JJ Miranda, PhD

JJ Miranda, PhD

Assistant Professor in Residence, Cellular and Molecular Pharmacology, UCSF


Phone: (415) 734-4861
1650 Owens Street
San Francisco, CA 94107

UCSF Profiles

Cancer Center Membership

Affiliate Member

Research Summary

The goal of the proposed research is to discover connections between host and pathogen genomes. My successful background in molecular chromosome biology prepares me to execute this project. As a graduate student at Harvard, I determined the structure of a 10-protein complex that links segregating chromatids to microtubules during mitosis. I trained with Stephen Harrison, a structural virologist. Although I didn’t work on molecular virology then, exposure to the field would lay the groundwork for my current research. Immediately after obtaining my PhD, I because a Sandler Fellow at UCSF, a special opportunity that gave me principal investigator status, protected research funding, and an opportunity to explore a risky new endeavor. Here my laboratory characterized structures of the CTCF family of genome-organizing proteins. Germane to this proposal, we were the first to publish ChIP-seq data identifying transcription factor binding sites on a virus genome-wide. We now wish to extend these results from the pathogen genome to the hosthogen genome.


Reed College, Portland, OR, B.A., 05/01, Biochemistry and Molecular Biology
Harvard University, Cambridge, MA, Ph.D., 03/07, Biochemistry

Professional Experience

  • 2001-2006
    Research Assistant and Teaching Fellow, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
  • 2006-2011
    Assistant Research Biochemist, Cellular and Molecular Pharmacology, University of California, San Francisco, CA
  • 2011-present
    Assistant Investigator, Gladstone Institute of Virology and Immunology, San Francisco, CA
  • 2011-present
    Assistant Professor in Residence, Cellular and Molecular Pharmacology, University of California, San Francisco, CA

Honors & Awards

  • 2001
    Class of '21 Award, Reed College, Portland, OR
  • 2002-2005
    Graduate Research Fellowship, National Science Foundation
  • 2003, 2004
    Certificate of Distinction in Teaching, Harvard University, Cambridge, MA

Selected Publications

  1. Phan AT, Fernandez SG, Somberg JJ, Keck KM, Miranda JL. Epstein-Barr virus latency type and spontaneous reactivation predict lytic induction levels. Biochem Biophys Res Commun. 2016 May 20; 474(1):71-5.
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  2. Fernandez SG, Miranda JL. Bendamustine reactivates latent Epstein-Barr virus. Leuk Lymphoma. 2016 May; 57(5):1208-10.
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  3. Holdorf MM, Cooper SB, Yamamoto KR, Miranda JJ. Occupancy of chromatin organizers in the Epstein-Barr virus genome. Virology. 2011 Jun 20; 415(1):1-5.
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  4. Cho US, Corbett KD, Al-Bassam J, Bellizzi JJ, De Wulf P, Espelin CW, Miranda JJ, Simons K, Wei RR, Sorger PK, Harrison SC. Molecular structures and interactions in the yeast kinetochore. Cold Spring Harb Symp Quant Biol. 2010; 75:395-401.
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  5. Campbell AE, Martinez SR, Miranda JJ. Molecular architecture of CTCFL. Biochem Biophys Res Commun. 2010 Jun 4; 396(3):648-50.
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  6. Martinez SR, Miranda JL. CTCF terminal segments are unstructured. Protein Sci. 2010 May; 19(5):1110-6.
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  7. Miranda JJ, King DS, Harrison SC. Protein arms in the kinetochore-microtubule interface of the yeast DASH complex. Mol Biol Cell. 2007 Jul; 18(7):2503-10.
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  8. Miranda JL. Conservation and diversity of ancient hemoglobins in Bacteria. Biochem Biophys Res Commun. 2006 May 12; 343(3):924-7.
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  9. Miranda JJ, Maillett DH, Soman J, Olson JS. Thermoglobin, oxygen-avid hemoglobin in a bacterial hyperthermophile. J Biol Chem. 2005 Nov 4; 280(44):36754-61.
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  10. Miranda JJ, De Wulf P, Sorger PK, Harrison SC. The yeast DASH complex forms closed rings on microtubules. Nat Struct Mol Biol. 2005 Feb; 12(2):138-43.
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  11. Miranda JJ. Position-dependent interactions between cysteine residues and the helix dipole. Protein Sci. 2003 Jan; 12(1):73-81.
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  12. Williams KE, Carver TA, Miranda JJ, Kautiainen A, Vogel JS, Dingley K, Baldwin MA, Turteltaub KW, Burlingame AL. Attomole detection of in vivo protein targets of benzene in mice: evidence for a highly reactive metabolite. Mol Cell Proteomics. 2002 Nov; 1(11):885-95.
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  13. Ziegler M, Miranda JJ, Andersen UN, Johnson DW, Leary JA, Raymond KN. Combinatorial Libraries of Metal-Ligand Assemblies with an Encapsulated Guest Molecule Coordination Number Incommensurate Cluster Formation, Part 17. Financial support of this work was provided by NSF CHE-9709621 and a NATO-NSF exchange grant SRG 951516. We thank the Miller Foundation for a fellowship to M.Z. Part 16: R. M. Yeh, M. Ziegler, D. W. Johnson, A. J. Terpin, K. N. Raymond, Inorg. Chem. 2001, in press. Angew Chem Int Ed Engl. 2001 Feb 16; 40(4):733-736.
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  14. Miranda JJ. Highly reactive cysteine residues in rodent hemoglobins. Biochem Biophys Res Commun. 2000 Aug 28; 275(2):517-23.
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  15. Yu Z, Friso G, Miranda JJ, Patel MJ, Lo-Tseng T, Moore EG, Burlingame AL. Structural characterization of human hemoglobin crosslinked by bis(3,5-dibromosalicyl) fumarate using mass spectrometric techniques. Protein Sci. 1997 Dec; 6(12):2568-77.
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