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101.  Liu, L. X., N. Heveker, O. T. Fackler, S. Arold, S. Le Gall, K. Janvier, B. M. Peterlin, C. Dumas, O. Schwartz, S. Benichou, and R. Benarous. 2000. Mutation of a conserved residue (D123) required for oligomerization of human immunodeficiency virus type 1 Nef protein abolishes interaction with human thioesterase and results in impairment of Nef biological functions. J Virol. 74:5310-5319. 
102. Nekrep, N., N. Jabrane-Ferrat, and B. M. Peterlin. 2000. Mutations in the bare lymphocyte syndrome define critical steps in the assembly of the regulatory factor X complex.Mol Cell Biol20:4455-4461. 
103. Okamoto, H., T. Cujec, M. Okamoto, B. M. Peterlin, M. Baba, and T. Okamoto. 2000. Fluoroquinoline derivatives, K-37, inhibits RNA-dependent transactivation by Tat of human immunodeficiency virus without affecting DNA-dependent transactivation. Virology 272:272-278.  
104. Okamoto, H., T. P. Cujec, B. M. Peterlin, and T. Okamoto. 2000. HIV-1 replication is inhibited by a pseudo-substrate peptide that blocks Tat transactivation. Virology.270:337-344.
105. Taube, R., K. Fujinaga, D. Irwin, J. Wimmer, M. Geyer, and B. M. Peterlin. 2000. Interactions between equine cyclin T1, Tat, and TAR are disrupted by a leucine-to-valine substitution found in human cyclin T1. J. Virol.  74:892-898. 
106. Fackler, O.T., B.M. Peterlin, and K. Weis.  2001.  Lessons from HIV: Movement of macromolecules inside the cell.  Curr. Mol. Med.1:1-7.
107. Geyer, M., and B. M. Peterlin, 2001, Domain assembly, surface accessibility and sequence conservation in full length HIV-1 Nef.  FEBS letters 24823:1-5. 
108. Geyer, M., and B. M. Peterlin. 2001.  Structure-function relationship in HIV-1 Nef.  EMBO Reports 2:580-585.
109. Kanazawa, S., and B.M. Peterlin, 2001.  Repression of MHC determinants in HIV infection. Microbes Infect. 3:1-7.
110. Mandic, R., O. T. Fackler, M. Geyer, and B. M. Peterlin. 2001. Negative factor from SIV binds to the catalytic subunit of the V-ATPase to internalize CD4 and to increase viral infectivity. Mol. Biol. Cell12:463-473.  
111. Barboric, M., R. Nissen, S. Kanazawa, N. Jabrane-Ferrat, and B.M. Peterlin 2001. NF-kB Associates with P-TEFb to stimulate transcriptional elongation by RNA Polymerase II. Mol. Cell 8:327-337. 
112. Fackler, O.T., P. d’Aloja, A.S. Baur, M. Federico, and B.M. Peterlin. 2001.  Nef from HIV-1F12 acts as a dominant negative inhibitor of virus production and virion infectivity.  J. Virol. 75:6601-6608.  
113. Fackler, O.T., D. Wolf, H.O. Weber, B. Laffert, P. D’Aloja, B. Schuler-Thurner, S. Geffin, K. Saksela, M. Geyer, B.M. Peterlin, G. Schuler, and A. S. Baur.  2001.  A natural variability in the proline-rich motif of Nef modulates HIV-1 replication in primary T cells.  Curr. Biol. 11:1294-1299.. 
114. Kanazawa, S., and B.M. Peterlin. 2001.  Combinations of dominant negative CIITA, p300 or Cdk9 proteins block the expression of MHC II genes.  Internat. Immunol.13:951-958. 
115. Nekrep, N., M. Geyer, and B.M. Peterlin.  2001.  Analysis of ankyrin repeats reveals how a single point mutation in RFXANK results in bare lymphocyte syndrome. Mol. Cell. Biol. 21:5531-5540. 
116. Zheng, Y-H., A. Plemenitas, T. Linnemann, O.T. Fackler, and B.M. Peterlin. 2001.  Nef increases infectivity of HIV via lipid rafts.  Curr. Biol. 11:875-879. 
117. Taube, R., X. Lin, D. Irwin, K. Fujinaga, and B.M.Peterlin. 2002. Interaction between P-TEFb and C-terminal domain of RNA polymerase II activates transcription from sites upstream and downstream of target genes.  Mol. Cell. Biol. 22:321-331. 
118. Geyer, M.O. Fackler, and B. M. Peterlin.  2002.  Subunit H of the V-ATPase involved in endocytosis shows homology to b-adaptin.  Mol. Biol. Cell 13:2045-2056. 
119. Jabrane-Ferrat, N., N. Nekrep, G. Tosi, L. Esserman, and B.M. Peterlin. 2002.  MHC II transcriptional platform:  Assembly of nuclear factor Y and regulatory factor X (RFX) on DNA requires RFX5 dimers.  Mol. Cell. Biol. 22:5616-5625 . 
120. Lind, K.E., Z. Du, K. Fujinaga, B.M. Peterlin, T.L. James.  2002. Structure-based computational database screening, In vitro assay, and NMR assessment of compounds that target TAR RNA.  Chem Biol. 9: 185-193. 
121. Geyer, M., H.F. Yu, O.T. Fackler, and B.M. Peterlin. 2002. V1H binds to AP2 and connects Nef to the endocytic machinery.  J. Biol. Chem. 277:28521-28529. 
122. Lin, X., R. Taube, K. Fujinaga, and B.M. Peterlin. 2002. P-TEFb  containing Cyclin K and Cdk9 activates transcription via RNA.  J. Biol. Chem277:16873-16878. 
123. Linnemann T., Zheng Y.H., Mandic R., B.M. Peterlin.  2002.  Interaction between Nef and Phosphatidylinositol-3-Kinase Leads to Activation of p21-Activated Kinase and Increased Production of HIV. Virology. 15: 246-255. 
124. Eming, R., K. Visconti, F. Hall, C. Sekine, K. Kobayashi, Q. Chen, A. Cope, S. Kanazawa, M. Peterlin, A. Rijnders, A. Boots, J. Meijerink, and G. Sonderstrup.2002. Humanized mice as a model for rheumatoid arthritis. Arthritis Res. 4 Suppl. 3:S133-140.  
125. Greene, W.C.  and B.M. Peterlin. 2002.  Charting HIV’s remarkable voyage through the cell: Basic science as a passport to future therapy.  Nature Med. 8: 673-680. 
126. Tosi, G. and B.M. Peterlin. 2002.  Phosphorylation of CIITA directs its oligomerization, accumulation and increased activity on MHCII promoters.  EMBO J. 21:5467-5476.  
127. Fujinaga, K., J.D. Irwin and B.M. Peterlin.  2002. Optimized chimeras between kinase inactive, mutant Cdk9 and truncated cyclin T1 proteins inhibit efficiently Tat transactivation and HIV replication.  J. Virol. 76:10873-10881.  
128. Fujinaga, K., R. Taube, J.D. Irwin and B.M. Peterlin.  2002. A minimal chimera between human cyclin T1 and Tat binds TAR and activates HIV transcription in murine cells.J. Virol. 76:12934-12939.  
129. Nekrep, N., N. Jabrane-Ferrat, H. Wolf, M. Eibl, M. Geyer and B.M. Peterlin.  2002. Point mutation in a winged-helix DNA-binding motif causes atypical bare lymphocyte syndrome. Nature Immunol. 3:1075-1081.   
130. Fujinaga, K., D. Irwin, R. Taube, T. Kurosu and B.M. Peterlin. 2003. Dynamics of HIV transcription: P-TEFb phosphorylates RD and dissociates negative effectors from TAR. Mol. Cell. Biol. 24:787-795.  
131. Jabrane-Ferrat, N., N. Nekrep, G. Tosi, L. Esserman and B.M. Peterlin. 2003.  MHCII enhanceosome: How is CIITA recruited to DNA-bound activators?  Internat. Immunol. 15:467-475. 
132. Kanazawa, S., L Souchek, G. Evan and B.M. Peterlin. 2003.  P-TEFb mediates transcriptional elongation and cell fates by cMyc.  Oncogene 22:5707-5711.  
133. Lin X., Yen, Y.S. Irwin, D., J. Romeo, L. Huang and B.M. Peterlin.  2003.  Transcriptional profiles of latent HIV in infected individuals:  Effects of Tat on the host and reservoir. J. Virol. 77:8227-8236. 
134. Nekrep, N., J.D. Fontes, M. Geyer and B.M. Peterlin. 2003.  How the lymphocyte loses its clothes.   Immunity 18:453-458.  
135. Peterlin, B.M. and D. Trono. 2003.  Hide, shield and strike back:  How HIV-infected cells avoid immune eradication.  Nat. Rev. Immunol3:97-107. 
136. Uematsu, K., S. Kanazawa, L. You, B. He, Z. Xu, K. Li, B.M. Peterlin, F. McCormick and D.M. Jablons.  2003. Mesotheliomas have over expression of b-catenin through activation of Dvl, and transcriptional activity of b -catenin is correlated to tumorigenicity.  Cancer Res. 63: 4547-4551. 
137. Zhang, F., M. Barboric, K.A. Blackwell, and B. M. Peterlin.  2003.  A model for repression: CTD analogs and PIE-1 block transcriptional elongation by P-TEFb. Genes Dev. 17:748-758. 
138. Zheng, Y.H., and B.M. Peterlin. 2002. Human p32 protein relieves a post-transcriptional block to HIV replication in murine cells.  Nat.Cell. Biol. 5:611-618  
139. Zheng, Y.H., A. Plemenitas, C.J. Fielding, and B.M. Peterlin.  2003. Nef increases the synthesis of and transports cholesterol to lipid rafts and HIV-1 progeny virions. Proc. Natl. Acad. Sci. USA 100:8460-8465. 
140. Costa, L.J., Y.H. Zheng, J. Sabotic, J. Mak, O.T. Fackler, B.M. Peterlin.  2004. Nef binds p6* in GagPol for optimal production and infectivity of HIV-1, J. Virol. 78:5311-5323.  
141. Drozina, G., J. Kohoutek, N. Jabrane-Ferrat and B. M. Peterlin. 2004. MHCII expression in B cells and in disease. Curr. Topics Microbiol. Immunol. 290:147-170.
142. Kurosu, T., and B.M. Peterlin. 2004.  VP16 and ubiquitin: Binding of P-TEFb via its activation domain and ubiquitin facilitates elongation of transcription of target genes. Curr. Biol., 14:1112-1116.  
143. Zheng, Y-H., D. Irwin, T. Kurosu, K. Tokunaga, T. Sata and B.M. Peterlin. 2004.  Human APOBEC3F is another host factor that blocks human immunodeficiency virus type 1 replication. J. Virol. 78:6073-6076.  
144. Kurosu, T., F. Zhang and B.M. Peterlin. 2004.  Transcriptional activity and substrate recognition of cyclin T2 from P-TEFb.  Gene 343:173-179. 
145. Barboric, M., and B.M. Peterlin. 2005.  A new paradigm in eukaryotic biology: Tat and the control of transcriptional elongation. PLoS Biol 3:e76.
146. Zheng, Y-H., N. Lovsin and B.M. Peterlin. 2004.  Newly identified host factors modulate HIV infection.  Imm. Letters 15:225-234. 
147. Zheng, Y-H. and B.M. Peterlin. 2005. Intracellular immunity to HIV-1: newly defined retroviral battles inside infected cells. Retrovirology2:25-38.
148. Barboric, M., F. Zhang, M. Besenicar, A. Plemenitas and B.M. Peterlin. 2005.  Ubiquitylation of Cdk9 by Skp2 faciliates optimal Tat transactivation.  J. Virol. 79:11135-11141.
149. Barboric, M., J. Kohoutek, J.P. Price, D. Blazek, D.H. Price, and B.M.Peterlin. 2005. Interplay between 7SK snRNA and oppositely charged regions in HEXIM1 direct the inhibition of P-TEFb. Embo J 24:4291-303.

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