8957536.
Srinivasan C, Phan BN, Lawler AJ, Ramamurthy E, Kleyman M, Brown AR, Kaplow IM, Wirthlin ME, Pfenning AR. Addiction-Associated Genetic Variants Implicate Brain Cell Type- and Region-Specific Cis-Regulatory Elements in Addiction Neurobiology. J Neurosci. 2021 Oct 27;41(43):9008-9030. doi: 10.1523/JNEUROSCI.2534-20.2021. Epub 2021 Aug 30. PMID: 34462306; PMCID: PMC8549541.
Seney ML, Kim SM, Glausier JR, Hildebrand MA, Xue X, Zong W, Wang J, Shelton MA, Phan BN, Srinivasan C, Pfenning AR, Tseng GC, Lewis DA, Freyberg Z, Logan RW. Transcriptional Alterations in Dorsolateral Prefrontal Cortex and Nucleus Accumbens Implicate Neuroinflammation and Synaptic Remodeling in Opioid Use Disorder. Biol Psychiatry. 2021 Oct 15;90(8):550-562. doi: 10.1016/j.biopsych.2021.06.007. Epub 2021 Jun 12. PMID: 34380600; PMCID: PMC8463497.
Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN, Serrato VL, Gutiérrez-Millán E, Aguilar-Ordoñez I, Jaffe AE, Collado-Torres L. Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses. BMC Bioinformatics. 2021 Jul 22;22(1):381. doi: 10.1186/s12859-021-04283-5. Erratum for: BMC Bioinformatics. 2021 May 1;22(1):224. doi: 10.1186/s12859-021-04142-3. PMID: 34294043; PMCID: PMC8299680.
Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN, Serrato VL, Gutiérrez-Millán E, Aguilar-Ordoñez I, Jaffe AE, Collado-Torres L. SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. BMC Bioinformatics. 2021 May 1;22(1):224. doi: 10.1186/s12859-021-04142-3. Erratum in: BMC Bioinformatics. 2021 Jul 22;22(1):381. doi: 10.1186/s12859-021-04283-5. PMID: 33932985; PMCID: PMC8088074.
Perez JL, Ozpinar A, Kano H, Phan B, Niranjan A, Lunsford LD. Salvage Stereotactic Radiosurgery in Breast Cancer Patients with Multiple Brain Metastases. World Neurosurg. 2019 May;125:e479-e486. doi: 10.1016/j.wneu.2019.01.108. Epub 2019 Jan 31. PMID: 30710716.
Chen HC, Polisetty TS, Zhu K, Phan BN, Durr NJ, Tian J, Mahoney NR. A quantitative analysis of factors influencing lower lid retraction and involutional ectropion. J Plast Reconstr Aesthet Surg. 2019 Jan;72(1):137-171. doi: 10.1016/j.bjps.2018.10.020. Epub 2018 Nov 2. PMID: 30467002.
Rasero J, Verstynen TD, DuPont CM, Kraynak TE, Barinas-Mitchell E, Scudder MR, Kamarck TW, Sentis AI, Leckie RL, Gianaros PJ. Stressor-evoked brain activity, cardiovascular reactivity, and subclinical atherosclerosis in midlife adults. medRxiv [Preprint]. 2024 Feb 6:2024.02.05.24302236. doi: 10.1101/2024.02.05.24302236. PMID: 38370849; PMCID: PMC10871357.
Sentis AI, Rasero J, Gianaros PJ, Verstynen TD. Cortical and subcortical brain networks predict prevailing heart rate. bioRxiv [Preprint]. 2024 Jan 7:2023.09.23.559114. doi: 10.1101/2023.09.23.559114. Update in: Psychophysiology. 2024 Jul 1:e14641. doi: 10.1111/psyp.14641. PMID: 38260308; PMCID: PMC10802251.
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
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