EMERMAN LAB -- Publications
hutch_rainier2

2017

Baldauf, H.-M., Stegmann, L., Schwarz, S.-M., Ambiel, I., Trotard, M., Martin, M. , Burggraf, M., Lenzi, G.M., Lejk, H., Pan, X., Fregoso, O.I. , Lim, E.S. , Abraham, L., Nguyen, L. , Rutsch, F., König, R., Kim, B. , Emerman, M., Fackler, O.T.,  Keppler, O.T. (2017) Vpx overcomes a SAMHD1-independent block to HIV reverse transcription that is specific to resting CD4 T cells. Proc. Natl. Acad. Sci. USA 114 (10) 2729–2734. abstract/full text

Adolph, M., Ara, A., Feng, Y., Wittkopp, C., Emerman, M., Fraser, J., Chelico, L., (2017)  Cytidine deaminase efficiency of the lentiviral viral restriction factor APOBEC3C correlates with dimerization. Nucl Acid Res, 45 (6): 3378-3394. abstract/full text

The KT Jeang Retrovirology prize 2017: Michael Emerman.  Retrovirology (2017) 14:37. abstract/full text

2016

McLaughlin, R.N., Gable, J.T., Wittkopp, C.J., Emerman, M., and  Malik, H.S. (2016)  Conservation and innovation of APOBEC3A restriction functions during primate volution. Mol Bio Evo, 33(8):1889-1901. abstract/full text

Fregoso, O.I, and Emerman, M. (2016) Activation of the DNA Damage Response Is a Conserved Function of HIV-1 and HIV-2 Vpr That is Indepedent of SLX4 Recruitment. mBio, 7(5):e01433-16. abstract/full text

Wittkopp, C.J., Madison A.B., Wu, L.I., Chelico, C. and Emerman, M. (2016) A Single Nucleotide Polymorphism in Human APOBEC3C Enhances Restriction of Lentiviruses. PLOS Pathog, 12(10):e1005865. abstract/full text 


2015

 Mitchell, P.S., Young, Y.M., Emerman, M., and Malik, H.S. (2015)  Evolutionary Analyses Suggest a Function of MxB Immunity Proteins Beyond Lentivirus Restriction. PLOS Pathog, 11(12):e1005304. abstract/full text

Etienne, L., Bibollet-Ruche, F., Sudmant, P.H., Wu, Li.I. Hahn, B.H and Emerman, M. (2015) The role of the antiviral APOBEC3 gene family in protecting chimpanzees against lentiviruses from monkeys. PLOS Pathog, 11(9):e1005149. abstract/full text


2014

Matsen, F.A., Small, C.T., Soliven, K.  Engel, G.A., Ferroz, M.M., Wang, X, Craing, K.L., Hasan, M.K., Emerman, M., Linial, M.L., and Jones-Englel, L. (2014) A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses. PLOS Comput Biol, 10(2):e1003493. abstract/full text

Emerman, M.  (2014) Author-initiated repurposing of reviews: the Streamline Reviews initiative at Virology.  Learned Publishing, 27(2):104-106. abstract

Refsland, E. W., Hultquist. J.F.,  Luengas. E.M., Ikeda. T., Shaban, N.M., Law, E.K.,  Brown, W., L., Reilly, C., Emerman, M., and Harris, R.S. (2014) Natural Polymorphisms in Human APOBEC3H and HIV-1Vif Combine in Primary T Lymphocytes to Affect Viral G to-A Mutation Levels and Infectivity. PLOS Genet, 10(11):e1004761. abstract/full text


2013

Spragg, C.J. and Emerman, M. (2013) Antagonism of SAMHD1 is actively maintained in natural infections of Simian Immunodeficiency Virus, Proc. Natl. Acad. Sci. USA, 110:21136-21141. abstract/full text

Etienne, L., and Emerman, M. (2013) The mongoose, the pheasant, the pox, and the retrovirus. PLOS Biology, 11(8):e1001641. abstract/full text

Compton, A.A., Malik, H.S. and Emerman, M. (2013) Host Gene Evolution Traces the Evolutionary History of Ancient Primate Lentiviruses. Phil. Trans. of the Royal Society B, 368(1626):20120496. abstract/full text

Fregoso, O.I., Ahn, J., Wang, C., Mehrens, J., Skowronski, J., and Emerman, M. (2013) Evolutionary Toggling of Vpx/Vpr Specificity Results in Divergent Recognition of the Restriction Factor SAMHD1. PLOS Pathog, 9(7):e1003496. abstract/full text

Etienne, L., Hahn, B.H., Sharp, P.M., Matsen, F.A., and Emerman, M. (2013) Gene loss and adaptation to hominids underlie the ancient origin of HIV-1. Cell Host Microbe, 14:85-92. abstract/full text

Duggal, N. K., Fu, W., Akey, J.M. and Emerman, M. (2013) Identification and antiviral activity of common polymorphisms in the APOBEC3 locus in human populations. Virology, 443:329-337. abstract/full text

Compton, A.A., and Emerman, M. (2013) Convergence and divergence in the evolution of the APOBEC3G-Vif interaction reveal ancient origins of Simian Immunodeficiency Viruses. PLoS Pathog 9(1):e1003135. abstract / full text

Malfavon-Borja, R., Wu, L.I., Emerman, M., and Malik, H.S. (2013) Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. Proc. Natl. Acad. Sci. USA, 2013 Jan 14 . abstract / full text


2012

Mitchell, P.S., Corinna, P., Emerman, M., Haller, O. Malik, H.S., Kochs, G. (2012) Evolution-guided identification of antiviral specificity determinants in the broadly acting innate immunity factor MxA. Cell Host Microbe, 12:598-604. abstract / full text

Lim, E.S, Wu, L.I., Malik, H.S., and Emerman, M. (2012) The function and evolution of the restriction factor viperin in primates was not driven by lentiviruses Retrovirology, 9:55. abstract/full text

Duggal, N.K., and Emerman M. (2012) Evolutionary conflicts between viruses and restriction factors shape immunity. Nature Reviews Immunology 12(10):687-95. abstract/full text

Lim, E.S, Fregoso, O.I., McCoy, C.O., Matsen, F.A., Malik, H.S., and Emerman, M. (2012) The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx. Cell Host Microbe. 11(2):194-204. abstract/full text

Compton, A.A., Hirsch, V.M., and Emerman, M. (2012) The host restriction factor. APOBEC3G and retroviral Vif protein coevolve due to ongoing genetic conflict. Cell Host Microbe, 11:91-98. abstract/full text


2011

Patel, M.R., Emerman, M., and Malik H.S. (2011) Paleovirology—ghosts and gifts of viruses past. Curr Op Virol, 1(4): 304-309. abstract/full text

Duggal, N. K., Malik, H. S., and Emerman, M. (2011) Positive selection of Apobec3DE in chimpanzees has driven breadth in anti-viral activity. J. Virol, 85: 11361-11371. abstract/full text

Emerman, M. (2011) The little book of viruses. PLoS Biol, 9(9):e1001139. full text

Lim, E.S. and Emerman, M. (2011) HIV: Going for the watchman. Nature, 474:587-588. full text

Li, M.M., and Emerman, M. (2011) Polymorphism in human APOBEC3H affects a dominant phenotype of subcellular localization and antiviral activity. J. Virol, 85:8179-8207.  abstract/full text

Tareen S.U. and Emerman, M.  (2011) Trim5 TAKes on Pattern Recognition. Cell Host Microbe, 9: 349-350.  abstract/full text

Tareen S.U. and Emerman, M. (2011) Human Trim5α has additional activities that are uncoupled from retroviral capsid recognition. Virology, 409:113-120. abstract/full text

Yu, S.F., Lujan, P., Jackson, D.L. , Emerman, M., and Linial, M.L. (2011) The DEAD-box RNA Helicase DDX6 is Required for Efficient Encapsidation of a Retroviral Genome. PLoS Pathog, 7(10):e1002303. full text


2010

Lim, E.S., Malik, H.S., and Emerman, M. (2010) Ancient adaptive evolution shaped functions of Vpu and Nef in human immunodeficiency virus and primate lentiviruses. J. Virol 84:7124-7134. abstract/full text

Emerman, M. and Malik, H.S. (2010) Paleovirology--modern consequences of ancient viruses. PLoS Bio, 8(2):e1000301. free text

Li, M.M, Wu, L.I., and Emerman, M. (2010) The range of human APOBEC3H sensitivity to lentiviral Vif proteins. J. Virol, 84(1):88-95. abstract/full text


2009

Tareen, S.U., Sawyer, S.L., Malik, H.S., and Emerman, M. (2009) An expanded clade of rodent Trim5 genes. Virology, 385: 473-483. abstract/full text

Voronin, Y, Holte, S, Overbaugh, J., and Emerman, M. (2009) Genetic Drift of HIV Populations in Culture. PLoS Genetics, 5(3):e1000431. full text

Yamashita, M. and Emerman, M. (2009) Cellular restriction targeting viral capsids perturbs HIV-1 infection of non-dividing cells. J. Virol, 83:11673-11681. abstract/full text

Lim, E.S. and Emerman, M. (2009) Simian immunodeficiency virus from african green monkeys (SIVagm) does not antagonize endogenous levels of African green monkey Tetherin/BST-2. J. Viro,l 83:11673-11681. abstract/full text


2008

OhAinle, M., Kerns, J.A., Li. M.M.H., Malik, H.S., and Emerman, M. (2008) Anti-retroelement activity of APOBEC3H Was Lost Twice in Recent Human Evolution. Cell Host Microbe, 4(12):249-259. abstract/full text

Lin, T-Y. and Emerman, M. (2008) Determinants of Cyclophilin A-dependent TRIM5α restriction against HIV-1. Virology, 379:335-341. abstract/full text

Malim, M.H. and Emerman, M. (2008) HIV-1 accessory proteins - ensuring viral survival in a hostile environment. Cell Host Microbe, 3:388-398. abstract/full text

Kerns, J.A., Emerman, M., and Malik, H.S. (2008) Positive selection and increased antiviral activity associated with the PARP-containing isoform of human Zinc-finger Antiviral Protein. PLoS Genetics, 4 (1): e21. full text


2007

Sawyer, S.L., Emerman, M., and Malik, H.S. (2007) Discordant Evolution of the Adjacent  Antiretroviral Genes TRIM22 and TRIM5 in Mammals. PLoS Pathog, 3(12):1918-1929. abstract/full text

Yamashita, M., Perez, O., Hope, T.J., and Emerman, M. (2007) Evidence for Direct Involvement of the Capsid Protein in HIV Infection of Nondividing cells. PLoS Pathog., 3(10):1502-1510. abstract/full text

Voronin, Y., Chohan, B., Emerman, M., and Overbaugh, J. (2007) Primary Isolates of Human Immunodeficiency Virus 1 (HIV-1) are Usually Dominated by the Major Variants Found in Blood. J. Virol, 81:10232-10241. abstract/ full text

Kaiser, S.M., Malik, H.S., and Emerman, M. (2007) Restriction of an Exinct Retrovirus by the Human Trim5a Antiviral Protein. Science 316:1756-1758. abstract /full text


2006

Yamashita, M., and Emerman, M. (2006) Retroviral Infection of Non-dividing Cells: Old and New Perspectives. Virology, 344:88-93. abstract

Kaiser, S.M., and Emerman, M. (2006) Uracil DNA Glycosylase is Dispensable for HIV-1 Replication and Does Not Contribute to the Antiviral Effects of the Cytidine Deaminase, Apobec3G. J. Virol, 80:875-882. abstract/full text

Sawyer, S.L., Wu, L., Akey, J.M., Emerman, M., and Malik, H.S. (2006) High Frequency Persistence of an Impaired Allele of the Retroviral Defense Gene TRIM5a in Humans. Current Biology, 16:95-100. abstract

OhAinle, M., Kerns, J.A., Malik, H.S., and Emerman, M. (2006) Adaptive Evolution and Antiviral Activity of the Conserved Mammalian Cytidine Deaminase APOBEC3H. J. Virol, 80:3853-3862. abstract/full text

Emerman, M. (2006) How Trim5α defends against retroviral invasions. Proc. Nat. Acad. Sci. (USA), 103: 5249-5250. abstract / full text

Lewinski MK, Yamashita M, Emerman M, Ciuffi A, Marshall H, et al. (2006) Retroviral DNA Integration: Viral and Cellular Determinants of Target-Site Selection. PLoS Pathog 2(6): e60 full text

Lin, T-Y. , Emerman, M. (2006) Cyclophilin A interacts with diverse lentiviral capsids. Retrovirology 3: 70. abstract


2005

Sawyer, S.L., Wu, L., Emerman, M., and Malik, H.S. (2005) Positive selection in primate Trim5a identifies a critical species-specific retroviral restriction. Proc. Natl. Acad. Sci. USA, 102:2832-2837. abstract/full text

Yamashita, M., and Emerman, M. (2005) The Cell Cycle Independence of HIV Infections is Not Determined by Known Karyophilic Viral Elements. PLoS Pathog, 1(3): 170-178. abstract/full text

Voronin, Y., Overbaugh, J., and Emerman, M. (2005) SIV Variants that Differ in Pathogenicity Differ in Fitness under Rapid Cell-turnover Conditions. J. Virol, 79:15091-15098. abstract/full text


2004

Goh, W.C., Manel, N. , and Emerman, M. (2004) The Human Immunodeficiency Virus Vpr Protein Binds Cdc25C: Implications for G2 arrest. Virology, 318: 338-351. abstract

Kaiser, S.M., and Emerman, M. (2004) Controlling lentiviruses: Single amino acid changes can determine specificity. Proc. Natl. Acad. Sci. USA, 101:3725-3726. abstract/full text

Yamashita, M., and Emerman, M. (2004) Capsid is a dominant determinant of retroviral infectivity in non-dividing cells. J. Virol, 78:5670-5678. abstract/full text

Sawyer, S.L., Emerman, M., and Malik H. S. (2004) Ancient, Positive Selection of the Antiviral DNA Editing Enzyme Apobec3G in Primates. PLoS Biology, 2: 1278-1285. abstract/full text


2003

Gummuluru, S., and Emerman, M. (2003) AIDS 2002, A Year in Review: Advances in HIV molecular biology. AIDS, 16:S17-S24. abstract

Gummuluru, S., Rogel M., Stamatatos, L., and Emerman, M. (2003) Binding of human immunodeficiency virus type 1 to immature dendritic cells can occur independently of DC-SIGN and mannose binding C-type lectin receptors via a cholesterol dependent pathway. J. Virol, 77:12865-12874. abstract/full text


2002

Lewinsohn, D.A., Lines, R., Lewinshohn, D.M., Riddell, S. R., Greenberg, P.D., Emerman, M., and Bartz, S.R. (2002) HIV-1 Vpr does not inhibit CTL-mediated apoptosis of HIV-1 infected cells. Virology, 294:13-30.

Somasundaran, M., Sharkey, M., Brichacek, B., Luzuraga, K. Emerman, M. Sullivan, J., and Stevenson, M. (2002) Evidence for a cytopathogenicity determinant within HIV-1 Vpr. Proc. Natl. Acad. Sci. USA, 99:9503-9508.

Gummuluru, S., KewalRamani, V.N., and Emerman, M. (2002) Dendritic Cell Mediated viral transfer to T cells is required for HIV-1 Persistence in the Face of Rapid Cell Turnover. J. Virol, 76:10692-10701.

McDonald, D. , Vodicka, M. , Lucero, G. , Svitkina, T.M. , Borisy, G.G., Emerman, M., and Hope, T.J. (2002) Visualization of the intracellular behavior of HIV in living cells. Journal of Cell Biology, 159:441-452.

Dvorin, J.D., Bell, P., Maul, G.G., Yamashita, M., Emerman, M., and Malim, M. H. (2002) Reassessment of the roles of integrase and the central DNA flap in human immunodeficiency virus type-1 nuclear import. J. Virol, 76:12087-12096.


2001

Malim, M. H. and Emerman, M. (2001) HIV-1 sequence variation: drift, shift, and attenuation. Cell, 104:469-472.

Bouyac-Bertoia, M., Dvorin, J.D., Fouchier, R.A.M., Jenkins, Y., Meyer, B.E., Wu, L.I., Emerman, M., Malim, M.H. (2001) HIV-1 infection requires a functional integrase NLS. Molecular Cell, 7:1025-1035.


2000

Emerman, M. (2000) Learning from Lentiviruses. Nature Genetics, 24:8-9.

Holte, S. and Emerman, M. (2000) A competition model for viral inhibition of host cell proliferation. Mathematical Biosciences, 166:69-84.

Harrington R. Wu L. Pullen H. Emerman M. (2000) Direct detection of infectious HIV-1 in blood using a centrifugation-indicator cell assay. Journal of Virological Methods, 88:111-115.

Gummuluru, S., Kinsey, C. M., Emerman, M. (2000). In vitro rapid turnover assay for HIV-1 replication selects for cell-to-cell spread. J. Virol, 74:10882-10891.


1999

Bartz, S.R. and Emerman, M. (1999) HIV-1 Tat induces apoptosis and increases sensitivity to apoptotic signals by up-regulating FLICE/Caspace-8. J. Virol, 73: 1956-1963.

Goh, W.C., Markee, J., Akridge, R.E, Meldorf, M., Musey, L., Karchmer, T., Krone, M., Collier, A., Corey, L., Emerman, M., and McElrath, M.J. (1999) Protection against HIV-1 infection in persons with repeated exposure: evidence for T cell immunity in the absence of inherited CCR5 co-receptor defects. J. Infect. Dis, 179:548-557.

Gummuluru, S. and Emerman, M. (1999) Cell Cycle and Vpr-Mediated Regulation of HIV-1 Expression in Primary and Transformed T Cell Lines. J. Virol, 73:5422-5430.


1998

Goh, W. C, Rogel, M.E, Kinsey, C.M. , Michael, S.F., Fultz, P.N., Nowak, M.A., Hahn, B.H., and Emerman, M. (1998) HIV-1 Vpr increases viral expression by manipulation of the cell cycle: a mechanism for selection of Vpr in vivo. Nature Medicine, 4:65-70.

Vodicka, M.A., Koepp, D.M., Silver, P.A., and Emerman, M. (1998) HIV-1 Vpr interacts with the nuclear transport pathway to promote macrophage infection. Genes & Dev, 12:175-185.

Emerman, M. and Malim, M.H. (1998) HIV-1 regulatory/accessory genes: keys to unraveling viral and host cell biology. Science, 280:1880-1884.


Selected Previous Publications

Selig, L., Benichou, S., Rogel, M. E. , Wu, L. I. , Vodicka, M. A., Sire, J., Benarous, R., and Emerman, M. (1997) Uracil DNA glycosylase specifically interacts with Vpr of both human immunodeficiency virus type 1 and simian immunodeficiency virus of sooty mangabeys, but binding does not correlate with cell cycle arrest. J. Virol, 71:4842-4846.

Stivahtis, G.L., Soares, M.A., Vodicka, M.A., Hahn, B.H., and Emerman, M. (1997) Conservation and host-specificity of Vpr-mediated cell cycle arrest suggest a fundamental role in primate lentiviral evolution and biology. J. Virol, 71:4331-4338.

Vodicka, M.A., Goh, W. C. , Wu, L.I. , Rogel, M.E., Bartz, S.R. Schweickart, V.L., Raport , C.J., and Emerman, M. (1997) Indicator cell Lines for detection of primary strains of human and simian immunodeficiency viruses. Virology, 233:193-198.

Bartz, S.R., Rogel, M.E., and Emerman, M. (1996) HIV-1 Vpr cell cycle control: Vpr is cytostatic and mediates G2 accumulation by a mechanism which differs from DNA damage checkpoint control. J. Virol, 70:2324-2331.

KewalRamani, V.N., and Emerman, M. (1996) Vpx association with mature core structures of HIV-2. Virology, 218:159-168.

Emerman, M. (1996) HIV, Vpr, and the cell cycle. Current Biology, 6:1096-1103.

Fletcher, T.M., Brichacek, B., Sharova, N., Newman, M.A., Stivahatis, G., Sharp, P.M., Emerman, M., Hahn, B.H., and Stevenson, M.A. (1996) Nuclear import and cell cycle arrest functions of the HIV-1 Vpr protein are encoded by two separate genes in HIV-2/SIVSM. EMBO J, 15:101-111.

Sharp, P.M., Bailes, E., Stevenson, M.A., Emerman, M., and Hahn, B.H. (1996) Gene acquisition in HIV and SIV. Nature, 383:586-587.

Rogel, M.E., Wu, L.I., and Emerman, M. (1995) The HIV-1 vpr gene prevents cell proliferation during chronic infection. J. Virol, 69:882-888.

Heinzinger, N., Bukrinsky, M., Haggerty, S., Ragland, A., KewalRamani, V., Lee, M., Gendelman, H., Ratner, L., Stevenson, M., and Emerman, M. (1994) The Vpr protein of HIV-1 influences nuclear targeting of viral nucleic acids in non-dividing host cells. Proc. Natl. Acad. Sci. (USA), 91:7311-7315.

Lewis, P., and Emerman, M. (1994) Passage through mitosis is required for onco-retroviruses, but not for the human immunodeficiency virus. J. Virol, 68: 510-516.

Deminie, C., and Emerman, M. (1993) Incorporation of human immunodeficiency virus Gag proteins into murine leukemia virus virions. J. Virol, 67:6499-6506.

Bukrinsky, M.I., Haggerty, S., Dempsey, M.P., Sharova, N., Adzubei, A., Spitz, L., Lewis, P., Goldfarb, D., Emerman, M., and Stevenson, M. (1993) A nuclear targeting signal within HIV-1 matrix protein that governs infection of non-dividing cells. Nature, 365:666-669.

Lewis, P., Hensel, M., and Emerman, M. (1992) Human immunodeficiency virus infection of cells arrested in the cell-cycle. EMBO J, 11:3053-3058.

Kimpton, J., and Emerman, M. (1992) Detection of replication competent and pseudotyped HIV with a sensitive cell line on the basis of activation of an integrated ß-galactosidase gene. J. Virol, 66:2232-2239.

Peden, K., Emerman, M., and Montagnier, L. (1991) Changes in growth properties on passage in tissue culture of viruses derived from infectious molecular clones of HIV-1/LAI, HIV-1/MAL, and HIV-1/ELI. Virology, 185:661-672.

Emerman, M., Vazeux, R., and Peden, K. (1989) The rev gene product of the human immunodeficiency virus affects envelope-specific RNA localization. Cell, 57:1155-1165.

Cordonnier, A., Montagnier, L., and Emerman, M. (1989) Single amino acid changes in the human immunodeficiency virus envelope affect viral tropism and receptor binding. Nature, 340:571-574.

Guyader, M., Emerman, M., Sonigo, P., Clavel, F., Montagnier, L, and Alizon, M. (1987) Genome organization and transactivation of the human immunodeficiency virus type 2. Nature, 326:662-669.

Emerman, M., Guyader, M., Montagnier, L., Baltimore, D., and Muesing, M.A. (1987) The specificity of the human immunodeficiency virus type 2 transactivator is different from that of the human immunodeficiency virus type 1. The EMBO J, 6:3755-3760.

Emerman, M. and Temin, H.M. (1986) Comparison of promoter suppression in avian and murine retrovirus vectors. Nuc. Acid Res, 14:9381-9396.

Emerman, M. and Temin, H.M. (1984) Genes with promoters in retrovirus vectors can be independently suppressed by an epigenetic mechanism. Cell, 39: 459-4.