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Justin J Brumbaugh

TitleAsst Professor
InstitutionUniversity of Colorado Boulder
DepartmentBiology-MCD Instruction

    Collapse Biography 
    Collapse education and training
    Harvard Medical School/Massachusetts General Hospital, Boston, MA, USAPostdoctoral12/2018Stem Cell Biology
    University of Wisconsin, Madison, WI, USAPhD12/2011Biochemistry
    European Molecular Biology Laboratory (EMBL), Heidelberg, Germany08/2006Biochemistry
    Penn State University, State College, PA, USABS05/2004Biochemistry and Molecular Biology
    Collapse awards and honors
    2020Boettcher Foundation Webb-Waring Biomedical Research Award, Boettcher Foundation
    2019Next Generation Leader, The International Society for Stem Cell Research
    2014 - 2017NRSA Kirchstein Postdoctoral Fellowship, NIH
    2014Tosteson & Fund for Medical Discovery Postdoctoral Fellowship, Massachusetts General Hospital Executive Committee on Research
    2006 - 2009NSF Graduate Research Fellowship, National Science Foundation
    2004Fulbright Scholar, Fulbright Program
    2000 - 2004Schreyer Honors Scholar, Penn State Honors College

    Collapse Overview 
    Collapse overview
    Development is extraordinary feat in complex organisms. Numerous cell types with highly specific functions arise from a single cell, the zygote. During this process, the embryo must strike a fine balance between replenishing stem cell populations (i.e., self-renewal) and appropriate induction of specialized cells (differentiation). Remarkably, all of these decisions take place largely without changing the genomic content of the cells involved, which underscores the importance of intricate and dynamic regulatory mechanisms in development. Understanding these mechanisms is crucial for both basic science and medicine. Our lab seeks to develop and apply novel and innovative tools to study the molecular determinants of cell fate.

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    List All   |   Timeline
    1. Brumbaugh J, Aguado BA, Lysaght T, Goldstein LSB. Human fetal tissue is critical for biomedical research. Stem Cell Reports. 2023 12 12; 18(12):2300-2312. PMID: 37977142.
      View in: PubMed
    2. Serdyukova K, Swearingen AR, 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. 2023 11 01; 150(21). PMID: 37846748.
      View in: PubMed
    3. Scott AK, Casas E, Schneider SE, Swearingen AR, Van Den Elzen CL, Seelbinder B, Barthold JE, Kugel JF, Stern JL, Foster KJ, Emery NC, Brumbaugh J, Neu CP. Mechanical memory stored through epigenetic remodeling reduces cell therapeutic potential. Biophys J. 2023 04 18; 122(8):1428-1444. PMID: 36871159.
      View in: PubMed
    4. Seelbinder B, Ghosh S, Schneider SE, Scott AK, Berman AG, Goergen CJ, Margulies KB, Bedi KC, Casas E, Swearingen AR, Brumbaugh J, Calve S, Neu CP. Nuclear deformation guides chromatin reorganization in cardiac development and disease. Nat Biomed Eng. 2021 12; 5(12):1500-1516. PMID: 34857921.
      View in: PubMed
    5. Brumbaugh J, Di Stefano B, Sardina JL. Editorial: Chromatin Regulation in Cell Fate Decisions. Front Cell Dev Biol. 2021; 9:734020. PMID: 34540846.
      View in: PubMed
    6. Brumbaugh J, Di Stefano B, Hochedlinger K. Reprogramming: identifying the mechanisms that safeguard cell identity. Development. 2019 12 02; 146(23). PMID: 31792064.
      View in: PubMed
    7. Brumbaugh J, Kim IS, Ji F, Huebner AJ, Di Stefano B, Schwarz BA, Charlton J, Coffey A, Choi J, Walsh RM, Schindler JW, Anselmo A, Meissner A, Sadreyev RI, Bernstein BE, 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. Nat Cell Biol. 2019 11; 21(11):1449-1461. PMID: 31659274.
      View in: PubMed
    8. Di Stefano B, Luo EC, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Rabano Jim?nez I, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC, Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW, Hochedlinger K. The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. Cell Stem Cell. 2019 11 07; 25(5):622-638.e13. PMID: 31588046.
      View in: PubMed
    9. 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 ES. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. Cell. 2019 02 07; 176(4):928-943.e22. PMID: 30712874.
      View in: PubMed
    10. Sardina JL, Collombet S, Tian TV, G?mez A, Di Stefano B, Berenguer C, Brumbaugh J, Stadhouders R, Segura-Morales C, Gut M, Gut IG, 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. 2018 11 01; 23(5):727-741.e9. PMID: 30220521.
      View in: PubMed
    11. Di Stefano B, Ueda M, Sabri S, Brumbaugh J, Huebner AJ, Sahakyan A, Clement K, Clowers KJ, Erickson AR, Shioda K, Gygi SP, Gu H, Shioda T, Meissner A, Takashima Y, Plath K, Hochedlinger K. Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells. Nat Methods. 2018 09; 15(9):732-740. PMID: 30127506.
      View in: PubMed
    12. Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K. Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling. Cell. 2018 01 11; 172(1-2):106-120.e21. PMID: 29249356.
      View in: PubMed
    13. Choi J, Huebner AJ, Clement K, Walsh RM, Savol A, Lin K, Gu H, Di Stefano B, Brumbaugh J, Kim SY, Sharif J, Rose CM, Mohammad A, Odajima J, Charron J, Shioda T, Gnirke A, Gygi S, Koseki H, Sadreyev RI, Xiao A, Meissner A, Hochedlinger K. Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells. Nature. 2017 08 10; 548(7666):219-223. PMID: 28746311.
      View in: PubMed
    14. Choi J, Clement K, Huebner AJ, Webster J, Rose CM, Brumbaugh J, Walsh RM, Lee S, Savol A, Etchegaray JP, Gu H, Boyle P, Elling U, Mostoslavsky R, Sadreyev R, Park PJ, Gygi SP, Meissner A, Hochedlinger K. DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell. 2017 05 04; 20(5):706-719.e7. PMID: 28366588.
      View in: PubMed
    15. Liu LL, 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 Rep. 2016 12 20; 17(12):3395-3406. PMID: 28009305.
      View in: PubMed
    16. Borkent M, Bennett BD, Lackford B, Bar-Nur O, Brumbaugh J, Wang L, Du Y, Fargo DC, Apostolou E, Cheloufi S, Maherali N, Elledge SJ, Hu G, Hochedlinger K. A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2. Stem Cell Reports. 2016 05 10; 6(5):704-716. PMID: 26947976.
      View in: PubMed
    17. Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K. The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 2015 Dec 10; 528(7581):218-24. PMID: 26659182.
      View in: PubMed
    18. Bar-Nur O, Verheul C, Sommer AG, Brumbaugh J, Schwarz BA, Lipchina I, Huebner AJ, Mostoslavsky G, Hochedlinger K. Lineage conversion induced by pluripotency factors involves transient passage through an iPSC stage. Nat Biotechnol. 2015 Jul; 33(7):761-8. PMID: 26098450.
      View in: PubMed
    19. Bar-Nur O, Brumbaugh J, Verheul C, Apostolou E, Pruteanu-Malinici I, Walsh RM, Ramaswamy S, Hochedlinger K. Small molecules facilitate rapid and synchronous iPSC generation. Nat Methods. 2014 Nov; 11(11):1170-6. PMID: 25262205.
      View in: PubMed
    20. Brumbaugh J, Russell JD, Yu P, Westphall MS, Coon JJ, Thomson JA. NANOG is multiply phosphorylated and directly modified by ERK2 and CDK1 in vitro. Stem Cell Reports. 2014 Jan 14; 2(1):18-25. PMID: 24678451.
      View in: PubMed
    21. Honarpour N, Rose CM, Brumbaugh J, Anderson J, Graham RL, Sweredoski MJ, Hess S, Coon JJ, Deshaies RJ. F-box protein FBXL16 binds PP2A-B55a and regulates differentiation of embryonic stem cells along the FLK1+ lineage. Mol Cell Proteomics. 2014 Mar; 13(3):780-91. PMID: 24390425.
      View in: PubMed
    22. Brumbaugh J, Hochedlinger K. Removing reprogramming roadblocks: Mbd3 depletion allows deterministic iPSC generation. Cell Stem Cell. 2013 Oct 03; 13(4):379-81. PMID: 24094318.
      View in: PubMed
    23. Van Etten J, Schagat TL, Hrit J, Weidmann CA, Brumbaugh J, Coon JJ, Goldstrohm AC. Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs. J Biol Chem. 2012 Oct 19; 287(43):36370-83. PMID: 22955276.
      View in: PubMed
    24. Bailey DJ, Rose CM, McAlister GC, Brumbaugh J, Yu P, Wenger CD, Westphall MS, Thomson JA, Coon JJ. Instant spectral assignment for advanced decision tree-driven mass spectrometry. Proc Natl Acad Sci U S A. 2012 May 29; 109(22):8411-6. PMID: 22586074.
      View in: PubMed
    25. Brumbaugh J, Hou Z, Russell JD, Howden SE, Yu P, Ledvina AR, Coon JJ, Thomson JA. Phosphorylation regulates human OCT4. Proc Natl Acad Sci U S A. 2012 May 08; 109(19):7162-8. PMID: 22474382.
      View in: PubMed
    26. Brumbaugh J, Rose CM, Phanstiel DH, Thomson JA, Coon JJ. Proteomics and pluripotency. Crit Rev Biochem Mol Biol. 2011 Dec; 46(6):493-506. PMID: 21999516.
      View in: PubMed
    27. Phanstiel DH, Brumbaugh J, Wenger CD, Tian S, Probasco MD, Bailey DJ, Swaney DL, Tervo MA, Bolin JM, Ruotti V, Stewart R, Thomson JA, Coon JJ. Proteomic and phosphoproteomic comparison of human ES and iPS cells. Nat Methods. 2011 Sep 11; 8(10):821-7. PMID: 21983960.
      View in: PubMed
    28. McAlister GC, Phanstiel DH, Brumbaugh J, Westphall MS, Coon JJ. Higher-energy collision-activated dissociation without a dedicated collision cell. Mol Cell Proteomics. 2011 May; 10(5):O111.009456. PMID: 21393638.
      View in: PubMed
    29. 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. 2009 Nov 25; 16(11):1190-6. PMID: 19942142.
      View in: PubMed
    30. Brumbaugh J, Phanstiel D, Coon JJ. Unraveling the histone's potential: a proteomics perspective. Epigenetics. 2008 Sep; 3(5):254-7. PMID: 18849650.
      View in: PubMed
    31. Phanstiel D, Brumbaugh J, Berggren WT, Conard K, Feng X, Levenstein ME, McAlister GC, Thomson JA, Coon JJ. Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells. Proc Natl Acad Sci U S A. 2008 Mar 18; 105(11):4093-8. PMID: 18326628.
      View in: PubMed
    32. 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. 2006 Jan 11; 128(1):24-5. PMID: 16390103.
      View in: PubMed
    33. Brumbaugh J, Schleifenbaum A, Stier G, Sattler M, Schultz C. Single- and dual-parameter FRET kinase probes based on pleckstrin. Nat Protoc. 2006; 1(2):1044-55. PMID: 17406341.
      View in: PubMed
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