Search PubMed for a current list of publications.

  1. Brumbaugh, J., Di Stefano, B., Hochedlinger, K. Reprogramming: identifying the mechanisms that safeguard cell identity. Development. 146(23), 2019. PMID:31792064
  2. 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
  3. 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
  4. 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
  5. 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. S1934-5909, 30401-3406 (2018). PMID:30220521
  6. 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):732-740 (2018). PMID:30127506
  7. 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, 106-120 (2018). PMID:29249356
  8. 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, 219-223 (2017). PMID:28746311
  9. 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 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell (2017). PMID:28366588
  10. 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), 3395-3406 (2016). PMID:28009305
  11. 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), 704-16 (2016). PMID:26947976
  12. 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), 218-224 (2015). PMID:26659182
  13. 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. Nat Biotech 33 (7), 761-768 (2015). PMID:26098450
  14. 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. Nat Methods 11, 1170-1176 (2014). PMID:25262205
  15. 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 Embryonic Stem Cells along the FLK1+ Lineage. Mol Cell Proteomics 13 (3), 780-791 (2014). PMID:24390425
  16. 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), 18-25 (2014). PMID:24678451
  17. Brumbaugh, J., Hochedlinger, K. Removing reprogramming roadblocks: Mbd3 depletion allows deterministic iPSC generation. Cell Stem Cell 13 (4), 379-381 (2013). PMID:24094318
  18. 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), 36370-36383 (2012). PMID:22955276
  19. 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. Proc Natl Acad Sci U S A 109, 8411-8416 (2012).  PMID:22586074
  20. 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. Proc Natl Acad Sci U S A 109, 7162-7168 (2012).  PMID:22474382
  21. Brumbaugh, J., Rose, C.M., Phanstiel, D.H., Thomson, J.A. & Coon, J.J. Proteomics and pluripotency. Crit Rev Biochem Mol Biol 46, 493-506 (2011).  PMID:21999516
  22. 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, 821-827 (2011).  PMID:21983960
  23. McAlister, G.C., Phanstiel, D.H., Brumbaugh, J., Westphall, M.S. & Coon, J.J. Higher-energy collision-activated dissociation without a dedicated collision cell. Mol Cell Proteomics 10, O111 009456 (2011).  PMID:21393638
  24. 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, 1190-1196 (2009).  PMID:19942142
  25. Brumbaugh, J., Phanstiel, D. & Coon, J.J. Unraveling the histone's potential: a proteomics perspective. Epigenetics 3, 254-257 (2008).  PMID:18849650
  26. 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 embryonic stem cells. Proc Natl Acad Sci U S A 105, 4093-4098 (2008).  PMID:18326628
  27. Brumbaugh, J., Schleifenbaum, A., Stier, G., Sattler, M. & Schultz, C. Single- and dual-parameter FRET kinase probes based on pleckstrin. Nat Protoc 1, 1044-1055 (2006).  PMID:17406341
  28. 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, 24-25 (2006).  PMID:16390103