{"id":25,"date":"2018-09-07T22:35:23","date_gmt":"2018-09-07T22:35:23","guid":{"rendered":"http:\/\/staff.washington.edu\/rbreth\/?page_id=25"},"modified":"2025-10-13T22:11:03","modified_gmt":"2025-10-13T22:11:03","slug":"publications","status":"publish","type":"page","link":"https:\/\/faculty.washington.edu\/jendavis\/publications\/","title":{"rendered":"Selected Publications"},"content":{"rendered":"\n

2023<\/p>\n\n\n\n

202<\/strong>5<\/p>\n\n\n\n

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Bretherton, R. C., Reichardt, I. M., Zabrecky, K. A., Nagle, A., Bailey, L. R., Bugg, D., Smolgovsky, S., Gifford, A.L., … & Davis, J<\/strong>. (2025). Preventing hypocontractility-induced fibroblast expansion alleviates dilated cardiomyopathy.\u00a0Science<\/em>, eadv9157. https:\/\/doi.org\/10.1126\/science.adv9157<\/p>\n\n\n\n

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Tune T, Kooiker KB, Davis J<\/strong>, Daniel T, Moussavi-Harami F. Bayesian estimation of muscle mechanisms and therapeutic targets using variational autoencoders. Biophys J. 2025 Jan 7;124(1):179-191. https:\/\/doi.org\/10.1016\/j.bpj.2024.11.3310<\/p>\n\n\n\n

202<\/strong>4<\/p>\n\n\n\n

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Bailey L.R.J, Bugg D., Reichardt I.M., Orta\u00e7 C.D., Nagle A., Gunaje J., Martinson A., Johnson R., MacCoss M.J., Sakamoto T., Kelly D.P., Regnier M., Davis J<\/strong>. (2024). MBNL1 Regulates Programmed Postnatal Switching Between Regenerative and Differentiated Cardiac States. Circulation. Jun 4;149(23):1812-1829. https:\/\/doi.org\/10.1161\/circulationaha.123.066860<\/a><\/p>\n\n\n\n

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Seeing is Believing: Muscleblind-like 1 Is Necessary For Mammalian Cardiomyocyte Maturation. Editorial by Khalid B. Dar, PhD and Shah R. Ali, MD<\/figcaption><\/figure>\n\n\n\n

Bugg D., Davis J<\/strong>. Sox9-coordinated cellular neighborhoods generate fibrosis. (2024). Cell Stem Cell. 2;31(5):589-590. https:\/\/doi.org\/10.1016\/j.stem.2024.04.009 <\/p>\n\n\n\n

2023<\/h2>\n\n\n\n
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Cai S., Zhao M., Zhou B., Yoshii A., Bugg D., Villet O., Sahu A., Olson G.S., Davis J<\/strong>., Tian R. (2023). Mitochondrial dysfunction in macrophages promotes inflammation and suppresses repair after myocardial infarction. J Clin Invest. 15;133(4):e159498. https:\/\/doi.org\/10.1172\/jci159498<\/a><\/p>\n\n\n\n

Bretherton R.C., Haack A.J., Kopyeva I., Rahman F., Kern J.D., Bugg D., Theberge A.B., Davis J<\/strong>., DeForest C.A. (2023). User-Controlled 4D Biomaterial Degradation with Substrate-Selective Sortase Transpeptidases for Single-Cell Biology. Adv Mater. 35(19):e2209904. https:\/\/doi.org\/10.1002\/adma.202209904<\/a><\/p>\n\n\n\n

Nelson A.R., Bugg D., Davis J<\/strong>., Saucerman J.J. (2023). Network model integrated with multi-omic data predicts MBNL1 signals that drive myofibroblast activation. iScience. 26(4):106502. https:\/\/doi.org\/10.1016\/j.isci.2023.106502<\/a><\/p>\n\n\n\n

Kooiker KB, Mohran S, Turner KL, Ma W, Martinson A, Flint G, Qi L, Gao C, Zheng Y, McMillen TS, Mandrycky C, Mahoney-Schaefer M, Freeman JC, Costales Arenas EG, Tu AY, Irving TC, Geeves MA, Tanner BCW, Regnier M, Davis J<\/strong>, Moussavi-Harami F. Danicamtiv Increases Myosin Recruitment and Alters Cross-Bridge Cycling in Cardiac Muscle. Circ Res. 2023 Aug 18;133(5):430-443. https:\/\/doi.org\/10.1161\/circresaha.123.322629<\/p>\n\n\n\n

Asencio A, Malingen S, Kooiker KB, Powers JD, Davis J<\/strong>, Daniel T, Moussavi-Harami F. Machine learning meets Monte Carlo methods for models of muscle’s molecular machinery to classify mutations. J Gen Physiol. 2023 May 1;155(5):e202213291. https:\/\/doi.org\/10.1085\/jgp.202213291<\/p>\n\n\n\n

<\/a><\/p>\n\n\n\n

2022 <\/h2>\n\n\n\n
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Bugg, D., Bailey, L.R.J., Bretherton, R.C., Beach, K.E., Reichardt, I.M., Robeson, K.Z., Reese, A.C., Gunaje, J., Flint, G., DeForest, C.A., Stempien-Otero, A., Davis, J.<\/strong> (2022). MBNL1 drives dynamic transitions between fibroblasts and myofibroblasts in cardiac wound healing. Cell Stem Cell, 29(3), 419-433 https:\/\/doi.org\/10.1016\/j.stem.2022.01.012<\/a><\/p>\n\n\n\n

Featured in ISCRM News<\/a><\/p>\n\n\n\n

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Bailey, L.R.J. & Davis, J.<\/strong> (2022). If these myocytes could talk, they would speak the language of metabolites. Journal of Clinical Investigation. <\/em>https:\/\/doi.org\/10.1172\/JCI156296<\/a><\/p>\n\n\n\n

Ngwenyama N., Kaur K., Bugg D., Theall B., Aronovitz M., Berland R., Panagiotidou S., Genco C., Perrin M.A., Davis J.<\/strong>, Alcaide P. (2022). Antigen presentation by cardiac fibroblasts promotes cardiac dysfunction. Nat Cardiovasc Res. 1(8):761-774. https:\/\/doi.org\/10.1038\/s44161-022-00116-7<\/a><\/p>\n\n\n\n

2021<\/h2>\n\n\n\n
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Mijailovich, S.M., Prodanovic, M., Poggesi, C., Powers, J.D., Davis, J., <\/strong>Geeves, M.A., Regnier, M. (2021). The effect of variable troponin C mutation thin filament incorporation on cardiac muscle twitch contractions. Journal of Molecular and Cellular Cardiology<\/em>, (155) 112-124 https:\/\/doi.org\/10.1016\/j.yjmcc.2021.02.009<\/a><\/p>\n\n\n\n

Reichardt, I.M., Robeson, K.Z., Regnier, M., Davis, J.M.<\/strong> (2021). Controlling cardiac fibrosis through cardiac fibroblast state space modulation. Cellular Signaling<\/em>, (79) 109888 https:\/\/doi.org\/10.1016\/j.cellsig.2020.109888<\/a><\/p>\n\n\n\n

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El-Nachef, D., Bugg, D., Beussman, K., Martinson, A., Murry, C., Sniadecki, N., & Davis, J.<\/strong> (2021). Engrafted Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Undergo Clonal Expansion In Vivo. Circulation<\/em>, (143), 1635-1638. <\/a>https:\/\/doi.org\/10.1161\/CIRCULATIONAHA.119.044974<\/a><\/p>\n\n\n\n

Featured in ISCRM News<\/a><\/p>\n\n\n\n

2020<\/h2>\n\n\n\n
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Powers, J. D., Kooiker, K. B., Mason, A. B., Teitgen, A. E., Flint, G. V., Tardiff, J. C., Davis, J.M.<\/strong>, Moussavi-Harami, F. (2020). Modulating the tension-time integral of the cardiac twitch prevents dilated cardiomyopathy in murine hearts. JCI Insight<\/em>. https:\/\/doi.org\/10.1172\/jci.insight.142446<\/a><\/p>\n\n\n\n

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Bugg, D.*, Bretherton, R. C.*, Kim, P.*, Olszewski, E., Nagle, A., Schumacher, A. E., Chu, N., Gunaje, J., DeForest, C. A., Stevens, K., Kim, D.H., Davis, J. M.<\/strong> (2020). Infarct Collagen Topography Regulates Fibroblast Fate Via p38-Yap-TEAD Signals. Circulation Research<\/em>, (127) 1306-1322 https:\/\/doi.org\/10.1161\/CIRCRESAHA.119.316162<\/a><\/p>\n\n\n\n

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Bretherton, R.*, Bugg, D.*, Olszewski, E.*, & Davis, J.<\/strong> (2020). Regulators of cardiac fibroblast cell state. Matrix Biology<\/em>. (91-92) 117-135 https:\/\/doi.org\/10.1016\/j.matbio.2020.04.002<\/a><\/p>\n\n\n\n

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Mandrycky, C. J., Williams, N. P., Batalov, I., El-Nachef, D., de Bakker, B. S., Davis, J<\/strong>., \u2026 Sniadecki, N. J. (2020). Engineering Heart Morphogenesis. Trends in Biotechnology<\/em>. 38(8) 835-845 https:\/\/doi.org\/10.1016\/j.tibtech.2020.01.006<\/a><\/p>\n\n\n\n

Brady, E.L., Kirby, M.A., Olszewski, E., Grosjean, P., Johansson, F., Davis, J., <\/strong>Wang, R.K., Stevens, K.R. (2020). Guided vascularization in the rat heart leads to transient vessel patterning. APL Bioengineering, <\/em>(4) 016105. https:\/\/doi.org\/10.1063\/1.5122804<\/a><\/p>\n\n\n\n

El-Nachef, D., Shi, K., Beussman, K. M., Martinez, R., Regier, M. C., Everett, G. W., \u2026 Davis, J. <\/strong>(2020). A Rainbow Reporter Tracks Single Cells and Reveals Heterogeneous Cellular Dynamics among Pluripotent Stem Cells and Their Differentiated Derivatives. Stem Cell Reports<\/em>, 15<\/em>(1), 226\u2013241. https:\/\/doi.org\/10.1016\/j.stemcr.2020.06.005<\/a><\/p>\n\n\n\n

Featured in ISCRM News<\/a><\/p>\n\n\n\n

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Earlier Publications<\/h2>\n\n\n\n
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Reiger, M.C., Olszewski, E., Carter, C., Aitchison, J.D., Kaushansky, A., Davis, J.<\/strong>, Berthier, E., Beebe, D.J., Stevens, K.R. (2019) Spatial presentation of biological molecules to cells by localized diffusive transfer. Lab on a Chip, <\/em>19 2114-2126. https:\/\/doi.org\/10.1039\/C9LC00122K<\/a><\/p>\n\n\n\n

Kwong, J.Q., Huo, J., Bround, M.J., Boyer, J.G., Shwanekamp, J.A., Ghazal, N., Maxwell, J.T., Jang, Y.C., Khuchua, Z., Shi, K., Bers, D.M., Davis, J., <\/strong>Molkentin, J.D. (2018). The mitochondrial calcium uniporter underlies metabolic fuel preference in skeletal muscle. JCI Insight, <\/em>3(22). https:\/\/doi.org\/10.1172\/jci.insight.121689<\/a><\/p>\n\n\n\n

Liu, L., Shadish, J. A., Arakawa, C. K., Shi, K., Davis, J.<\/strong>, & DeForest, C. A. (2018). Cyclic Stiffness Modulation of Cell\u2010Laden Protein\u2013Polymer Hydrogels in Response to User\u2010Specified Stimuli Including Light. Advanced Biosystems<\/em>, 2<\/em>(12), 1800240. https:\/\/doi.org\/10.1002\/adbi.201800240<\/a><\/p>\n\n\n\n

Featured in ISCRM News<\/a><\/p>\n\n\n\n

Molkentin, J. D., Bugg, D.,<\/strong> Ghearing, N., Dorn, L. E., Kim, P., Sargent, M. A., \u2026 Davis, J. <\/strong>(2017). Fibroblast-Specific Genetic Manipulation of p38 Mitogen-Activated Protein Kinase In Vivo Reveals Its Central Regulatory Role in Fibrosis. Circulation<\/em>, 136<\/em>(6), 549\u2013561. https:\/\/doi.org\/10.1161\/CIRCULATIONAHA.116.026238<\/a><\/p>\n\n\n\n

Vanhoutte, D., Schips, T.G., Kwong, J.Q., Davis, J., <\/strong>… McNally, E.M., Molkentin, J.D. (2016) Thrombospondin expression in myofibers stabilizes muscle membranes. Elife. <\/em>https:\/\/doi.org\/10.7554\/elife.17589<\/a><\/p>\n\n\n\n

Stempien-Otero, A., Kim, D.-H., & Davis, J.<\/strong> (2016). Molecular networks underlying myofibroblast fate and fibrosis. Journal of Molecular and Cellular Cardiology<\/em>, 97<\/em>, 153\u2013161. https:\/\/doi.org\/10.1016\/J.YJMCC.2016.05.002<\/a><\/p>\n\n\n\n

Davis, J.<\/strong>, Davis, L. C., Correll, R. N., Makarewich, C. A., Schwanekamp, J. A., Moussavi-Harami, F., \u2026 Molkentin, J. D. (2016). A Tension-Based Model Distinguishes Hypertrophic versus Dilated Cardiomyopathy. Cell<\/em>, 165<\/em>(5), 1147\u20131159. https:\/\/doi.org\/10.1016\/J.CELL.2016.04.002<\/a><\/p>\n\n\n\n

Highlighted in Cell<\/a>,<\/em> Nature Reviews Cardiology<\/a><\/em>, and Trends in Molecular Medicine<\/em> and featured in Medical News Today<\/a><\/p>\n\n\n\n

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Davis, J.<\/strong>, Salomonis, N., Ghearing, N., Lin, S.-C. J., Kwong, J. Q., Mohan, A., \u2026 Molkentin, J. D. (2015). MBNL1-mediated regulation of differentiation RNAs promotes myofibroblast transformation and the fibrotic response. Nature Communications<\/em>, 6<\/em>(1), 10084. https:\/\/doi.org\/10.1038\/ncomms10084<\/a><\/p>\n\n\n\n

Davis, J.<\/strong>, & Molkentin, J. D. (2014). Myofibroblasts: trust your heart and let fate decide. Journal of Molecular and Cellular Cardiology<\/em>, 70<\/em>, 9\u201318. https:\/\/doi.org\/10.1016\/j.yjmcc.2013.10.019<\/a><\/p>\n\n\n\n

Goonasekera, S.A.*, Davis, J.*<\/strong>, … , Molkentin, J.D. (2014). Enhanced Ca2+<\/sup> influx from STIM1-Orai1 induces muscle pathology in mouse models of muscular dystrophy. Human Molecular Genetics, <\/em>23(14), 3706-3715. https:\/\/doi.org\/10.1093\/hmg\/ddu079<\/a><\/p>\n\n\n\n

Wang W., Barnabei M.S., Asp M.L., Heinis F.I., Arden E., Davis J.<\/strong>, Braunlin E., Li Q., Davis J.P., Potter J.D., Metzger J.M. (2013). Noncanonical EF-hand motif strategically delays Ca2+ buffering to enhance cardiac performance. Nature Medicine, <\/em>19(3):305-12. https:\/\/doi.org\/10.1038\/nm.3079<\/a><\/p>\n\n\n\n

Davis J<\/strong>, Kwong JQ, Kitsis RN, Molkentin JD. (2013). Apoptosis repressor with a CARD domain (ARC) restrains Bax-mediated pathogenesis in dystrophic skeletal muscle. PLoS One.<\/em> 8(12):e82053. https:\/\/doi.org\/10.1371\/journal.pone.0082053<\/a><\/p>\n\n\n\n

Davis, J<\/strong>., Burr, A. R., Davis, G. F., Birnbaumer, L., & Molkentin, J. D. (2012). A TRPC6-Dependent Pathway for Myofibroblast Transdifferentiation and Wound Healing In Vivo. Developmental Cell<\/em>, 23<\/em>(4), 705\u2013715. https:\/\/doi.org\/10.1016\/j.devcel.2012.08.017<\/a><\/p>\n\n\n\n

Davis, J.<\/strong>, Maillet, M., Miano, J. M., & Molkentin, J. D. (2012). Lost in Transgenesis. Circulation Research<\/em>, 111<\/em>(6), 761\u2013777. https:\/\/doi.org\/10.1161\/CIRCRESAHA.111.262717<\/a><\/p>\n\n\n\n

Kehat I., Davis J<\/strong>., Tiburcy M., Accornero F., Saba-El-Leil M.K., Maillet M., York A.J., Lorenz J.N., Zimmermann W.H., Meloche S., Molkentin J.D. (2011) Extracellular signal-regulated kinases 1 and 2 regulate the balance between eccentric and concentric cardiac growth. Circulation Research<\/em>, 108(2), 176-183. https:\/\/doi.org\/10.1161\/circresaha.110.231514<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

2023 2025 Bretherton, R. C., Reichardt, I. M., Zabrecky, K. A., Nagle, A., Bailey, L. R., Bugg, D., Smolgovsky, S., Gifford, A.L., … & Davis, J. (2025). Preventing hypocontractility-induced fibroblast expansion alleviates dilated cardiomyopathy.\u00a0Science, eadv9157. https:\/\/doi.org\/10.1126\/science.adv9157 Tune T, Kooiker KB, Davis J, Daniel T, Moussavi-Harami F. Bayesian estimation of muscle mechanisms and therapeutic targets using<\/p>\n

Read More<\/a><\/div>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"spay_email":""},"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/Paz0C3-p","_links":{"self":[{"href":"https:\/\/faculty.washington.edu\/jendavis\/wp-json\/wp\/v2\/pages\/25"}],"collection":[{"href":"https:\/\/faculty.washington.edu\/jendavis\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/faculty.washington.edu\/jendavis\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/faculty.washington.edu\/jendavis\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/faculty.washington.edu\/jendavis\/wp-json\/wp\/v2\/comments?post=25"}],"version-history":[{"count":23,"href":"https:\/\/faculty.washington.edu\/jendavis\/wp-json\/wp\/v2\/pages\/25\/revisions"}],"predecessor-version":[{"id":360,"href":"https:\/\/faculty.washington.edu\/jendavis\/wp-json\/wp\/v2\/pages\/25\/revisions\/360"}],"wp:attachment":[{"href":"https:\/\/faculty.washington.edu\/jendavis\/wp-json\/wp\/v2\/media?parent=25"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}