Main Publications List

* Equal contribution / ** Co-corresponding author

1. Chromatin accessibility landscape of articular knee cartilage reveals aberrant enhancer regulation in osteoarthritis.
   Liu Y*, Chang JC*, Hon CC, Fukui N, Tanaka N, Zhang Z, Lee MTM**, Minoda A**.
   Sci Rep., 8(1):15499. (2018)
2. JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.
   Handoko L*, Kaczkowski B*, Hon CC, Lizio M, Wakamori M, Matsuda T, Ito T, Jeyamohan P, Sato Y, Sakamoto K, Yokoyama S, Kimura H, Minoda A**, Umehara T**.
   Epigenetics., 13(4):410-431. (2018)
3. Peripheral PDGFRα⁺gp38⁺ mesenchymal cells support the differentiation of fetal liver-derived ILC2.
   Koga S, Hozumi K, Hirano KI, Yazawa M, Terooatea T, Minoda A, Nagasawa T, Koyasu S, Moro K.
   J Exp Med., 215(6):1609-1626. (2018)
4. Priming of lineage-specifying genes by Bcl11b is required for lineage choice in post-selection thymocytes.
   Kojo S, Tanaka H, Endo TA, Muroi S, Liu Y, Seo W, Tenno M, Kakugawa K, Naoe Y, Nair K, Moro K, Katsuragi Y, Kanai A, Inaba T, Egawa T, Venkatesh B, Minoda A, Kominami R, Taniuchi I.
   Nat Commun., 8(1):702 (2017)
5. Identification of chromatin marks at TERRA promoter and encoding region.
   Negishi Y, Kawaji H, Minoda A**, Usui K.
   Biochem Biophys Res Commun., 467(4):1052-7. (2015)
6. Comparative analysis of metazoan chromatin organization.
   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 GH, Park PJ. *Co-second authors
   Nature, 512(7515):449-452 (2014)
7. Impact of sequencing depth in ChIP-seq experiments
   Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ.
   Nucleic Acids Res., 42(9):e74 (2014)
8. Nature and function of insulator protein binding sites in the Drosophila genome.
   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 GH, Pirrotta V.
   Genome Res., 22(11):2188-2198 (2012)
9. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.
   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 GH, Park PJ, Elgin SC.
   PLoS Genet., 8(9):e1002954 (2012)
10. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context.
    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 GH, Pirrotta V, Kuroda MI, Park PJ.
    PLoS Genet., 8(4):e1002646 (2012)
11. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.
    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 GH, Park PJ.
    Nature, 471(7339):480-485 (2011)
12. Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair.
    Chiolo I, Minoda A, Colmenares SU, Polyzos A, Costes SV, Karpen GH.
    Cell, 144(5):732-744 (2011)
13. An assessment of histone-modification antibody quality.
    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 GH, Hawkins RD, Lieb JD.
    *Co-first authors
    Nat Struct Mol Biol., 18(1):91-93 (2011)
14. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin.
    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 GH. *Co-first authors
    Genome Res., 21(2):147-163 (2011)
15. Identification of functional elements and regulatory circuits by Drosophila modENCODE.
    modENCODE Consortium, 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 GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M.
    Science, 330(6012):1787-1797 (2010)