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    Karpen, Gary

    TitleBiologist Senior Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentBiological Systems & Eng
    Address1 Cyclotron Road
    Berkeley CA 94720
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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Zhang W, Karpen G, Zhang Q. Exploring the role of CENP-A Ser18 phosphorylation in CIN and Tumorigenesis. Cell Cycle. 2017; 16(24):2323-2325. PMID: 28980868.
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      2. Takada M, Zhang W, Suzuki A, Kuroda TS, Yu Z, Inuzuka H, Gao D, Wan L, Zhuang M, Hu L, Zhai B, Fry CJ, Bloom K, Li G, Karpen G, Wei W, Zhang Q. FBW7 Loss Promotes Chromosomal Instability and Tumorigenesis via Cyclin E1/CDK2-Mediated Phosphorylation of CENP-A. Cancer Res. 2017 Sep 15; 77(18):4881-4893. PMID: 28760857.
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      3. Colmenares SU, Swenson JM, Langley SA, Kennedy C, Costes SV, Karpen G. Drosophila Histone Demethylase KDM4A Has Enzymatic and Non-enzymatic Roles in Controlling Heterochromatin Integrity. Dev Cell. 2017 Jul 24; 42(2):156-169.e5. PMID: 28743002.
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      4. Lee YCG, Karpen G. Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution. Elife. 2017 Jul 11; 6. PMID: 28695823.
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      5. Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen G. Phase separation drives heterochromatin domain formation. Nature. 2017 Jul 13; 547(7662):241-245. PMID: 28636597.
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      6. Zhang W, Mao JH, Zhu W, Jain AK, Liu K, Brown JB, Karpen G. Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy. Nat Commun. 2016 Aug 31; 7:12619. PMID: 27577169.
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      7. Janssen A, Breuer GA, Brinkman EK, van der Meulen AI, Borden SV, van Steensel B, Bindra RS, LaRocque JR, Karpen G. A single double-strand break system reveals repair dynamics and mechanisms in heterochromatin and euchromatin. Genes Dev. 2016 Jul 15; 30(14):1645-57. PMID: 27474442.
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      8. Mao JH, Langley SA, Huang Y, Hang M, Bouchard KE, Celniker SE, Brown JB, Jansson JK, Karpen G, Snijders AM. Identification of genetic factors that modify motor performance and body weight using Collaborative Cross mice. Sci Rep. 2015 Nov 09; 5:16247. PMID: 26548763; PMCID: PMC4637864.
      9. Ryu T, Spatola B, Delabaere L, Bowlin K, Hopp H, Kunitake R, Karpen G, Chiolo I. Heterochromatic breaks move to the nuclear periphery to continue recombinational repair. Nat Cell Biol. 2015 Nov; 17(11):1401-11. PMID: 26502056; PMCID: PMC4628585.
      10. Zhang P, Lo A, Huang Y, Huang G, Liang G, Mott J, Karpen G, Blakely EA, Bissell MJ, Barcellos-Hoff MH, Snijders AM, Mao JH. Identification of genetic loci that control mammary tumor susceptibility through the host microenvironment. Sci Rep. 2015 Mar 09; 5:8919. PMID: 25747469; PMCID: PMC4352890.
      11. Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, Booth BW, Pfeiffer BD, George RA, Svirskas R, Krzywinski M, Schein J, Accardo MC, Damia E, Messina G, Méndez-Lago M, de Pablos B, Demakova OV, Andreyeva EN, Boldyreva LV, Marra M, Carvalho AB, Dimitri P, Villasante A, Zhimulev IF, Rubin GM, Karpen G, Celniker SE. The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res. 2015 Mar; 25(3):445-58. PMID: 25589440; PMCID: PMC4352887.
      12. Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen G, Park PJ. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. PMID: 25164756; PMCID: PMC4227084.
      13. Langley SA, Karpen G, Langley CH. Nucleosomes shape DNA polymorphism and divergence. PLoS Genet. 2014 Jul; 10(7):e1004457. PMID: 24991813; PMCID: PMC4081404.
      14. Snijders AM, Langley S, Mao JH, Bhatnagar S, Bjornstad KA, Rosen CJ, Lo A, Huang Y, Blakely EA, Karpen G, Bissell MJ, Wyrobek AJ. An interferon signature identified by RNA-sequencing of mammary tissues varies across the estrous cycle and is predictive of metastasis-free survival. Oncotarget. 2014 Jun 30; 5(12):4011-25. PMID: 24994117; PMCID: PMC4147302.
      15. Rout MP, Karpen G. Editorial overview: Cell nucleus: the nucleus: a dynamic organelle. Curr Opin Cell Biol. 2014 Jun; 28:iv-vii. PMID: 24908378.
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      16. Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen G, Kuroda MI, Park PJ. Impact of sequencing depth in ChIP-seq experiments. Nucleic Acids Res. 2014 May; 42(9):e74. PMID: 24598259; PMCID: PMC4027199.
      17. Dunleavy EM, Zhang W, Karpen G. Solo or doppio: how many CENP-As make a centromeric nucleosome? Nat Struct Mol Biol. 2013 Jun; 20(6):648-50. PMID: 23739165.
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      18. Earnshaw WC, Allshire RC, Black BE, Bloom K, Brinkley BR, Brown W, Cheeseman IM, Choo KH, Copenhaver GP, Deluca JG, Desai A, Diekmann S, Erhardt S, Fitzgerald-Hayes M, Foltz D, Fukagawa T, Gassmann R, Gerlich DW, Glover DM, Gorbsky GJ, Harrison SC, Heun P, Hirota T, Jansen LE, Karpen G, Kops GJ, Lampson MA, Lens SM, Losada A, Luger K, Maiato H, Maddox PS, Margolis RL, Masumoto H, McAinsh AD, Mellone BG, Meraldi P, Musacchio A, Oegema K, O'Neill RJ, Salmon ED, Scott KC, Straight AF, Stukenberg PT, Sullivan BA, Sullivan KF, Sunkel CE, Swedlow JR, Walczak CE, Warburton PE, Westermann S, Willard HF, Wordeman L, Yanagida M, Yen TJ, Yoda K, Cleveland DW. Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Res. 2013 Apr; 21(2):101-6. PMID: 23580138; PMCID: PMC3627038.
      19. Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB, Tolstorukov MY, Kuroda MI, Pirrotta V, Karpen G, Park PJ, Elgin SC. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet. 2012 Sep; 8(9):e1002954. PMID: 23028361; PMCID: PMC3447959.
      20. Schwartz YB, Linder-Basso D, Kharchenko PV, Tolstorukov MY, Kim M, Li HB, Gorchakov AA, Minoda A, Shanower G, Alekseyenko AA, Riddle NC, Jung YL, Gu T, Plachetka A, Elgin SC, Kuroda MI, Park PJ, Savitsky M, Karpen G, Pirrotta V. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res. 2012 Nov; 22(11):2188-98. PMID: 22767387; PMCID: PMC3483548.
      21. Alekseyenko AA, Ho JW, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SC, Karpen G, Pirrotta V, Kuroda MI, Park PJ. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet. 2012; 8(4):e1002646. PMID: 22570616; PMCID: PMC3343056.
      22. Zhang W, Colmenares SU, Karpen G. Assembly of Drosophila centromeric nucleosomes requires CID dimerization. Mol Cell. 2012 Jan 27; 45(2):263-9. PMID: 22209075; PMCID: PMC3299411.
      23. Mellone BG, Grive KJ, Shteyn V, Bowers SR, Oderberg I, Karpen G. Assembly of Drosophila centromeric chromatin proteins during mitosis. PLoS Genet. 2011 May; 7(5):e1002068. PMID: 21589899; PMCID: PMC3093364.
      24. Dunleavy EM, Almouzni G, Karpen G. H3.3 is deposited at centromeres in S phase as a placeholder for newly assembled CENP-A in G1 phase. Nucleus. 2011 Mar-Apr; 2(2):146-57. PMID: 21738837; PMCID: PMC3127096.
      25. Chiolo I, Minoda A, Colmenares SU, Polyzos A, Costes SV, Karpen G. Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. Cell. 2011 Mar 04; 144(5):732-44. PMID: 21353298; PMCID: PMC3417143.
      26. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen G, Park PJ. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24; 471(7339):480-5. PMID: 21179089; PMCID: PMC3109908.
      27. Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen G. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011 Feb; 21(2):147-63. PMID: 21177972; PMCID: PMC3032919.
      28. Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen G, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. PMID: 21177974; PMCID: PMC3192495.
      29. Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SC, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ, Karpen G, Hawkins RD, Lieb JD. An assessment of histone-modification antibody quality. Nat Struct Mol Biol. 2011 Jan; 18(1):91-3. PMID: 21131980; PMCID: PMC3017233.
      30. Williamson A, Wickliffe KE, Mellone BG, Song L, Karpen G, Rape M. Identification of a physiological E2 module for the human anaphase-promoting complex. Proc Natl Acad Sci U S A. 2009 Oct 27; 106(43):18213-8. PMID: 19822757; PMCID: PMC2775311.
      31. Karpen G. Preparation of high-molecular-weight DNA from Drosophila embryos. Cold Spring Harb Protoc. 2009 Jul; 2009(7):pdb.prot5254. PMID: 20147219.
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      32. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen G, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH. Unlocking the secrets of the genome. Nature. 2009 Jun 18; 459(7249):927-30. PMID: 19536255; PMCID: PMC2843545.
      33. Mellone BG, Zhang W, Karpen G. Frodos found: Behold the CENP-a "Ring" bearers. Cell. 2009 May 01; 137(3):409-12. PMID: 19410539; PMCID: PMC3192489.
      34. Peng JC, Karpen G. Heterochromatic genome stability requires regulators of histone H3 K9 methylation. PLoS Genet. 2009 Mar; 5(3):e1000435. PMID: 19325889; PMCID: PMC2654965.
      35. Allshire RC, Karpen G. Epigenetic regulation of centromeric chromatin: old dogs, new tricks? Nat Rev Genet. 2008 Dec; 9(12):923-37. PMID: 19002142; PMCID: PMC2586333.
      36. Erhardt S, Mellone BG, Betts CM, Zhang W, Karpen G, Straight AF. Genome-wide analysis reveals a cell cycle-dependent mechanism controlling centromere propagation. J Cell Biol. 2008 Dec 01; 183(5):805-18. PMID: 19047461; PMCID: PMC2592830.
      37. Peng JC, Karpen G. Epigenetic regulation of heterochromatic DNA stability. Curr Opin Genet Dev. 2008 Apr; 18(2):204-11. PMID: 18372168; PMCID: PMC2814359.
      38. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen G, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 08; 450(7167):203-18. PMID: 17994087.
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      39. Smith CD, Shu S, Mungall CJ, Karpen G. The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Science. 2007 Jun 15; 316(5831):1586-91. PMID: 17569856; PMCID: PMC2819280.
      40. Hoskins RA, Carlson JW, Kennedy C, Acevedo D, Evans-Holm M, Frise E, Wan KH, Park S, Mendez-Lago M, Rossi F, Villasante A, Dimitri P, Karpen G, Celniker SE. Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science. 2007 Jun 15; 316(5831):1625-8. PMID: 17569867; PMCID: PMC2825053.
      41. Zhang W, Mellone BG, Karpen G. A specialized nucleosome has a "point" to make. Cell. 2007 Jun 15; 129(6):1047-9. PMID: 17574019; PMCID: PMC2950099.
      42. Peng JC, Karpen G. H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability. Nat Cell Biol. 2007 Jan; 9(1):25-35. PMID: 17159999; PMCID: PMC2819265.
      43. Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen G. Improved repeat identification and masking in Dipterans. Gene. 2007 Mar 01; 389(1):1-9. PMID: 17137733; PMCID: PMC1945102.
      44. Blower MD, Daigle T, Kaufman T, Karpen G. Drosophila CENP-A mutations cause a BubR1-dependent early mitotic delay without normal localization of kinetochore components. PLoS Genet. 2006 Jul; 2(7):e110. PMID: 16839185; PMCID: PMC1500813.
      45. Mellone B, Erhardt S, Karpen G. The ABCs of centromeres. Nat Cell Biol. 2006 May; 8(5):427-9. PMID: 16691204.
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      46. Heun P, Erhardt S, Blower MD, Weiss S, Skora AD, Karpen G. Mislocalization of the Drosophila centromere-specific histone CID promotes formation of functional ectopic kinetochores. Dev Cell. 2006 Mar; 10(3):303-15. PMID: 16516834; PMCID: PMC3192491.
      47. Sullivan BA, Karpen G. Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nat Struct Mol Biol. 2004 Nov; 11(11):1076-83. PMID: 15475964; PMCID: PMC1283111.
      48. Le HD, Donaldson KM, Cook KR, Karpen G. A high proportion of genes involved in position effect variegation also affect chromosome inheritance. Chromosoma. 2004 Mar; 112(6):269-76. PMID: 14767778; PMCID: PMC3116012.
      49. Fyodorov DV, Blower MD, Karpen G, Kadonaga JT. Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo. Genes Dev. 2004 Jan 15; 18(2):170-83. PMID: 14752009; PMCID: PMC324423.
      50. Konev AY, Yan CM, Acevedo D, Kennedy C, Ward E, Lim A, Tickoo S, Karpen G. Genetics of P-element transposition into Drosophila melanogaster centric heterochromatin. Genetics. 2003 Dec; 165(4):2039-53. PMID: 14704184; PMCID: PMC1462875.
      51. Sun X, Le HD, Wahlstrom JM, Karpen G. Sequence analysis of a functional Drosophila centromere. Genome Res. 2003 Feb; 13(2):182-94. PMID: 12566396; PMCID: PMC420369.
      52. Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ, Sullivan BA, Sutton GG, Yasuhara JC, Wakimoto BT, Myers EW, Celniker SE, Rubin GM, Karpen G. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol. 2002; 3(12):RESEARCH0085. PMID: 12537574; PMCID: PMC151187.
      53. Dernburg AF, Karpen G. A chromosome RNAissance. Cell. 2002 Oct 18; 111(2):159-62. PMID: 12408860.
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      54. Yan CM, Dobie KW, Le HD, Konev AY, Karpen G. Efficient recovery of centric heterochromatin P-element insertions in Drosophila melanogaster. Genetics. 2002 May; 161(1):217-29. PMID: 12019236; PMCID: PMC1462106.
      55. Blower MD, Sullivan BA, Karpen G. Conserved organization of centromeric chromatin in flies and humans. Dev Cell. 2002 Mar; 2(3):319-30. PMID: 11879637; PMCID: PMC3192492.
      56. Donaldson KM, Lui A, Karpen G. Modifiers of terminal deficiency-associated position effect variegation in Drosophila. Genetics. 2002 Mar; 160(3):995-1009. PMID: 11901117; PMCID: PMC1462006.
      57. Sullivan B, Karpen G. Centromere identity in Drosophila is not determined in vivo by replication timing. J Cell Biol. 2001 Aug 20; 154(4):683-90. PMID: 11514585; PMCID: PMC2196454.
      58. Maggert KA, Karpen G. The activation of a neocentromere in Drosophila requires proximity to an endogenous centromere. Genetics. 2001 Aug; 158(4):1615-28. PMID: 11514450; PMCID: PMC1461751.
      59. Blower MD, Karpen G. The role of Drosophila CID in kinetochore formation, cell-cycle progression and heterochromatin interactions. Nat Cell Biol. 2001 Aug; 3(8):730-9. PMID: 11483958; PMCID: PMC3229202.
      60. Sullivan BA, Blower MD, Karpen G. Determining centromere identity: cyclical stories and forking paths. Nat Rev Genet. 2001 Aug; 2(8):584-96. PMID: 11483983.
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      61. Hari KL, Cook KR, Karpen G. The Drosophila Su(var)2-10 locus regulates chromosome structure and function and encodes a member of the PIAS protein family. Genes Dev. 2001 Jun 01; 15(11):1334-48. PMID: 11390354; PMCID: PMC312712.
      62. Dobie KW, Kennedy CD, Velasco VM, McGrath TL, Weko J, Patterson RW, Karpen G. Identification of chromosome inheritance modifiers in Drosophila melanogaster. Genetics. 2001 Apr; 157(4):1623-37. PMID: 11290718; PMCID: PMC1461595.
      63. Lopez JM, Karpen G, Orr-Weaver TL. Sister-chromatid cohesion via MEI-S332 and kinetochore assembly are separable functions of the Drosophila centromere. Curr Biol. 2000 Aug 24; 10(16):997-1000. PMID: 10985388.
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      64. Maggert KA, Karpen G. Acquisition and metastability of centromere identity and function: sequence analysis of a human neocentromere. Genome Res. 2000 Jun; 10(6):725-8. PMID: 10854406.
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      65. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen G, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC. The genome sequence of Drosophila melanogaster. Science. 2000 Mar 24; 287(5461):2185-95. PMID: 10731132.
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      66. Dobie KW, Hari KL, Maggert KA, Karpen G. Centromere proteins and chromosome inheritance: a complex affair. Curr Opin Genet Dev. 1999 Apr; 9(2):206-17. PMID: 10322137.
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      67. Murphy TD, Karpen G. Centromeres take flight: alpha satellite and the quest for the human centromere. Cell. 1998 May 01; 93(3):317-20. PMID: 9590164.
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      68. Williams BC, Murphy TD, Goldberg ML, Karpen G. Neocentromere activity of structurally acentric mini-chromosomes in Drosophila. Nat Genet. 1998 Jan; 18(1):30-7. PMID: 9425896.
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      69. Sun X, Wahlstrom J, Karpen G. Molecular structure of a functional Drosophila centromere. Cell. 1997 Dec 26; 91(7):1007-19. PMID: 9428523; PMCID: PMC3209480.
      70. Karpen G, Allshire RC. The case for epigenetic effects on centromere identity and function. Trends Genet. 1997 Dec; 13(12):489-96. PMID: 9433139.
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      71. Cook KR, Murphy TD, Nguyen TC, Karpen G. Identification of trans-acting genes necessary for centromere function in Drosophila melanogaster using centromere-defective minichromosomes. Genetics. 1997 Mar; 145(3):737-47. PMID: 9055083; PMCID: PMC1207858.
      72. Donaldson KM, Karpen G. Trans-suppression of terminal deficiency-associated position effect variegation in a Drosophila minichromosome. Genetics. 1997 Feb; 145(2):325-37. PMID: 9071587; PMCID: PMC1207798.
      73. Karpen G, Le MH, Le H. Centric heterochromatin and the efficiency of achiasmate disjunction in Drosophila female meiosis. Science. 1996 Jul 05; 273(5271):118-22. PMID: 8658180.
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      74. Le MH, Duricka D, Karpen G. Islands of complex DNA are widespread in Drosophila centric heterochromatin. Genetics. 1995 Sep; 141(1):283-303. PMID: 8536977; PMCID: PMC1206727.
      75. Murphy TD, Karpen G. Localization of centromere function in a Drosophila minichromosome. Cell. 1995 Aug 25; 82(4):599-609. PMID: 7664339; PMCID: PMC3209481.
      76. Murphy TD, Karpen G. Interactions between the nod+ kinesin-like gene and extracentromeric sequences are required for transmission of a Drosophila minichromosome. Cell. 1995 Apr 07; 81(1):139-48. PMID: 7720069.
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      77. Thompson-Stewart D, Karpen G, Spradling AC. A transposable element can drive the concerted evolution of tandemly repetitious DNA. Proc Natl Acad Sci U S A. 1994 Sep 13; 91(19):9042-6. PMID: 8090766; PMCID: PMC44743.
      78. Cook KR, Karpen G. A rosy future for heterochromatin. Proc Natl Acad Sci U S A. 1994 Jun 7; 91(12):5219-21. PMID: 8031404.
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      79. Karpen G. Position-effect variegation and the new biology of heterochromatin. Curr Opin Genet Dev. 1994 Apr; 4(2):281-91. PMID: 8032206.
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      80. Tower J, Karpen G, Craig N, Spradling AC. Preferential transposition of Drosophila P elements to nearby chromosomal sites. Genetics. 1993 Feb; 133(2):347-59. PMID: 8382177; PMCID: PMC1205324.
      81. Glaser RL, Karpen G, Spradling AC. Replication forks are not found in a Drosophila minichromosome demonstrating a gradient of polytenization. Chromosoma. 1992 Dec; 102(1):15-9. PMID: 1291225.
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      82. Karpen G, Spradling AC. Analysis of subtelomeric heterochromatin in the Drosophila minichromosome Dp1187 by single P element insertional mutagenesis. Genetics. 1992 Nov; 132(3):737-53. PMID: 1334894; PMCID: PMC1205211.
      83. Spradling AC, Karpen G. Sixty years of mystery. Genetics. 1990 Dec; 126(4):779-84. PMID: 2127578; PMCID: PMC1204277.
      84. Karpen G, Spradling AC. Reduced DNA polytenization of a minichromosome region undergoing position-effect variegation in Drosophila. Cell. 1990 Oct 05; 63(1):97-107. PMID: 2208283; PMCID: PMC3229194.
      85. McKee BD, Karpen G. Drosophila ribosomal RNA genes function as an X-Y pairing site during male meiosis. Cell. 1990 Apr 06; 61(1):61-72. PMID: 2156630.
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      86. Karpen G, Schaefer JE, Laird CD. A Drosophila rRNA gene located in euchromatin is active in transcription and nucleolus formation. Genes Dev. 1988 Dec; 2(12B):1745-63. PMID: 3149250.
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      87. Schubiger G, Karpen G. Blastema formation in regulating imaginal disc fragments of Drosophila melanogaster. Prog Clin Biol Res. 1983; 110 Pt A:609-18. PMID: 6402788.
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      88. Karpen G, Schubiger G. Extensive regulatory capabilities of a Drosophila imaginal disk blastema. Nature. 1981 Dec 24; 294(5843):744-7. PMID: 6798471.
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      89. Abbott LC, Karpen G, Schubiger G. Compartmental restrictions and blastema formation during pattern regulation in Drosophila imaginal leg discs. Dev Biol. 1981 Oct 15; 87(1):64-75. PMID: 7286422.
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