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Finding, Conducting, and Nurturing Science: A Virologist's Memoir.

Skalka AMA.

Annu Rev Virol. 2017 Sep 29;4(1):1-35. doi: 10.1146/annurev-virology-101416-042011. Epub 2017 May 26.


Successes and challenges with retroviral enzymes.

Skalka AM, Andrake MD, Katz RA.

Postepy Biochem. 2016;62(3):280-285. Review.


The conformational feasibility for the formation of reaching dimer in ASV and HIV integrase: a molecular dynamics study.

Balasubramanian S, Rajagopalan M, Bojja RS, Skalka AM, Andrake MD, Ramaswamy A.

J Biomol Struct Dyn. 2017 Dec;35(16):3469-3485. doi: 10.1080/07391102.2016.1257955. Epub 2016 Nov 28.


Retroviral Integrase: Then and Now.

Andrake MD, Skalka AM.

Annu Rev Virol. 2015 Nov;2(1):241-64. doi: 10.1146/annurev-virology-100114-055043. Review.


Retroviral DNA Transposition: Themes and Variations.

Skalka AM.

Microbiol Spectr. 2014 Dec;2(5):MDNA300052014.


Intasome architecture and chromatin density modulate retroviral integration into nucleosome.

Benleulmi MS, Matysiak J, Henriquez DR, Vaillant C, Lesbats P, Calmels C, Naughtin M, Leon O, Skalka AM, Ruff M, Lavigne M, Andreola ML, Parissi V.

Retrovirology. 2015 Feb 7;12:13. doi: 10.1186/s12977-015-0145-9.


The interferon-inducible antiviral protein Daxx is not essential for interferon-mediated protection against avian sarcoma virus.

Haugh KA, Shalginskikh N, Nogusa S, Skalka AM, Katz RA, Balachandran S.

Virol J. 2014 May 28;11:100. doi: 10.1186/1743-422X-11-100.


HIV: Integration triggers death.

Skalka AM.

Nature. 2013 Jun 20;498(7454):305-6. doi: 10.1038/nature12254. Epub 2013 Jun 5. No abstract available.


Architecture and assembly of HIV integrase multimers in the absence of DNA substrates.

Bojja RS, Andrake MD, Merkel G, Weigand S, Dunbrack RL Jr, Skalka AM.

J Biol Chem. 2013 Mar 8;288(10):7373-86. doi: 10.1074/jbc.M112.434431. Epub 2013 Jan 14.


Retroviral DNA methylation and epigenetic repression are mediated by the antiviral host protein Daxx.

Shalginskikh N, Poleshko A, Skalka AM, Katz RA.

J Virol. 2013 Feb;87(4):2137-50. doi: 10.1128/JVI.02026-12. Epub 2012 Dec 5.


Localization of ASV integrase-DNA contacts by site-directed crosslinking and their structural analysis.

Peletskaya E, Andrake M, Gustchina A, Merkel G, Alexandratos J, Zhou D, Bojja RS, Satoh T, Potapov M, Kogon A, Potapov V, Wlodawer A, Skalka AM.

PLoS One. 2011;6(12):e27751. doi: 10.1371/journal.pone.0027751. Epub 2011 Dec 1.


Retroviral integrases promote fraying of viral DNA ends.

Katz RA, Merkel G, Andrake MD, Roder H, Skalka AM.

J Biol Chem. 2011 Jul 22;286(29):25710-8. doi: 10.1074/jbc.M111.229179. Epub 2011 May 27.


Architecture of a full-length retroviral integrase monomer and dimer, revealed by small angle X-ray scattering and chemical cross-linking.

Bojja RS, Andrake MD, Weigand S, Merkel G, Yarychkivska O, Henderson A, Kummerling M, Skalka AM.

J Biol Chem. 2011 May 13;286(19):17047-59. doi: 10.1074/jbc.M110.212571. Epub 2011 Mar 15.


Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the parvoviridae and circoviridae are more than 40 to 50 million years old.

Belyi VA, Levine AJ, Skalka AM.

J Virol. 2010 Dec;84(23):12458-62. doi: 10.1128/JVI.01789-10. Epub 2010 Sep 22.


Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes.

Belyi VA, Levine AJ, Skalka AM.

PLoS Pathog. 2010 Jul 29;6(7):e1001030. doi: 10.1371/journal.ppat.1001030.


Identification of a functional network of human epigenetic silencing factors.

Poleshko A, Einarson MB, Shalginskikh N, Zhang R, Adams PD, Skalka AM, Katz RA.

J Biol Chem. 2010 Jan 1;285(1):422-33. doi: 10.1074/jbc.M109.064667. Epub 2009 Oct 30.


Comparison of metal-dependent catalysis by HIV-1 and ASV integrase proteins using a new and rapid, moderate throughput assay for joining activity in solution.

Andrake MD, Ramcharan J, Merkel G, Zhao XZ, Burke TR Jr, Skalka AM.

AIDS Res Ther. 2009 Jun 29;6:14. doi: 10.1186/1742-6405-6-14.


Oligonucleotide-based assays for integrase activity.

Merkel G, Andrake MD, Ramcharan J, Skalka AM.

Methods. 2009 Apr;47(4):243-8. doi: 10.1016/j.ymeth.2008.10.024. Epub 2008 Nov 14. Review.


Nuclear import of Avian Sarcoma Virus integrase is facilitated by host cell factors.

Andrake MD, Sauter MM, Boland K, Goldstein AD, Hussein M, Skalka AM.

Retrovirology. 2008 Aug 7;5:73. doi: 10.1186/1742-4690-5-73.


Identification of cellular proteins that maintain retroviral epigenetic silencing: evidence for an antiviral response.

Poleshko A, Palagin I, Zhang R, Boimel P, Castagna C, Adams PD, Skalka AM, Katz RA.

J Virol. 2008 Mar;82(5):2313-23. Epub 2007 Dec 19.


Mode of inhibition of HIV-1 Integrase by a C-terminal domain-specific monoclonal antibody.

Ramcharan J, Colleluori DM, Merkel G, Andrake MD, Skalka AM.

Retrovirology. 2006 Jun 21;3:34.


Targeting Tn5 transposase identifies human immunodeficiency virus type 1 inhibitors.

Ason B, Knauss DJ, Balke AM, Merkel G, Skalka AM, Reznikoff WS.

Antimicrob Agents Chemother. 2005 May;49(5):2035-43.


Retroviral DNA integration and the DNA damage response.

Skalka AM, Katz RA.

Cell Death Differ. 2005 Aug;12 Suppl 1:971-8. Review.


Caffeine inhibits human immunodeficiency virus type 1 transduction of nondividing cells.

Daniel R, Marusich E, Argyris E, Zhao RY, Skalka AM, Pomerantz RJ.

J Virol. 2005 Feb;79(4):2058-65.


Effects of cell cycle status on early events in retroviral replication.

Katz RA, Greger JG, Skalka AM.

J Cell Biochem. 2005 Apr 1;94(5):880-9. Review.


Genome-wide analyses of avian sarcoma virus integration sites.

Narezkina A, Taganov KD, Litwin S, Stoyanova R, Hayashi J, Seeger C, Skalka AM, Katz RA.

J Virol. 2004 Nov;78(21):11656-63.


Histone H2AX is phosphorylated at sites of retroviral DNA integration but is dispensable for postintegration repair.

Daniel R, Ramcharan J, Rogakou E, Taganov KD, Greger JG, Bonner W, Nussenzweig A, Katz RA, Skalka AM.

J Biol Chem. 2004 Oct 29;279(44):45810-4. Epub 2004 Aug 11.


Integrase-specific enhancement and suppression of retroviral DNA integration by compacted chromatin structure in vitro.

Taganov KD, Cuesta I, Daniel R, Cirillo LA, Katz RA, Zaret KS, Skalka AM.

J Virol. 2004 Jun;78(11):5848-55.


Transduction of terminally differentiated neurons by avian sarcoma virus.

Greger JG, Katz RA, Taganov K, Rall GF, Skalka AM.

J Virol. 2004 May;78(9):4902-6.


Characterization of a naphthalene derivative inhibitor of retroviral integrases.

Daniel R, Myers CB, Kulkosky J, Taganov K, Greger JG, Merkel G, Weber IT, Harrison RW, Skalka AM.

AIDS Res Hum Retroviruses. 2004 Feb;20(2):135-44.


The base excision repair enzyme MED1 mediates DNA damage response to antitumor drugs and is associated with mismatch repair system integrity.

Cortellino S, Turner D, Masciullo V, Schepis F, Albino D, Daniel R, Skalka AM, Meropol NJ, Alberti C, Larue L, Bellacosa A.

Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):15071-6. Epub 2003 Nov 12.


Evidence that the retroviral DNA integration process triggers an ATR-dependent DNA damage response.

Daniel R, Kao G, Taganov K, Greger JG, Favorova O, Merkel G, Yen TJ, Katz RA, Skalka AM.

Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4778-83. Epub 2003 Apr 4.


Metal-dependent inhibition of HIV-1 integrase.

Neamati N, Lin Z, Karki RG, Orr A, Cowansage K, Strumberg D, Pais GC, Voigt JH, Nicklaus MC, Winslow HE, Zhao H, Turpin JA, Yi J, Skalka AM, Burke TR Jr, Pommier Y.

J Med Chem. 2002 Dec 19;45(26):5661-70.


Functional oligomeric state of avian sarcoma virus integrase.

Bao KK, Wang H, Miller JK, Erie DA, Skalka AM, Wong I.

J Biol Chem. 2003 Jan 10;278(2):1323-7. Epub 2002 Nov 21.


Transduction of interphase cells by avian sarcoma virus.

Katz RA, Greger JG, Darby K, Boimel P, Rall GF, Skalka AM.

J Virol. 2002 Jun;76(11):5422-34.


Mapping the epitope of an inhibitory monoclonal antibody to the C-terminal DNA-binding domain of HIV-1 integrase.

Yi J, Cheng H, Andrake MD, Dunbrack RL Jr, Roder H, Skalka AM.

J Biol Chem. 2002 Apr 5;277(14):12164-74. Epub 2002 Jan 22.


Characterization of retrovirus-host DNA junctions in cells deficient in nonhomologous-end joining.

Taganov K, Daniel R, Katz RA, Favorova O, Skalka AM.

J Virol. 2001 Oct;75(19):9549-52.


Role of DNA end distortion in catalysis by avian sarcoma virus integrase.

Katz RA, DiCandeloro P, Kukolj G, Skalka AM.

J Biol Chem. 2001 Sep 7;276(36):34213-20. Epub 2001 Jul 5.


Computational analysis of retrovirus-induced scid cell death.

Daniel R, Litwin S, Katz RA, Skalka AM.

J Virol. 2001 Apr;75(7):3121-8.


Wortmannin potentiates integrase-mediated killing of lymphocytes and reduces the efficiency of stable transduction by retroviruses.

Daniel R, Katz RA, Merkel G, Hittle JC, Yen TJ, Skalka AM.

Mol Cell Biol. 2001 Feb;21(4):1164-72. Erratum in: Mol Cell Biol 2001 Apr;21(7):2617.


Modeling the late steps in HIV-1 retroviral integrase-catalyzed DNA integration.

Brin E, Yi J, Skalka AM, Leis J.

J Biol Chem. 2000 Dec 15;275(50):39287-95.


Atomic Resolution Structures of the Core Domain of Avian Sarcoma Virus Integrase and Its D64N Mutant.

Lubkowski J, Dauter Z, Yang F, Alexandratos J, Merkel G, Skalka AM, Wlodawer A.

Biochemistry. 1999 Nov 9;38(45):15060. No abstract available.


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