Publications

for a current list of publications.

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  • Brumbaugh, J.*, Aguado, B.A., Lysaght, T., Goldstein, L.S.B. Human fetal tissue is critical for biomedical research. Stem Cell Reports. 2023. PMID: 37977142 (*denotes corresponding authorship)

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  • Serdyukova, K., Swearingen, A.R., Coradin., M., Nevo, M., Tran, H., Bajric, E., Brumbaugh, J. Leveraging dominant-negative histone H3 K-to-M mutations to study chromatin during differentiation and development. Development. 150(21), 2023. PMID: 37846748

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  • Scott, A.K., Casas, E., Schneider, S.E., Swearingen, A.R., Van Den Elzen, C.L., Seelbinder, B., Barthold, J.E., Kugel, J.F., Stern, J.L., Foster, K.J., Emery, N.C.,ÌýBrumbaugh, J., Neu, C.P. Mechanical memory stored through epigenetic remodeling reduces cell therapeutic potential. Biophysical Journal. 122(8), 2023. PMID: 36871159

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  • Witkowski, M.T., Lee, S., Wang, E., Lee, A.K., Talbot, A., Ma, C., Tsopoulidis, N., Brumbaugh, J., Zhao, Y., Roberts, K.G., Hogg, S.J., Nomikou, S., Ghebrechristos, Y.E., Thandapani, P., Mullighan, C.G., Hochedlinger, K., Chen, W., Abdel-Wahab, O., Eyquem, J., Aifantis, I. NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia. Nature Immunology. 23(10), 2022. PMID:Ìý36138187

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  • Seelbinder, B., Ghosh, S., Schneider, S.E., Scott, A., Berman, A.G., Goergen, C.J., Margulies, K.B., Bedi, K., Casas, E., Swearingen, A.R., Brumbaugh, J., Calve, S., Neu, C.P. Nuclear Deformation Guides Chromatin Reorganization in Cardiac Development and Disease. Nature Biomedical Engineering. 5(12), 2021. PMID:Ìý34857921

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  • Brumbaugh, J.*, Di Stefano, B.*, Sardina, J.L.*, Chromatin Regulation in Cell Fate Decisions. Frontiers in Cell and Developmental Biology. 9, 2021. PMID:Ìý34540846. (*denotes co-corresponding authorship; editorial)

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  • Brumbaugh, J., Di Stefano, B., Hochedlinger, K. Reprogramming: identifying the mechanisms that safeguard cell identity. Development. 146(23), 2019. PMID:31659274

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  • Brumbaugh, J.*, Soo Kim, I.*, Ji, F., Huebner, A.J., Di Stefano, B., Schwarz, B.A., Charlton, J., Coffey, A., Choi, J., Walsh, R.M., Schindler, J.W., Anselmo, A., Meissner, A., Sadreyev, R.I., Bernstein, B., Hock, H.*, Hochedlinger, K.* Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo. Nature Cell Biology. 21(11), 2019. PMID:31659274

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  • Di Stefano, B., Luo, E.C., Haggerty, C., Aigner, S., Charlton, J., Brumbaugh, J., Ji, F., Rabano Jiménez, I., Clowers, K.J., Huebner, A.J., Clement, K., Lipchina, I., de Kort, M.A.C., Anselmo, A., Pulice, J., Gerli, M.F.M., Gu, H., Gygi, S.P., Sadreyev, R.I., Meissner, A., Yeo, G.W., Hochedlinger, K. The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. Cell Stem Cell. 25(5), 2019. PMID:31588046

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  • Schiebinger, G., Shu, J., Tabaka, M., Cleary, B., Subramanian, V., Solomon, A., Gould, J., Liu, S., Lin, S., Berube, P., Lee, L., Chen, J., Brumbaugh, J., Rigollet, P., Hochedlinger, K., Jaenisch, R., Regev, A., Lander, E.S. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. Cell. 176(4), 2019. PMID:30712874

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  • Sardina, J.L., Collombet, S., Tian, T.V., Gómez, A., Di Stefano, B., Berenguer, C., Brumbaugh, J., Stadhouders, R., Segura-Morales, C., Gut, M., Gut, I.G., Heath, S., Aranda, S., Di Croce, L., Hochedlinger, K., Thieffry, D., Graf, T. Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate. Cell Stem Cell. 23(5), 2018. PMID:30220521

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  • Di Stefano, B., Ueda, M., Sabri, S., Brumbaugh, J., Huebner, A.J., Sahakyan, A., Clement, K., Clowers, K.J., Erickson, A.R., Shioda, K., Gygi, S.P., Gu, H., Shioda, T., Meissner, A., Takashima, Y., Plath, K., Hochedlinger, K. Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells. Nature Methods. 15(9), 2018. PMID:30127506

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  • Brumbaugh, J.*, Di Stefano, B.*, Wang, X., Borkent, M., Forouzmand, E., Clowers, K.J., Schwarz, B.A., Kalocsay, M., Elledge, S., Gygi, S.P., Hu, G., Yongsheng, Y., Hochedlinger, K. Nudt21 controls cell fate by connecting alternative polyadenylation to chromatin signaling. Cell. 172(1-2), 2018. PMID:29249356

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  • Choi, J., Huebner, A.J., Clement, K., Walsh, R.M., Savol, A., Lin, K., Gu, H., Di Stefano, B., Brumbaugh, J., Kim, S., Sharif, J., Rose, C.M., Mohammad, A., Odajima, J., Charron, J., Shioda, T., Gnirke, A., Gygi, S.P., Koseki, H., Sadreyev, R., Xiao, A., Meissner, A., Hochedlinger, K. Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells. Nature. 548(7666), 2017. PMID:28746311

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  • Choi, J., Clement, K., Huebner, A.J., Webster, J., Rose, C.M., Brumbaugh, J., Walsh, R.M., Lee, S., Savol, A., Etchegaray, J.P., Gu, H., Boyle, P., Elling, U., Mostoslavsky, R., Sadreyev, R., Park, P.J., Gygi, S.P., Meissner, A., Hochedlinger, K. DUSP9 modulatesDNA hypomethylation in female mouse pluripotent stem cells. Cell Stem Cell. 20(5), 2017. PMID:28366588

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  • Liu, L.L., Brumbaugh, J., Bar-Nur, O., Smith, Z., Stadtfeld, M., Meissner, A., Hochedlinger, K., Michor, F. Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell Reports. 17(12), 2016. PMID:28009305

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  • Borkent, M., Bennett, B.D., Lackford, B., Bar-Nur, O., Brumbaugh, J., Wang, L., Du, Y., Fargo, D.C., Apostolou, E., Cheloufi, S., Maherali, N., Elledge, S.J., Hu, G., Hochedlinger, K. A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2. Stem Cell Reports. 6(5), 2016. PMID:26947976

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  • Cheloufi, S., Elling, U., Hopfgartner, B., Jung, Y.L., Murn, J., Ninova, M., Hubmann, M., Badeaux, A.I., Ang, C.E., Tenen, D., Wesche, D.J., Abazova, N., Hogue, M., Tasdemir, N., Brumbaugh, J., Rathert, P., Jude, J., Ferrari, F., Blanco, A., Fellner, M., Wenzel, D., Zinner, M., Vidal, S.E., Bell, O., Stadtfeld, M., Chang, H.Y., Almouzni, G., Lowe, S.W., Rinn, J., Wernig, M., Aravin, A., Shi, Y., Park, P.J., Penninger, J.M., Zuber, J., Hochedlinger, K. The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 528(7581), 2015. PMID:26659182 ÌýÌýÌýÌýÌýÌýÌýÌýÌý ÌýÌýÌýÌýÌýÌýÌýÌýÌýÌý

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  • Bar-Nur, O., Verheul, C., Sommer, A.G., Brumbaugh, J., Schwarz, B.A., Lipchina, I., Huebner, A.J., Mostoslavsky, G., Hochedlinger, K. Lineage conversion induced by pluripotency factors involves transient passage through an iPS cell stage. Nature Biotechnology. 33(7), 2015. PMID:26098450

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  • Bar-Nur, O.*, Brumbaugh, J.*, Verheul, C., Apostolou, E., Pruteanu-Malinici, I., Walsh, R.M., Ramaswamy, S., Hochedlinger, K. Small molecules facilitate rapid and synchronous iPSC generation. Nature Methods. 11(11), 2014. PMID:25262205

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  • Honarpour, N., Rose, C.M., Brumbaugh, J., Anderson, J., Graham, R.L.J., Sweredoski, M.J., Hess, S., Coon, J.J., Deshaies, R.J. F-box Protein FBXL16 Binds PP2A-B55α and Regulates Differentiation of ES Cells along the FLK1+ Lineage. Mol Cell Proteomics. 13(3), 2014. PMID:24390425

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  • Brumbaugh, J.*, Russell, J.D.*, Yu, P., Westphall, M.S., Coon, J.J., Thomson, J.A. NANOG is multiply phosphorylated and directly modified by ERK2 and CDK1 in vitro. Stem Cell Reports. 2(1), 2014. PMID:24678451

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  • Brumbaugh, J., Hochedlinger, K. Removing reprogramming roadblocks: Mbd3 depletion allows deterministic iPSC generation. Cell Stem Cell. 13(4), 2013. PMID:24094318

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  • Van Etten, J., Schagat, T.L., Hrit, J., Weidmann, C., Brumbaugh, J., Coon, J.J. & Goldstrohm, A.C. Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs. J Biol Chem. 287(43), 2012. PMID:22955276

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  • Bailey, D.J., Rose, C.M., McAlister, G.C., Brumbaugh, J., Yu, P., Wenger, C.D., Westphall, M.S., Thomson, J.A. & Coon, J.J. Instant spectral assignment for advanced decision tree-driven mass spectrometry. PNAS. 109(22), 2012. PMID:22586074

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  • Brumbaugh, J., Hou, Z., Russell, J.D., Howden, S.E., Yu, P., Ledvina, A.R., Coon, J.J. & Thomson, J.A. Phosphorylation regulates human OCT4. PNAS. 109(19), 2012. PMID:22474382Ìý ÌýÌýÌýÌý ÌýÌý

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  • Brumbaugh, J., Rose, C.M., Phanstiel, D.H., Thomson, J.A. & Coon, J.J. Proteomics and pluripotency. Crit Rev Biochem Mol Biol. 46(6), 2011. PMID:21999516

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  • Phanstiel, D.H.*, Brumbaugh, J.*, Wenger, C.D., Tian, S., Probasco, M.D., Bailey, D.J., Swaney, D.L., Tervo, M.A., Bolin, J.M., Ruotti, V., Stewart, R., Thomson, J.A. & Coon, J.J. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nature Methods. 8(10), 2011. PMID:21983960

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  • McAlister, G.C., Phanstiel, D.H., Brumbaugh, J., Westphall, M.S. & Coon, J.J. Higher-energy collsion-activated dissociation without a dedicated collision cell. Mol Cell Proteomics. 10(5), 2011. PMID:21393638

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  • Laketa, V., Zarbakhsh, S., Morbier, E., Subramanian, D., Dinkel, C., Brumbaugh, J., Zimmermann, P., Pepperkok, R. & Schultz, C. Membrane-permeant phosphoinositide derivatives as modulators of growth factor signaling and neurite outgrowth. Chem Biol. 16(11), 2009. PMID:19942142

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  • Brumbaugh, J., Phanstiel, D. & Coon, J.J. Unraveling the histone's potential: a proteomics perspective. Epigenetics. 3(5), 2008. PMID:18849650

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  • Phanstiel, D., Brumbaugh, J., Berggren, W.T., Conard, K., Feng, X., Levenstein, M.E., McAlister, G.C., Thomson, J.A. & Coon, J.J. Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human ES cells. PNAS. 105(11), 2008. PMID:18326628

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  • Brumbaugh, J., Schleifenbaum, A., Stier, G., Sattler, M. & Schultz, C. Single- and dual-parameter FRET kinase probes based on pleckstrin. Nature Protocols. 1(2), 2006. PMID:17406341

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  • Brumbaugh, J., Schleifenbaum, A., Gasch, A., Sattler, M. & Schultz, C. A dual parameter FRET probe for measuring PKC and PKA activity in living cells. J Am Chem Soc. 128(1), 2006. PMID:16390103

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