Karpen, Gary

TitleBiologist Senior Sci/Engr
InstitutionLawrence 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 09 15; 77(18):4881-4893. PMID: 28760857.
      View in: PubMed
    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 07 24; 42(2):156-169.e5. PMID: 28743002.
      View in: PubMed
    4. Lee YCG, Karpen G. Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution. Elife. 2017 07 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 07 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 07 15; 30(14):1645-57. PMID: 27474442; PMCID: PMC4973294 [Available on 01/15/17].
    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.
      View in: PubMed
    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. 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.
    19. 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.
    20. 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.
    21. 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.
    22. 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.
    23. 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.
    24. 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.
    25. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24; 330(6012):1787-97. PMID: 21177974.
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    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. 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.
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    29. 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.
    30. 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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    31. 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.
    32. 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.
    33. 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.
    34. 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.
    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.
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    36. Peng JC, Karpen G. Epigenetic regulation of heterochromatic DNA stability. Curr Opin Genet Dev. 2008 Apr; 18(2):204-11. PMID: 18372168; PMCID: PMC2814359.
    37. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007 Nov 08; 450(7167):203-18. PMID: 17994087.
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    38. 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.
    39. 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.
    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. 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.
    42. 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.
    43. 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.
    44. 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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    45. 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.
    46. 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.
    47. 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.
    48. 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.
    49. 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.
    50. 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.
    51. 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.
    52. Dernburg AF, Karpen G. A chromosome RNAissance. Cell. 2002 Oct 18; 111(2):159-62. PMID: 12408860.
      View in: PubMed
    53. 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.
    54. 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.
    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.

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