Miranda, J.L., 2023. Single-Cell Transcriptomics of Epstein-Barr Virus and Human Herpesvirus 6 Coinfection. Microbiol Resour Announc 12, e0034223. https://doi.org/10.1128/mra.00342-23

Rondeau, N.C., Miranda, J.L., 2021. Rheostat Coordination of Latent Kaposi Sarcoma-Associated Herpesvirus RNA Expression in Single Cells. J Virol 95, e0003221. https://doi.org/10.1128/JVI.00032-21

Rondeau, N.C., Finlayson, M.O., Miranda, J.L., 2020. Widespread Traces of Lytic Kaposi Sarcoma-Associated Herpesvirus in Primary Effusion Lymphoma at Single-Cell Resolution. Microbiol Resour Announc 9, e00851-20. https://doi.org/10.1128/MRA.00851-20

Yetming, K.D., Lupey-Green, L.N., Biryukov, S., Hughes, D.J., Marendy, E.M., Miranda, J.L., Sample, J.T., 2020. The BHLF1 Locus of Epstein-Barr Virus Contributes to Viral Latency and B-Cell Immortalization. J Virol 94, e01215-20. https://doi.org/10.1128/JVI.01215-20

Moquin, S.A., Thomas, S., Whalen, S., Warburton, A., Fernandez, S.G., McBride, A.A., Pollard, K.S., Miranda, J.L., 2018. The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation. J Virol 92, e01413-17. https://doi.org/10.1128/JVI.01413-17

Lupey-Green, L.N., Moquin, S.A., Martin, K.A., McDevitt, S.M., Hulse, M., Caruso, L.B., Pomerantz, R.T., Miranda, J.L., Tempera, I., 2017. PARP1 restricts Epstein Barr Virus lytic reactivation by binding the BZLF1 promoter. Virology 507, 220–230. https://doi.org/10.1016/j.virol.2017.04.006

Phan, A.T., Fernandez, S.G., Somberg, J.J., Keck, K.M., Miranda, J.L., 2016. Epstein-Barr virus latency type and spontaneous reactivation predict lytic induction levels. Biochem Biophys Res Commun 474, 71–75. https://doi.org/10.1016/j.bbrc.2016.04.070

Holdorf, M.M., Cooper, S.B., Yamamoto, K.R., Miranda, J.J.L., 2011. Occupancy of chromatin organizers in the Epstein-Barr virus genome. Virology 415, 1–5. https://doi.org/10.1016/j.virol.2011.04.004

Ibáñez de Garayo, M., Liu, W., Rondeau, N.C., Damoci, C.B., Miranda, J.J.L., 2021. Rationally repurposed nitroxoline inhibits preclinical models of Epstein-Barr virus-associated lymphoproliferation. J Antibiot (Tokyo) 74, 763–766. https://doi.org/10.1038/s41429-021-00433-2

He, A., Miranda, J.L., 2018. JQ1 reduces Epstein-Barr virus-associated lymphoproliferative disease in mice without sustained oncogene repression. Leuk Lymphoma 59, 1248–1251. https://doi.org/10.1080/10428194.2017.1372578

Phan, A.T., Martinez, D.M., Miranda, J.L., 2017. RNA-seq detects pharmacological inhibition of Epstein-Barr virus late transcription during spontaneous reactivation. Genom Data 13, 5–6. https://doi.org/10.1016/j.gdata.2017.05.012

Keck, K.M., Moquin, S.A., He, A., Fernandez, S.G., Somberg, J.J., Liu, S.M., Martinez, D.M., Miranda, J.L., 2017. Bromodomain and extraterminal inhibitors block the Epstein-Barr virus lytic cycle at two distinct steps. J Biol Chem 292, 13284–13295. https://doi.org/10.1074/jbc.M116.751644

Fernandez, S.G., Miranda, J.J.L., 2016. Bendamustine reactivates latent Epstein-Barr virus. Leuk Lymphoma 57, 1208–1210. https://doi.org/10.3109/10428194.2015.1079317

Germano, E.R., Flores, T., Freed, G.S., Kim, K., Tulinsky, G.H., Yang, A., Rose, O.J., Ray, C.A., Autry, A., Catallozzi, M., Mailloux, B.J., Miranda, J.L., 2024. Building-level wastewater surveillance localizes interseasonal influenza variation. mSphere e0060023. https://doi.org/10.1128/msphere.00600-23

Rondeau, N.C., Rose, O.J., Alt, E.R., Ariyan, L.A., Elikan, A.B., Everard, J.L., Schreier, A.R., Tessler, M.E., Tulinsky, G.H., Vo, J.R., Ray, C.A., Yang, C.Y., Miranda, J.L., Mailloux, B.J., 2023. Building-Level Detection Threshold of SARS-CoV-2 in Wastewater. Microbiol Spectr 11, e0292922. https://doi.org/10.1128/spectrum.02929-22

Rondeau, N.C., Rose, O.J., Ariyan, L.A., Mailloux, B.J., Miranda, J.L., 2021. Accessible and Validated Processing of SARS-CoV-2 from Wastewater. Microbiol Resour Announc 10, e0017421. https://doi.org/10.1128/MRA.00174-21

Henderson, D.J.P., Miranda, J.L., Emerson, B.M., 2017. The β-NAD+ salvage pathway and PKC-mediated signaling influence localized PARP-1 activity and CTCF Poly(ADP)ribosylation. Oncotarget 8, 64698–64713. https://doi.org/10.18632/oncotarget.19841

Campbell, A.E., Martinez, S.R., Miranda, J.J.L., 2010. Molecular architecture of CTCFL. Biochem Biophys Res Commun 396, 648–650. https://doi.org/10.1016/j.bbrc.2010.04.146

Martinez, S.R., Miranda, J.L., 2010. CTCF terminal segments are unstructured. Protein Sci 19, 1110–1116. https://doi.org/10.1002/pro.367

Cho, U.-S., Corbett, K.D., Al-Bassam, J., Bellizzi, J.J., De Wulf, P., Espelin, C.W., Miranda, J.J., Simons, K., Wei, R.R., Sorger, P.K., Harrison, S.C., 2010. Molecular structures and interactions in the yeast kinetochore. Cold Spring Harb Symp Quant Biol 75, 395–401. https://doi.org/10.1101/sqb.2010.75.040

Miranda, J.J.L., King, D.S., Harrison, S.C., 2007. Protein arms in the kinetochore-microtubule interface of the yeast DASH complex. Mol Biol Cell 18, 2503–2510. https://doi.org/10.1091/mbc.e07-02-0135

Miranda, J.J.L., De Wulf, P., Sorger, P.K., Harrison, S.C., 2005a. The yeast DASH complex forms closed rings on microtubules. Nat Struct Mol Biol 12, 138–143. https://doi.org/10.1038/nsmb896

Bach, D.M., Holzman, M.A., Wague, F., Miranda, J.L., Lopatkin, A.J., Mansfield, J.H., Snow, J.W., 2021. Thermal stress induces tissue damage and a broad shift in regenerative signaling pathways in the honey bee digestive tract. J Exp Biol 224, jeb242262. https://doi.org/10.1242/jeb.242262

Miranda, J.L., 2006. Conservation and diversity of ancient hemoglobins in Bacteria. Biochem Biophys Res Commun 343, 924–927. https://doi.org/10.1016/j.bbrc.2006.03.048

Miranda, J.J.L., Maillett, D.H., Soman, J., Olson, J.S., 2005b. Thermoglobin, oxygen-avid hemoglobin in a bacterial hyperthermophile. J Biol Chem 280, 36754–36761. https://doi.org/10.1074/jbc.M505918200

Miranda, J.J.L., 2003. Position-dependent interactions between cysteine residues and the helix dipole. Protein Sci 12, 73–81. https://doi.org/10.1110/ps.0224203

Williams, K.E., Carver, T.A., Miranda, J.J.L., Kautiainen, A., Vogel, J.S., Dingley, K., Baldwin, M.A., Turteltaub, K.W., Burlingame, A.L., 2002. Attomole detection of in vivo protein targets of benzene in mice: evidence for a highly reactive metabolite. Mol Cell Proteomics 1, 885–895. https://doi.org/10.1074/mcp.m200067-mcp200

Ziegler, M., Miranda, J.J., Andersen, U.N., Johnson, D.W., Leary, J.A., Raymond, K.N., 2001. Combinatorial Libraries of Metal-Ligand Assemblies with an Encapsulated Guest Molecule. Angew Chem Int Ed Engl 40, 733–736.

Miranda, J.J., 2000. Highly reactive cysteine residues in rodent hemoglobins. Biochem Biophys Res Commun 275, 517–523. https://doi.org/10.1006/bbrc.2000.3326

Yu, Z., Friso, G., Miranda, J.J., Patel, M.J., Lo-Tseng, T., Moore, E.G., Burlingame, A.L., 1997. Structural characterization of human hemoglobin crosslinked by bis(3,5-dibromosalicyl) fumarate using mass spectrometric techniques. Protein Sci 6, 2568–2577. https://doi.org/10.1002/pro.5560061209