JJ Miranda, PhD

Photo of JJ Miranda, PhD

Email JJ
(415) 502-2783

600 16th St
San Francisco, CA 94158

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  • Assistant Investigator, UCSF School of Medicine
  • Assistant Professor


The human genome is not a linear sequence, but rather a contorted knot of chromosomes in three-dimensional space. We hope to identify long-range interactions between the human host and HIV pathogen genomes. Components of such "hosthogen" bridges may be novel targets for drugs that disrupt viral latency.

Displaying 1 - 21 of 21

  1. Moquin SA, Thomas S, Whalen S, Warburton A, Fernandez SG, McBride AA, Pollard KS, Miranda JJL. The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation. J Virol. 2017 Nov 15. View on Pubmed
  2. He A, Miranda JL. JQ1 reduces Epstein-Barr virus-associated lymphoproliferative disease in mice without sustained oncogene repression. Leuk Lymphoma. 2018 May; 59(5):1248-1251. View on Pubmed
  3. Henderson DJP, Miranda JL, Emerson BM. The ß-NAD+ salvage pathway and PKC-mediated signaling influence localized PARP-1 activity and CTCF Poly(ADP)ribosylation. Oncotarget. 2017 Sep 12; 8(39):64698-64713. View on Pubmed
  4. Keck KM, Moquin SA, He A, Fernandez SG, Somberg JJ, Liu SM, Martinez DM, Miranda JL. Bromodomain and extraterminal inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps. J Biol Chem. 2017 08 11; 292(32):13284-13295. View on Pubmed
  5. Phan AT, Martinez DM, Miranda JL. RNA-seq detects pharmacological inhibition of Epstein-Barr virus late transcription during spontaneous reactivation. Genom Data. 2017 Sep; 13:5-6. View on Pubmed
  6. Lupey-Green LN, Moquin SA, Martin KA, McDevitt SM, Hulse M, Caruso LB, Pomerantz RT, Miranda JL, Tempera I. PARP1 restricts Epstein Barr Virus lytic reactivation by binding the BZLF1 promoter. Virology. 2017 07; 507:220-230. View on Pubmed
  7. 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 05 20; 474(1):71-75. View on Pubmed
  8. Fernandez SG, Miranda JJ. Bendamustine reactivates latent Epstein-Barr virus. Leuk Lymphoma. 2016 May; 57(5):1208-10. View on Pubmed
  9. 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. View on Pubmed
  10. 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. View on Pubmed
  11. Campbell AE, Martinez SR, Miranda JJ. Molecular architecture of CTCFL. Biochem Biophys Res Commun. 2010 Jun 04; 396(3):648-50. View on Pubmed
  12. Martinez SR, Miranda JL. CTCF terminal segments are unstructured. Protein Sci. 2010 May; 19(5):1110-6. View on Pubmed
  13. 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. View on Pubmed
  14. Miranda JL. Conservation and diversity of ancient hemoglobins in Bacteria. Biochem Biophys Res Commun. 2006 May 12; 343(3):924-7. View on Pubmed
  15. Miranda JJ, Maillett DH, Soman J, Olson JS. Thermoglobin, oxygen-avid hemoglobin in a bacterial hyperthermophile. J Biol Chem. 2005 Nov 04; 280(44):36754-61. View on Pubmed
  16. 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. View on Pubmed
  17. Miranda JJ. Position-dependent interactions between cysteine residues and the helix dipole. Protein Sci. 2003 Jan; 12(1):73-81. View on Pubmed
  18. 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. View on Pubmed
  19. 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. View on Pubmed
  20. Miranda JJ. Highly reactive cysteine residues in rodent hemoglobins. Biochem Biophys Res Commun. 2000 Aug 28; 275(2):517-23. View on Pubmed
  21. 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. View on Pubmed