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Page 1
A flexible cross-platform single-cell data processing pipeline.
Battenberg K, Kelly ST, Ras RA, Hetherington NA, Hayashi M, Minoda A. Battenberg K, et al. Among authors: minoda a. Nat Commun. 2022 Nov 11;13(1):6847. doi: 10.1038/s41467-022-34681-z. Nat Commun. 2022. PMID: 36369450 Free PMC article.
Functional annotation of human long noncoding RNAs via molecular phenotyping.
Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman … See abstract for full author list ➔ Ramilowski JA, et al. Among authors: minoda a. Genome Res. 2020 Jul;30(7):1060-1072. doi: 10.1101/gr.254219.119. Epub 2020 Jul 27. Genome Res. 2020. PMID: 32718982 Free PMC article.
Integrative analysis of scRNA-seq and scATAC-seq revealed transit-amplifying thymic epithelial cells expressing autoimmune regulator.
Miyao T, Miyauchi M, Kelly ST, Terooatea TW, Ishikawa T, Oh E, Hirai S, Horie K, Takakura Y, Ohki H, Hayama M, Maruyama Y, Seki T, Ishii H, Yabukami H, Yoshida M, Inoue A, Sakaue-Sawano A, Miyawaki A, Muratani M, Minoda A, Akiyama N, Akiyama T. Miyao T, et al. Among authors: minoda a. Elife. 2022 May 17;11:e73998. doi: 10.7554/eLife.73998. Elife. 2022. PMID: 35578835 Free PMC article.
Defining super-enhancers by highly ranked histone H4 multi-acetylation levels identifies transcription factors associated with glioblastoma stem-like properties.
Das ND, Chang JC, Hon CC, Kelly ST, Ito S, Lizio M, Kaczkowski B, Watanabe H, Katsushima K, Natsume A, Koseki H, Kondo Y, Minoda A, Umehara T. Das ND, et al. Among authors: minoda a. BMC Genomics. 2023 Sep 27;24(1):574. doi: 10.1186/s12864-023-09659-w. BMC Genomics. 2023. PMID: 37759202 Free PMC article.
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. Ho JW, et al. Among authors: minoda a. Nature. 2014 Aug 28;512(7515):449-52. doi: 10.1038/nature13415. Nature. 2014. PMID: 25164756 Free PMC article.
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. Riddle NC, et al. Among authors: minoda a. Genome Res. 2011 Feb;21(2):147-63. doi: 10.1101/gr.110098.110. Epub 2010 Dec 22. Genome Res. 2011. PMID: 21177972 Free PMC article.
Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians.
Hashimoto K, Kouno T, Ikawa T, Hayatsu N, Miyajima Y, Yabukami H, Terooatea T, Sasaki T, Suzuki T, Valentine M, Pascarella G, Okazaki Y, Suzuki H, Shin JW, Minoda A, Taniuchi I, Okano H, Arai Y, Hirose N, Carninci P. Hashimoto K, et al. Among authors: minoda a. Proc Natl Acad Sci U S A. 2019 Nov 26;116(48):24242-24251. doi: 10.1073/pnas.1907883116. Epub 2019 Nov 12. Proc Natl Acad Sci U S A. 2019. PMID: 31719197 Free PMC article.
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. Egelhofer TA, et al. Among authors: minoda a. Nat Struct Mol Biol. 2011 Jan;18(1):91-3. doi: 10.1038/nsmb.1972. Epub 2010 Dec 5. Nat Struct Mol Biol. 2011. PMID: 21131980 Free PMC article.
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. Kharchenko PV, et al. Among authors: minoda a. Nature. 2011 Mar 24;471(7339):480-5. doi: 10.1038/nature09725. Epub 2010 Dec 22. Nature. 2011. PMID: 21179089 Free PMC article.
57 results