Anna M. Skalka, PhD-Publications

Original Articles
Published symposia proceedings
Book chapters
Method papers
Scholarly reviews.
News and views
Textbooks

Original Articles

Andrake MD, Sauter MM, Boland K, Goldstein AD, Hussein M, Skalka AM. Nuclear import of Avian Sarcoma Virus integrase is facilitated by host cell factors. Retrovirology. 2008;5:73.
Poleshko A, Palagin I, Zhang R, Boimel P, Castagna C, Adams PD, Skalka AM, Katz RA. Identification of cellular proteins that maintain retroviral epigenetic silencing: evidence for an antiviral response. J Virol. 2008 Mar;82(5):2313-23.
Merkel G, Andrake MD, Ramcharan J, Skalka AM. Oligonucleotide-based assays for integrase activity. Methods. 2008 Nov 13.
Katz RA, Jack-Scott E, Narezkina A, Palagin I, Boimel P, Kulkosky J, Nicolas E, Greger JG, Skalka AM. High-frequency epigenetic repression and silencing of retroviruses can be antagonized by histone deacetylase inhibitors and transcriptional activators, but uniform reactivation in cell clones is restricted by additional mechanisms. J Virol. 2007 Mar;81(6):2592-604.
Ramcharan J, Colleluori DM, Merkel G, Andrake MD, Skalka AM. Mode of inhibition of HIV-1 Integrase by a C-terminal domain-specific monoclonal antibody. Retrovirology. 2006;3:34.
Ason B, Knauss DJ, Balke AM, Merkel G, Skalka AM, Reznikoff WS. Targeting Tn5 transposase identifies human immunodeficiency virus type 1 inhibitors. Antimicrob Agents Chemother. 2005 May;49(5):2035-43.
Daniel R, Marusich E, Argyris E, Zhao RY, Skalka AM, Pomerantz RJ. Caffeine inhibits human immunodeficiency virus type 1 transduction of nondividing cells. J Virol. 2005 Feb;79(4):2058-65.
Greger JG, Katz RA, Ishov AM, Maul GG, Skalka AM. The cellular protein daxx interacts with avian sarcoma virus integrase and viral DNA to repress viral transcription. J Virol. 2005 Apr;79(8):4610-8.
Daniel R, Ramcharan J, Rogakou E, Taganov KD, Greger JG, Bonner W, Nussenzweig A, Katz RA, Skalka AM. Histone H2AX is phosphorylated at sites of retroviral DNA integration but is dispensable for postintegration repair. J Biol Chem. 2004 Oct 29;279(44):45810-4.
Narezkina A, Taganov KD, Litwin S, Stoyanova R, Hayashi J, Seeger C, Skalka AM, Katz RA. Genome-wide analyses of avian sarcoma virus integration sites. J Virol. 2004 Nov;78(21):11656-116563.
Daniel R, Greger JG, Katz RA, Taganov KD, Wu X, Kappes JC, Skalka AM. Evidence that stable retroviral transduction and cell survival following DNA integration depend on components of the nonhomologous end joining repair pathway. J Virol. 2004 Aug;78(16):8573-81.
Daniel R, Myers CB, Kulkosky J, Taganov K, Greger JG, Merkel G, Weber IT, Harrison RW, Skalka AM. Characterization of a naphthalene derivative inhibitor of retroviral integrases. AIDS Res Hum Retroviruses. 2004 Feb;20(2):135-44.
Taganov KD, Cuesta I, Daniel R, Cirillo LA, Katz RA, Zaret KS, Skalka AM. Integrase-specific enhancement and suppression of retroviral DNA integration by compacted chromatin structure in vitro. J Virol. 2004 Jun;78(11):5848-55.
Greger JG, Katz RA, Taganov K, Rall GF, Skalka AM. Transduction of terminally differentiated neurons by avian sarcoma virus. J Virol. 2004 May;78(9):4902-6.
Katz RA, Greger JG, Boimel P, Skalka AM. Human immunodeficiency virus type 1 DNA nuclear import and integration are mitosis independent in cycling cells. J Virol. 2003 Dec;77(24):13412-7.
Cortellino S, Turner D, Masciullo V, Schepis F, Albino D, Daniel R, Skalka AM, Meropol NJ, Alberti C, Larue L, Bellacosa A. The base excision repair enzyme MED1 mediates DNA damage response to antitumor drugs and is associated with mismatch repair system integrity. Proc Natl Acad Sci USA. 2003 Dec 9;100(25):15071-6.
Daniel R, Kao G, Taganov K, Greger JG, Favorova O, Merkel G, Yen TJ, Katz RA, Skalka AM. Evidence that the retroviral DNA integration process triggers an ATR-dependent DNA damage response. Proc Natl Acad Sci USA. 2003 Apr 15;100(8):4778-83.
Bao KK, Wang H, Miller JK, Erie DA, Skalka AM, Wong I. Functional oligomeric state of avian sarcoma virus integrase. J Biol Chem. 2003 Jan 10;278(2):1323-7.
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. Metal-dependent inhibition of HIV-1 integrase. J Med Chem. 2002 Dec 19;45(26):5661-70.
Bao KK, Skalka AM, Wong I. Presteady-state analysis of avian sarcoma virus integrase. II. Reverse-polarity substrates identify preferential processing of the U3-U5 pair. J Biol Chem. 2002 Apr 5;277(14):12099-108.
Bao KK, Skalka AM, Wong I. Presteady-state analysis of avian sarcoma virus integrase. I. A splicing activity and structure-function implications for cognate site recognition. J Biol Chem. 2002 Apr 5;277(14):12089-98.
Katz RA, Greger JG, Darby K, Boimel P, Rall GF, Skalka AM. Transduction of interphase cells by avian sarcoma virus. J Virol. 2002 Jun;76(11):5422-34.
Yi J, Cheng H, Andrake MD, Dunbrack RL, Jr., Roder H, Skalka AM. Mapping the epitope of an inhibitory monoclonal antibody to the C-terminal DNA-binding domain of HIV-1 integrase. J Biol Chem. 2002 Apr 5;277(14):12164-74.
Katz RA, DiCandeloro P, Kukolj G, Skalka AM. Role of DNA end distortion in catalysis by avian sarcoma virus integrase. J Biol Chem. 2001 Sep 7;276(36):34213-20.
Taganov K, Daniel R, Katz RA, Favorova O, Skalka AM. Characterization of retrovirus-host DNA junctions in cells deficient in nonhomologous-end joining. J Virol. 2001 Oct;75(19):9549-52.
Daniel R, Litwin S, Katz RA, Skalka AM. Computational analysis of retrovirus-induced scid cell death. J Virol. 2001 Apr;75(7):3121-8.
Daniel R, Katz RA, Merkel G, Hittle JC, Yen TJ, Skalka AM. Wortmannin potentiates integrase-mediated killing of lymphocytes and reduces the efficiency of stable transduction by retroviruses. Mol Cell Biol. 2001 Feb;21(4):1164-72.
Yi J, Skalka AM. Mapping epitopes of monoclonal antibodies against HIV-1 integrase with limited proteolysis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Biopolymers. 2000;55(4):308-18.
Brin E, Yi J, Skalka AM, Leis J. Modeling the late steps in HIV-1 retroviral integrase-catalyzed DNA integration. J Biol Chem. 2000 Dec 15;275(50):39287-95.
Yi J, Arthur JW, Dunbrack RL, Jr., Skalka AM. An inhibitory monoclonal antibody binds at the turn of the helix-turn-helix motif in the N-terminal domain of HIV-1 integrase. J Biol Chem. 2000 Dec 8;275(49):38739-48.
Coleman J, Eaton S, Merkel G, Skalka AM, Laue T. Characterization of the self association of Avian sarcoma virus integrase by analytical ultracentrifugation. J Biol Chem. 1999 Nov 12;274(46):32842-6.
Chan AW, Kukolj G, Skalka AM, Bremel RD. Timing of DNA integration, transgenic mosaicism, and pronuclear microinjection. Mol Reprod Dev. 1999 Apr;52(4):406-13.
Lubkowski J, Dauter Z, Yang F, Alexandratos J, Merkel G, Skalka AM, Wlodawer A. Atomic resolution structures of the core domain of avian sarcoma virus integrase and its D64N mutant. Biochemistry. 1999 Oct 12;38(41):13512-22.
Lubkowski J, Dauter Z, Yang F, Alexandratos J, Merkel G, Skalka AM, Wlodawer A. Atomic resolution structures of the core domain of Avian Sarcoma Virus integrase and its D64N mutant. Biochemistry.1999 Nov 9;38(45):15060.
Yi J, Asante-Appiah E, Skalka AM. Divalent cations stimulate preferential recognition of a viral DNA end by HIV-1 integrase. Biochemistry. 1999 Jun 29;38(26):8458-68.
Daniel R, Katz RA, Skalka AM. A role for DNA-PK in retroviral DNA integration. Science. 1999 Apr 23;284(5414):644-7.
Hindmarsh P, Ridky T, Reeves R, Andrake M, Skalka AM, Leis J. HMG protein family members stimulate human immunodeficiency virus type 1 and avian sarcoma virus concerted DNA integration in vitro. J Virol. 1999 Apr;73(4):2994-3003.
Asante-Appiah E, Skalka AM. HIV-1 integrase: structural organization, conformational changes, and catalysis. Adv Virus Res. 1999;52:351-69.
Kukolj G, Katz RA, Skalka AM. Characterization of the nuclear localization signal in the avian sarcoma virus integrase. Gene. 1998 Nov 26;223(1-2):157-63.
Lubkowski J, Yang F, Alexandratos J, Merkel G, Katz RA, Gravuer K, Skalka AM, Wlodawer A. Structural basis for inactivating mutations and pH-dependent activity of avian sarcoma virus integrase. J Biol Chem. 1998 Dec 4;273(49):32685-9.
Asante-Appiah E, Seeholzer SH, Skalka AM. Structural determinants of metal-induced conformational changes in HIV-1 integrase. J Biol Chem. 1998 Dec 25;273(52):35078-87.
Bouck J, Litwin S, Skalka AM, Katz RA. In vivo selection for intronic splicing signals from a randomized pool. Nucleic Acids Res. 1998 Oct 1;26(19):4516-23.
Katz RA, Gravuer K, Skalka AM. A preferred target DNA structure for retroviral integrase in vitro. J Biol Chem. 1998 Sep 11;273(37):24190-5.
Bouck J, Fu XD, Skalka AM, Katz RA. Role of the constitutive splicing factors U2AF65 and SAP49 in suboptimal RNA splicing of novel retroviral mutants. J Biol Chem. 1998 Jun 12;273(24):15169-76.
Lubkowski J, Yang F, Alexandratos J, Wlodawer A, Zhao H, Burke TR, Jr., Neamati N, Pommier Y, Merkel G, Skalka AM. Structure of the catalytic domain of avian sarcoma virus integrase with a bound HIV-1 integrase-targeted inhibitor. Proc Natl Acad Sci USA. 1998 Apr 28;95(9):4831-6.
Asante-Appiah E, Merkel G, Skalka AM. Purification of untagged retroviral integrases by immobilized metal ion affinity chromatography. Protein Expr Purif. 1998 Feb 12(1):105-10.
Asante-Appiah E, Skalka AM. Molecular mechanisms in retrovirus DNA integration. Antiviral Res. 1997 Dec;36(3):139-56.
Bujacz G, Alexandratos J, Wlodawer A, Merkel G, Andrake M, Katz RA, Skalka AM. Binding of different divalent cations to the active site of avian sarcoma virus integrase and their effects on enzymatic activity. J Biol Chem. 1997 Jul 18;272(29):18161-8.
Asante-Appiah E, Skalka AM. A metal-induced conformational change and activation of HIV-1 integrase. J Biol Chem. 1997 Jun 27;272(26):16196-205.
Kukolj G, Jones KS, Skalka AM. Subcellular localization of avian sarcoma virus and human immunodeficiency virus type 1 integrases. J Virol. 1997 Jan;71(1):843-7.
Levy-Mintz P, Duan L, Zhang H, Hu B, Dornadula G, Zhu M, Kulkosky J, Bizub-Bender D, Skalka AM, Pomerantz RJ. Intracellular expression of single-chain variable fragments to inhibit early stages of the viral life cycle by targeting human immunodeficiency virus type 1 integrase. J Virol. 1996 Dec;70(12):8821-32.
Aiyar A, Hindmarsh P, Skalka AM, Leis J. Concerted integration of linear retroviral DNA by the avian sarcoma virus integrase in vitro: dependence on both long terminal repeat termini. J Virol. 1996 Jun;70(6):3571-80.
Ridky TW, Bizub-Bender D, Cameron CE, Weber IT, Wlodawer A, Copeland T, Skalka AM, Leis J. Programming the Rous sarcoma virus protease to cleave new substrate sequences. J Biol Chem. 1996 May 3;271(18):10538-44.
Katz RA, Merkel G, Skalka AM. Targeting of retroviral integrase by fusion to a heterologous DNA binding domain: in vitro activities and incorporation of a fusion protein into viral particles. Virology. 1996 Mar 1;217(1):178-90.
Bujacz G, Jaskolski M, Alexandratos J, Wlodawer A, Merkel G, Katz RA, Skalka AM. The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations. Structure. 1996 Jan 15;4(1):89-96.
Mirzabekov AD, Bernardi G, Cohen SN, Grunberg-Manago M, Kisselev LL, Rich A, Skalka AM, Szybalski W, Zachau HG. In memoriam Alexander A. Bayev, 1904-1994. Gene. 1995 Aug 30;162(1):1-3.
Andrake MD, Skalka AM. Multimerization determinants reside in both the catalytic core and C terminus of avian sarcoma virus integrase. J Biol Chem. 1995 Dec 8;270(49):29299-306.
Kukolj G, Skalka AM. Enhanced and coordinated processing of synapsed viral DNA ends by retroviral integrases in vitro. Genes Dev. 1995 Oct 15;9(20):2556-67.
Bujacz G, Jaskolski M, Alexandratos J, Wlodawer A, Merkel G, Katz RA, Skalka AM. High-resolution structure of the catalytic domain of avian sarcoma virus integrase. J Mol Biol. 1995 Oct 20;253(2):333-46.
Müller B, Bizub-Bender D, Andrake MD, Jones KS, Skalka AM. Monoclonal antibodies against Rous sarcoma virus integrase protein exert differential effects on integrase function in vitro. J Virol. 1995 Sep;69(9):5631-9.
Bouck J, Fu XD, Skalka AM, Katz RA. Genetic selection for balanced retroviral splicing: novel regulation involving the second step can be mediated by transitions in the polypyrimidine tract. Mol Cell Biol. 1995 May;15(5):2663-71.
Kulkosky J, Katz RA, Merkel G, Skalka AM. Activities and substrate specificity of the evolutionarily conserved central domain of retroviral integrase. Virology. 1995 Jan 10;206(1):448-56.
Cameron CE, Burstein H, Bizub-Bender D, Ridky T, Weber IT, Wlodawer A, Skalka AM, Leis J. Identification of amino acid residues of the retroviral aspartic proteinases important for substrate specificity and catalytic efficiency. Adv Exp Med Biol. 1995;362:399-406.
Bizub-Bender D, Kulkosky J, Skalka AM. Monoclonal antibodies against HIV type 1 integrase: clues to molecular structure. AIDS Res Hum Retroviruses. 1994 Sep;10(9):1105-15.
Cameron CE, Ridky TW, Shulenin S, Leis J, Weber IT, Copeland T, Wlodawer A, Burstein H, Bizub-Bender D, Skalka AM. Mutational analysis of the substrate binding pockets of the Rous sarcoma virus and human immunodeficiency virus-1 proteases. J Biol Chem. 1994 Apr 15;269(15):11170-7.
Kulkosky J, Skalka AM. Molecular mechanism of retroviral DNA integration. Pharmacol Ther. 1994;61(1-2):185-203.
Müller B, Jones KS, Merkel GW, Skalka AM. Rapid solution assays for retroviral integration reactions and their use in kinetic analyses of wild-type and mutant Rous sarcoma virus integrases. Proc Natl Acad Sci USA. 1993 Dec 15;90(24):11633-7.
Katz RA, Mack JP, Merkel G, Kulkosky J, Ge Z, Leis J, Skalka AM. Requirement for a conserved serine in both processing and joining activities of retroviral integrase. Proc Natl Acad Sci USA 1992 Aug 1;89(15):6741-5.
Vogt VM, Burstein H, Skalka AM. Proteolysis in the maturation of avian retroviruses does not require calcium. Virology 1992 Aug;189(2):771-4.
Jones KS, Coleman J, Merkel GW, Laue TM, Skalka AM. Retroviral integrase functions as a multimer and can turn over catalytically. J Biol Chem. 1992 Aug 15;267(23):16037-40.
Grinde B, Cameron CE, Leis J, Weber IT, Wlodawer A, Burstein H, Skalka AM. Analysis of substrate interactions of the Rous sarcoma virus wild type and mutant proteases and human immunodeficiency virus-1 protease using a set of systematically altered peptide substrates. J Biol Chem. 1992 May 15;267(14):9491-8.
Grinde B, Cameron CE, Leis J, Weber IT, Wlodawer A, Burstein H, Bizub D, Skalka AM. Mutations that alter the activity of the Rous sarcoma virus protease. J Biol Chem. 1992 May 15;267(14):9481-90.
Kulkosky J, Jones KS, Katz RA, Mack JP, Skalka AM. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol Cell Biol. 1992 May;12(5):2331-8.
Burstein H, Bizub D, Kotler M, Schatz G, Vogt VM, Skalka AM. Processing of avian retroviral gag polyprotein precursors is blocked by a mutation at the NC-PR cleavage site. J Virol. 1992 Mar;66(3):1781-5.
Burstein H, Bizub D, Skalka AM. Assembly and processing of avian retroviral gag polyproteins containing linked protease dimers. J Virol. 1991 Nov;65(11):6165-72.
Cochrane AW, Jones KS, Beidas S, Dillon PJ, Skalka AM, Rosen CA. Identification and characterization of intragenic sequences which repress human immunodeficiency virus structural gene expression. J Virol. 1991 Oct;65(10):5305-13.
Katzman M, Mack JP, Skalka AM, Leis J. A covalent complex between retroviral integrase and nicked substrate DNA. Proc Natl Acad Sci USA. 1991 Jun 1;88(11):4695-9.
Fu XD, Katz RA, Skalka AM, Maniatis T. The role of branchpoint and 3'-exon sequences in the control of balanced splicing of avian retrovirus RNA. Genes Dev. 1991 Feb;5(2):211-20.
Bizub D, Weber IT, Cameron CE, Leis JP, Skalka AM. A range of catalytic efficiencies with avian retroviral protease subunits genetically linked to form single polypeptide chains. J Biol Chem. 1991 Mar 15;266(8):4951-8.
Khan E, Mack JP, Katz RA, Kulkosky J, Skalka AM. Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucleic Acids Res. 1991 Feb 25;19(4):851-60.
Katz RA, Merkel G, Kulkosky J, Leis J, Skalka AM. The avian retroviral IN protein is both necessary and sufficient for integrative recombination in vitro. Cell. 1990 Oct 5;63(1):87-95.
Kulkosky J, Katz RA, Skalka AM. Terminal nucleotides of the preintegrative linear form of HIV-1 DNA deduced from the sequence of circular DNA junctions. J Acquir Immune Defic Syndr. 1990;3(9):852-8.
Katz RA, Skalka AM. Control of retroviral RNA splicing through maintenance of suboptimal processing signals. Mol Cell Biol. 1990 Feb;10(2):696-704.
Katzman M, Katz RA, Skalka AM, Leis J. The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration. J Virol. 1989 Dec;63(12):5319-27.
Skalka AM. Retroviral proteases: first glimpses at the anatomy of a processing machine. Cell. 1989 Mar 24;56(6):911-3.
Weber IT, Miller M, Jaskolski M, Leis J, Skalka AM, Wlodawer A. Molecular modeling of the HIV-1 protease and its substrate binding site. Science. 1989 Feb 17;243(4893):928-31.
Kotler M, Danho W, Katz RA, Leis J, Skalka AM. Avian retroviral protease and cellular aspartic proteases are distinguished by activities on peptide substrates. J Biol Chem. 1989 Feb 25;264(6):3428-35.
Bizub D, Fischberg-Bender E, Heimer EP, Felix A, Skalka AM. Detection of transforming ras proteins containing leucine at position 61 by a new mouse monoclonal antibody, ras(53-69)Leu61. Cancer Res. 1989 Nov 15;49(22):6425-31.
Bizub D, Blair D, Alvord G, Skalka AM. Correlation between H-ras p21TLeu61 protein content and tumorigenicity of NIH3T3 cells. Oncogene. 1988 Oct;3(4):443-8.
Kotler M, Katz RA, Skalka AM. Activity of avian retroviral protease expressed in Escherichia coli. J Virol. 1988 Aug;62(8):2696-700.
Leis, J, Baltimore, D, Bishop, JM, Coffin, J, Fleissner E, Goff SP, Vogt V, Robinson H, and Skalka, AM. Standardized and simplified nomenclature for proteins common to all retroviruses. J Virol. 62:1808-1809, 1988.
Katz RA, Kotler M, Skalka AM. cis-acting intron mutations that affect the efficiency of avian retroviral RNA splicing: implication for mechanisms of control. J Virol. 1988 Aug;62(8):2686-95.
Terry R, Soltis DA, Katzman M, Cobrinik D, Leis J, Skalka AM. Properties of avian sarcoma-leukosis virus pp32-related pol-endonucleases produced in Escherichia coli. J Virol. 1988 Jul;62(7):2358-65.
Soltis DA, Skalka AM. Independent expression of the α and β chains of ASLV reverse transcriptase in Escherichia coli: characterization of enzymatic activities. Proc Natl Acad Sci USA. 1988;85:3372-6.
Kotler M, Katz RA, Danho W, Leis J, Skalka AM. Synthetic peptides as substrates and inhibitors of a retroviral protease. Proc Natl Acad Sci USA. 1988 Jun;85(12):4185-9.
Fu XD, Katz RA, Skalka AM, Leis J. Site-directed mutagenesis of the avian retrovirus nucleocapsid protein, pp 12. Mutation which affects RNA binding in vitro blocks viral replication. J Biol Chem. 1988 Feb 15;263(5):2140-5.
Morris-Vasios C, Kochan JP, Skalka AM. Avian sarcoma-leukosis virus pol-endo proteins expressed independently in mammalian cells accumulate in the nucleus but can be directed to other cellular compartments. J Virol. 1988 Jan;62(1):349-53.
Katz RA, Skalka AM. A C-terminal domain in the avian sarcoma-leukosis virus pol gene product is not essential for viral replication. J Virol. 1988 Feb;62(2):528-33.
Bizub D, Heimer EP, Felix A, Chizzonite R, Wood A, Skalka AM, Slater D, Aldrich TH, Furth ME. Antisera to the variable region of ras oncogene proteins, and specific detection of H-ras expression in an experimental model of chemical carcinogenesis. Oncogene. 1987 May;1(2):131-42.
Shoeman RL, Young D, Pottathil R, Victor J, Conroy RR, Crowl RM, Coleman T, Heimer E, Lai C-Y, Ganguly K, Reddy EP, Skalka AM, Pine PR, Khan FR, Weissbach H. Comparison of recombinant HIV gag precurson and gag/env fusion proteins and a synthetic env peptide as diagnostic reagents. Anal Biochem. 1987;161:370-99.
Katz RA, Fu XD, Skalka AM, Leis J. Avian retrovirus nucleocapsid protein, pp12, produced in Escherichia coli has biochemical properties identical to unphosphorylated viral protein. Gene. 1986;50(1-3):361-9.
Cobrinik D, Katz R, Terry R, Skalka AM, Leis J. Avian sarcoma and leukosis virus pol-endonuclease recognition of the tandem long terminal repeat junction: minimum site required for cleavage is also required for viral growth. J Virol. 1987 Jun;61(6):1999-2008.
Alexander F, Leis J, Soltis DA, Crowl RM, Danho W, Poonian MS, Pan YC, Skalka AM. Proteolytic processing of avian sarcoma and leukosis viruses pol-endo recombinant proteins reveals another pol gene domain. J Virol. 1987 Feb;61(2):534-42.
Katz RA, Terry RW, Skalka AM. A conserved cis-acting sequence in the 5' leader of avian sarcoma virus RNA is required for packaging. J Virol. 1986 Jul;59(1):163-7.
Bizub D, Wood AW, Skalka AM. Mutagenesis of the Ha-ras oncogene in mouse skin tumors induced by polycyclic aromatic hydrocarbons. Proc Natl Acad Sci USA. 1986 Aug;83(16):6048-52.
Kramer RA, Schaber MD, Skalka AM, Ganguly K, Wong-Staal F, Reddy EP. HTLV-III gag protein is processed in yeast cells by the virus pol-protease. Science. 1986 Mar 28;231(4745):1580-4.
Katz RA, Cullen BR, Malavarca R, Skalka AM. Role of the avian retrovirus mRNA leader in expression: evidence for novel translational control. Mol Cell Biol. 1986 Feb;6(2):372-9.
Butnick NZ, Miyamoto C, Chizzonite R, Cullen BR, Ju G, Skalka AM. Regulation of the human c-myc gene: 5' noncoding sequences do not affect translation. Mol Cell Biol. 1985 Nov;5(11):3009-16.
Langer-Safer PR, Lehrman SR, Skalka AM. v-src inhibits differentiation via an extracellular intermediate(s). Mol Cell Biol. 1985 Oct;5(10):2847-50.
Duyk G, Longiaru M, Cobrinik D, Kowal R, deHaseth P, Skalka AM, Leis J. Circles with two tandem long terminal repeats are specifically cleaved by pol gene-associated endonuclease from avian sarcoma and leukosis viruses: nucleotide sequences required for site-specific cleavage. J Virol. 1985 Nov;56(2):589-99.
Smith EJ, Bizub D, Scholl DR, Skalka AM. Characterization of a solitary long terminal repeat of avian endogenous virus origin. Virology. 1984 Apr 30;134(2):493-6.
Bizub D, Katz RA, Skalka AM. Nucleotide sequence of noncoding regions in Rous-associated virus-2: comparisons delineate conserved regions important in replication and oncogenesis. J Virol. 1984 Feb;49(2):557-65.
Duyk G, Leis J, Longiaru M, Skalka AM. Selective cleavage in the avian retroviral long terminal repeat sequence by the endonuclease associated with the alpha beta form of avian reverse transcriptase. Proc Natl Acad Sci USA. 1983 Nov;80(22):6745-9.
Cullen BR, Skalka AM, Ju G. Endogenous avian retroviruses contain deficient promoter and leader sequences. Proc Natl Acad Sci USA. 1983 May;80(10):2946-50.
Leis J, Duyk G, Johnson S, Longiaru M, Skalka A. Mechanism of action of the endonuclease associated with the alpha beta and beta beta forms of avian RNA tumor virus reverse transcriptase. J Virol. 1983 Feb;45(2):727-39.
Scholl DR, Kahn S, Malavarca R, Astrin S, Skalka AM. Nucleotide sequence of the long terminal repeat and flanking cellular sequences of avian endogenous retrovirus ev-2: variation in Rous-associated virus-0 expression cannot be explained by differences in primary sequence. J Virol. 1983 Feb;45(2):868-71.
Tsichlis PN, Donehower L, Hager G, Zeller N, Malavarca R, Astrin S, Skalka AM. Sequence comparison in the crossover region of an oncogenic avian retrovirus recombinant and its nononcogenic parent: genetic regions that control growth rate and oncogenic potential. Mol Cell Biol. 1982 Nov;2(11):1331-8.
Neel BG, Gasic GP, Rogler CE, Skalka AM, Ju G, Hishinuma F, Papas T, Astrin SM, Hayward WS. Molecular analysis of the c-myc locus in normal tissue and in avian leukosis virus-induced lymphomas. J Virol. 1982 Oct;44(1):158-66.
Skalka AM, Boone L, Junghans R, Luk D. Genetic recombination in avian retroviruses. J Cell Biochem. 1982;19(3):293-304.
Junghans RP, Boone LR, Skalka AM. Products of reverse transcription in avian retrovirus analyzed by electron microscopy. J Virol. 1982 Aug;43(2):544-54.
Junghans RP, Boone LR, Skalka AM. Retroviral DNA H structures: displacement-assimilation model of recombination. Cell. 1982 Aug;30(1):53-62.
Ju G, Hishinuma F, Skalka AM. Nucleotide sequence analysis of avian retroviruses: structural similarities with transposable elements. Fed Proc. 1982 Aug;41(10):2659-61.
Takeya T, Hanafusa H, Junghans RP, Ju G, Skalka AM. Comparison between the viral transforming gene (src) of recovered avian sarcoma virus and its cellular homolog. Mol Cell Biol. 1981 Nov;1(11):1024-37.
Lerner TL, Skalka AM, Hanafusa H. Integration of Rous sarcoma virus DNA into chicken embryo fibroblasts: no preferred proviral acceptor site in the DNA of clones of singly infected transformed chicken cells. J Virol. 1981 Nov;40(2):421-30.
Kopchick JJ, Ju G, Skalka AM, Stacey DW. Biological activity of cloned retroviral DNA in microinjected cells. Proc Natl Acad Sci USA. 1981 Jul;78(7):4383-7.
Hishinuma F, DeBona PJ, Astrin S, Skalka AM. Nucleotide sequence of acceptor site and termini of integrated avian endogenous provirus ev1: integration creates a 6 bp repeat of host DNA. Cell. 1981 Jan;23(1):155-64.
Boone LR, Skalka AM. Viral DNA synthesized in vitro by avian retrovirus particles permeabilized with melittin. I. Kinetics of synthesis and size of minus- and plus-strand transcripts. J Virol. 1981 Jan;37(1):109-16.
Boone LR, Skalka AM. Viral DNA synthesized in vitro by avian retrovirus particles permeabilized with melittin. II. Evidence for a strand displacement mechanism in plus-strand synthesis. J Virol. 1981 Jan;37(1):117-26.
Baez M, Taussig R, Zazra JJ, Young JF, Palese P, Reisfeld A, Skalka AM. Complete nucleotide sequence of the influenza A/PR/8/34 virus NS gene and comparison with the NS genes of the A/Udorn/72 and A/FPV/Rostock/34 strains. Nucleic Acids Res. 1980 Dec 11;8(23):5845-58.
Ju G, Skalka AM. Nucleotide sequence analysis of the long terminal repeat (LTR) of avian retroviruses: structural similarities with transposable elements. Cell. 1980 Nov;22(2 Pt 2):379-86.
Ju G, Boone L, Skalka AM. Isolation and characterization of recombinant DNA clones of avian retroviruses: size heterogeneity and instability of the direct repeat. J Virol. 1980 Mar;33(3):1026-33.
Boone LR, Skalka AM. Two species of full-length cDNA are synthesized in high yield by melittin-treated avian retrovirus particles. Proc Natl Acad Sci USA. 1980 Feb;77(2):847-51.
Nisen P, Medford R, Mansour J, Purucker M, Skalka A, Shapiro L. Cell-cycle-associated rearrangement of inverted repeat DNA sequences. Proc Natl Acad Sci USA. 1979 Dec;76(12):6240-4.
McClements W, Hanafusa H, Tilghman S, Skalka AM. Structural studies on oncornavirus-related sequences in chicken genomic DNA: two-step analyses of EcoRI and Bgl I restriction digests and tentative mapping of a ubiquitous endogenous provirus digests and tentative mapping of a ubiquitous endogenous provirus. Proc Natl Acad Sci USA. 1979 May;76(5):2165-9.
Sawin VL, Skalka AM, Wray W. Simultaneous observation of quinacrine bands and silver grains on radiolabeled metaphase chromosomes. Histochemistry. 1978 Dec 28;59(1):1-8.
Folkmanis A, Maltzman W, Mellon P, Skalka A, Echols H. The essential role of the cro gene in lytic development by bacteriophage lambda. Virology. 1977 Sep;81(2):352-62.
McClements W, Skalka AM. Analysis of chicken ribosomal RNA genes and construction of lambda hybrids containing gene fragments. Science. 1977 Apr 8;196(4286):195-7.
Skalka A, Shapiro L. In situ immunoassays for gene translation products in phage plaques and bacterial colonies. Gene. 1976;1(1):65-79.
Ray U, Skalka AM. Lysogenization of Escherichia coli by bacteriophage lambda: complementary activity of the hosts' DNA polymerase I and ligase and bacteriophage replication proteins O and P. J Virol. 1976;18:511-7.
Sogo JM, Greenstein M, Skalka A. The circle mode of replication of bacteriophage lambda: the role of covalently closed templates and the formation of mixed catenated dimers. J Mol Biol. 1976 May 25;103(3):537-62.
Dawson P, Hohn B, Hohn T, Skalka A. Functional empty capsid precursors produced by lambda mutant defective for late lambda DNA replication. J Virol. 1976 Feb;17(2):576-83.
Greenstein M, Skalka A. Replication of bacteriophage lambda DNA: in vivo studies of the interaction between the viral gamma protein and the host recBC DNAase. J Mol Biol. 1975 Oct 5;97(4):543-9.
Dawson P, Skalka A. Bacteriophage lambda head morphogenesis: studies on the role of DNA. J Mol Biol. 1975 Apr 5;93(2):167-80.
Reuben R, Gefter M, Enquist L, Skalka A. New method for large-scale preparation of covalently closed lambda DNA molecules. J Virol. 1974 Nov;14(5):1104-7.
Enquist LW, Skalka A. Replication of bacteriophage lambda DNA dependent on the function of host and viral genes. I. Interaction of red, gam and rec. J Mol Biol. 1973 Apr 5;75(2):185-212.
Skalka AM, Hanson P. Comparisons of the distribution of nucleotides and common sequences in DNA from selected bacteriophages. J Virol. 1972;9(583-593).
Skalka A, Poonian M, Bartl P. Concatemers in DNA replication: electron microscopic studies of partially denatured intracellular lambda DNA. J Mol Biol. 1972 Mar 14;64(3):541-50.
Yamagishi H, Skalka A. Distribution of nucleotides in Escherichia coli DNA from lambda-transducing phages. J Mol Biol. 1971 Jun 14;58(2):417-30.
Skalka AM. Annual reports of research in progress appear in Carnegie Institute Year Books (Washington, DC) 64:529; 66:565; 66:650, 657, 660; 67:556; 1965, 1966, 1967, 1968.
Bear PD, Skalka A. The molecular origin of lambda prophage mRNA. Proc Natl Acad Sci USA. 1969 Feb;62(2):385-8.
Skalka A. Nucleotide distribution and functional orientation in the deoxyribonucleic acid of phage phi 80. J Virol. 1969 Feb;3(2):150-6.
Skalka A, Burgi E, Hershey AD. Segmental distribution of nucleotides in the DNA of bacteriophage lambda. J Mol Biol. 1968 May 28;34(1):1-16.
Skalka A, Butler B, Echols H. Genetic control of transcription during development of phage gamma. Proc Natl Acad Sci USA. 1967 Aug;58(2):576-83.
Smith MG, Skalka A. Some properties of DNA from phage-infected bacteria. J Gen Physiol. 1966 Jul;49(6):127-42.
Skalka, A. Regional and temporal control of genetic transcription in phage lambda. Proc Natl Acad Sci USA. 55:1190-1195, 1966.
Skalka A, Fowler AV, Hurwitz J. The effect of histones on the enzymatic synthesis of ribonucleic acid. J Biol Chem. 1966 Feb 10;241(3):588-96.
Skalka AM. The effect of histones on the enzymatic reactions involved in RNA and DNA synthesis. PhD Dissertation. 1964; New York University.
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Published Symposia Proceedings

Skalka AM. Advances in cell and molecular biology. In: Biotechnology: Science, Engineering, and Ethical Challenges for the 21st Century (Rudolph, F.B., McIntire, L.V., eds.), pp. 15-27. Joseph Henry Press, Washington, D.C., 1996.
Cameron CE., Burstein H, Bizub-Bender D, Ridky T, Weber IT, Wlodawer A, Skalka AM, Leis J. Identification of amino acid residues of the retroviral aspartic proteinase important for substrate specificity and catalytic efficiency. In: Proceedings of the 5th International Conference on Aspartic Proteinases (Takahashi, K., ed.), pp. 399-406, 1994.
Jones KS, Kulkosky J, Skalka AM. Analyses of HIV integration components. The Symposium Volume on Advances in Molecular Biology and Targeted Treatment of AIDS (Kumar A. ed). Plenum Press, New York, 1991.
Skalka AM, Bizub D, Kotler M, Katz RA, Leis J, Cameron C, Danho W, Wlodawer A, Weber I, Miller M, Jaskølski M, Rao M. Biochemical and physical studies of retroviral protease. Proceedings for the First Roche Symposium, Clinical Pharmacology, (Zuckschwerdt Verland Munich), 1989.
Skalka AM, Duyk G, Longiaru M, De Haseth P, Terry R, Leis J. Integrative recombination – a role for the retroviral reverse transcriptase. Cold Spring Harbor Symp. Quant. Biol., Recombination at the DNA Level, 49:651-659, 1984.
Skalka AM, Tsichlis PN, Malavarca R, Cullen B, Ju G. Viral sequences determining the oncogenicity of avian leukosis viruses. In: Oncogenes and Retroviruses. Evaluation of Basic Findings and Clinical Potential (O'Connor, T.E., Rauscher, F.J., Jr., eds.), pp. 105-118. Roswell Park Memorial Institute, September, 1982. Alan R. Liss, NY, 1983.
Skalka AM, Ju G, Hishinuma F, DeBona, P, Astrin, S. Structural analogies among avian retroviral DNAs and transposable elements. Cold Spring Harbor Symp. Quant. Biol. 45:739-746, 1981.
Skalka AM, DeBona P, Hishinuma F, McClements W. Avian endogenous proviral DNA: analysis of integrated ev-1 and a related gs- chf- provirus purified by molecular cloning. Cold Spring Harbor Symp. Quant. Biol. 44:1097-1104, 1980.
McClements, W, Tilghman S., Crouch R, Skalka AM. Cloning and analysis of rDNA from higher eukaryotes. In: The International Symposium on Genetic Engineering, (Boyer, H.W., Nicosia, S., eds.), pp. 117-126. Elsevier/North Holland Biochemical Press, 1978.
Skalka AM, Shapiro L. Screening for recombinant DNAs with in situ immunoassays. ICN-UCLA Symposia on Molecular and Cellular Biology. In: Eukaryotic Genetics System, (Wilcox, G., Abelson, J., Fox, J.F., eds.), vol. VIII, pp. 75-84. Academic Press, 1977.
Skalka AM, Greenstein, M, Reuben R. Molecular mechanisms in the control of λ DNA replication: interaction between phage and host functions. 1975 ICN-UCLA Winter Conference on Molecular and Cellular Biology. In: DNA Synthesis and Its Regulation, (Goulian, M., Hanawalt, P., Fox, C.F., eds.), vol. 3, pp. 460-485. W. A. Benjamin, Inc., Menlo Park, CA, 1975.
Skalka AM. A replicator's view of recombination (and repair). In: Mechanism and Recombination, (Grell, R.F., ed.), pp. 421-432. Plenum Press, NY, 1974.
Skalka AM, Enquist LW. Overlapping pathways for replication, recombination and repair in bacteriophage lambda. In: Mechanism and Regulation of DNA Replication, pp. 181-200. Plenum Press, NY, 1974.
Skalka AM. Multiple units of transcription in phage lambda. Cold Spring Harbor Symp. Quant. Biol. 31:377-379, 1966.
Hurwitz, J, Evans A, Babinet C, Skalka AM. On the copying of DNA in the RNA polymerase reaction. Cold Spring Harbor Symp. Quant. Biol. 28:59-65, 1963.
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Book Chapters

Katz RA, Daniel R, Skalka AM. Host factors that affect provirus stability and silencing. HIV-1 Integrase: Mechanisms of Action and Inhibitor Design (Wand, B., Neamati, N., eds.), Chapter 9. John Wiley and Sons, Inc., United Kingdom, in press.
Andrake MD, Skalka, AM. Retroviral Integrases. In: Wiley Encyclopedia of Molecular Medicine (Creighton, T., ed.), vol. 5, pp. 1780-1784. John Wiley and Sons, Inc., New York, NY, 2002.
Skalka AM. The pecularities of Lambda DNA. We Can Sleep Later. Alfred D. Hershey and the Origins of Molecular Biology (Stahl FW, ed.), pp. 73-80. Cold Spring Harbor Press, Cold Spring Harbor, NY, 2000.
Alexandratos J, Bujacz G, Jaskolski M, Wlodawer A, Merkel G, Katz RA, Skalka AM. Crystal structure of avian sarcoma virus integrase with bound essential cations. In: Techniques in Protein Chemistry VIII, pp. 417-425. Academic Press, 1997.
Bujacz G, Jaskolski J, Alexandratos J, Wlodawer A, Merkel G, Katz RA, Skalka AM. Crystal structure of the catalytic domain of avian sarcoma virus integrase. In: Techniques in Protein Chemistry VII, (Marshak DR, ed.), pp. 383-390. Academic Press, 1996.
Skalka AM. The endonuclease activity associated with reverse transcriptase of avian sarcoma and leukosis virus (ASLV). In: Reverse Transcriptase (Skalka AM, Goff S, eds.), pp. 193-204. Cold Spring Harbor Press, Cold Spring Harbor, NY, 1993.
Boone LR, Skalka .M. Strand displacement synthesis by reverse transcriptase. In: Reverse Transcriptase (Skalka AM, Goff S, eds.), pp. 119-134. Cold Spring Harbor Press, Cold Spring Harbor, NY, 1993.
Skalka AM. A tapestry of transposition. The Dynamic Genome: Barbara McClintock’s Ideas In The Century Of Genetics (Federoff N, Botstein D, eds.), pp. 173-183. Cold Spring Harbor Laboratory Press, 1992.
Skalka AM. Risk assessment for genetic experimentation and application. In: Introduction Of Genetically Modified Organisms Into The Environment (Mooney HA, Bernardi G, eds.). SCOPE, John Wiley & Sons, Ltd, 1990.
Leis J, Bizub D, Weber IT., Cameron C, Katz RA., Wlodawer, A., Skalka, A.M. Structure-function analysis of retroviral aspartic protease. In: Current Communications in Molecular Biology: Viral Proteinases As Targets For Chemotherapy (Kråusslich H, Oroszlan S, Wimmer E, eds.), pp. 235-243. Cold Spring Harbor Press, Cold Spring Harbor, NY, 1989.
Skalka AM. Integrative recombination of retroviral DNA. In: Genetic Recombination, (Kucherlapati R, Smith GR, eds.), vol. 94, pp. 701-724. ASM Publishers, 1988.
Skalka AM. DNA replication-bacteriophage lambda. In: Current Topics in Microbiology and Immunology, vol. 78, pp. 201-237. Springer-Verlag, 1977.
Skalka AM. Origin of DNA concatemers during growth (of lambda). In: The Bacteriophage λ, (Hershey AD, ed.), pp. 535-547. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1971.
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Methods Papers

Merkel G, Andrake MD, Ramcharan J, Skalka AM. Oligonucleotide-based assays for integrase activity. Mechanistic and pharmacological analyses of HIV-1 integration. Methods (Engelman, A., ed.), Elsevier Editorial Systems, 2008. Epub ahead of print.
Anderson D, Shapiro L, Skalka AM. In situ immunoassays for translation products. In: Methods in Enzymology (Wu, R., ed.), vol. 68, pp.428-436. Academic Press, NY, 1979.
Skalka AM, Bartl P. Identification of repeating units in DNA concatemers. In: Methods in Enzymology (Grossman L, Moldave K, eds.), Part E, vol. 29, pp. 459-466. Academic Press, NY, 1974.
Skalka AM. A method for the breakage of DNA and resolution of the fragments. In: Methods in Enzymology, Nucleic Acids, (Grossman L, Moldave K, eds.), part D, vol. 21, pp. 341-350. Academic Press, NY, 1971.
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Scholarly Reviews

Ramcharan J, Skalka AM. Strategies for Identification of HIV-1 Integrase Inhibitors. Future Virology 1:2006.
Katz RA, Greger JG, Skalka AM. Effects of cell cycle status on early events in retroviral replication. J. Cell. Biochem. 94:880-889, 2005.
Skalka AM, Katz RA. Retroviral DNA integration and the DNA damage response. Cell Death Diff. 12:971-978, 2005.
Asante-Appiah E, Skalka AM. HIV-1 integrase: structural organization, conformational changes and catalysis. In: Advances in Virus Research, vol. 52. Academic Press, NY, 1999.
Andrake MD, Skalka AM. Retroviral Integrase: putting the pieces together. J. Biol. Chem. 271:19633-19636, 1996.
Kulkosky J, Skalka AM. Molecular mechanism of retroviral DNA integration. Pharmacol. Ther. 61:185-203, 1994.
Katz RA, Skalka AM. The Retroviral Enzymes. Annu. Rev. Biochem. 63:133-173, 1994.
Skalka AM. Retroviral DNA integration: lessons for transposon shuffling. Gene 135:175-182, 1993.
Skalka AM. Retroviral Enzymes – attractive targets for antiviral therapy. Adv. Oncol. 8:2-6, 1992.
Katz R, Skalka AM. Generation of diversity in retroviruses. Ann. Rev. Genet. 24:409-445, 1990.
Kulkosky J, Skalka AM. HIV DNA Integration: observations and Inferences. J. AIDS 3:839-851, 1990.
Leis J, Weber I, Wlodawer A, Skalka AM. Structure-function analysis of the Rous sarcoma virus-specific proteinase. ASM News 56:77-81, 1990.
Skalka AM, Nuss D. (editors). Comments on Special Virology. BioEssays 5:243-244, 1986.
Skalka AM, Leis J. Retroviral DNA integration. BioEssays 1:206-210, 1984.
Enquist LW, Skalka AM. Replication of bacteriophage lambda DNA. Trends Biochem. Sci. 3:279-283, 1978.
Skalka AM. Current status of coliphage λ EK2 vectors. Gene 3:29-38, 1978.
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News and Views

Skalka AM. Second Opinion - Lobbying for Research $$. Washington Post, Jun 1993 9:25, page 6.
Weissbach H, Skalka AM. Recombinant DNA - A new tool for the pharmacologist. Trends in Pharmacological Sciences, Oct 1979 pp. 32-33.
Skalka AM. Second report of the COGENE Working Group on Risk Assessment. Report on Wye Conference. In: Recombinant DNA and Experimentation (Morgan J, Whelan WJ, eds.). Pergamon Press, NY, 1979.
Szybalski W, Skalka AM. Nobel prizes and restriction enzymes (An editorial). Gene 1978 4:181-182, 1978.
Skalka AM, Bernardi G, Sgaramella V. First report to COGENE from the Working Group on Risk Assessment. The Committee on Genetic Experimentation, July 1978.
Skalka AM. Recombinant DNA Research. Research Management, January 1978 pp. 9-13.
Skalka AM., Weissbach, A., Bartl, P. Genetic recombination:Genetic, physical, and biochemical aspects. Science. 1974 183:1218-1219.
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Books/Issues Edited

Skalka AM. (ed.) Seminars in Virology: Retroviral DNA Integration. In: Advances in Virus Research, vol 52. Academic Press, NY, 1999.
Goff S, Skalka AM. (eds.) Reverse Transcriptase. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1993.
Reddy EP, Skalka AM, Curran T. (eds.). The Oncogene Handbook. Elsevier, NY, 1988.
Cullen B, Gage LP, Siddiqui MAQ, Skalka AM, Weissbach, H. (eds). Mechanisms of Control of Gene Expression. Alan R Liss, Inc, NY, 1987.
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Textbooks

Flint SJ, Enquist LW, Racaniello VR., Skalka, AM. Principles of Virology. Molecular Biology, Pathogenesis and Control of Animal iruses, 2nd edition, 918 pages. ASM Press, Washington, DC, 2004.
Flint SJ, Enquist LW, Krug RM, Racaniello VR, Skalka AM. Principles of Virology. Molecular Biology, Pathogenesis, and Control. ASM Press, 2000.
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