1. Miyashita A†, Hatsuta H, Kikuchi M, Nakaya A, Saito Y, Tsukie T, Hara N, Ogishima S, Kitamura N, Akazawa K, Kakita A, Takahashi H, Murayama S, Ihara Y, Ikeuchi T, Kuwano R (2014) Genes associated with the progression of neurofibrillary tangles in Alzheimer’s disease. Transl Psychiatry (accepted).
2. Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S†, FANTOM Consortium. (2014) Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proc Natl Acad Sci U S A. 111(14):5289-94.
3. Arner E†, Forrest AR, Ehrlund A, Mejhert N, Itoh M, Kawaji H, Lassmann T, Laurencikiene J, Rydén M, Arner P†, FANTOM Consortium. (2014) Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. PLoS One. 9(3):e80274.
4. FANTOM Consortium and the RIKEN PMI and CLST (DGT). (2014) A promoter-level mammalian expression atlas. Nature 507(7493):462-70.
5. Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F; FANTOM Consortium, Forrest AR†, Carninci P†, Rehli M†, Sandelin A†, Kawaji H, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmid C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple CA, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furuno M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Nozaki T, Ogishima S, Ohkura N, Ohmiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Satoh H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, ‘t Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyoda H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verardo R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Hume DA, Hayashizaki Y. (2014) An atlas of active enhancers across human cell types and tissues. Nature 507(7493):455-61.
6. Katayama T†, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kala M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. (2014) BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics. 5(1):5.
7. Kikuchi M, Ogishima S†, Miyamoto T, Miyashita A, Kuwano R, Nakaya J, Tanaka H. (2013) Identification of unstable network modules reveals disease modules associated with the progression of Alzheimer’s disease. PLoS One. 8(11):e76162.
8. Nishio Y†, Ogishima S†, Ichikawa M, Yamada Y, Usuda Y, Masuda T, Tanaka H. (2013) Analysis of L-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli. BMC Syst Biol. 7:92.
9. Ogishima S†, Mizuno S, Kikuchi M, Miyashita A, Kuwano R, Tanaka H, Nakaya J. (2013) A map of Alzheimer’s disease-signaling pathways: a hope for drug target discovery. Clin Pharmacol Ther. 93(5):399-401.
10. Katayama T†, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T. (2013) The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics. 4(1):6.
11. Mizuno S, Iijima R, Ogishima S, Kikuchi M, Matsuoka Y, Ghosh S, Miyamoto T, Miyashita A, Kuwano R, Tanaka H. (2012) AlzPathway: a comprehensive map of signaling pathways of Alzheimer’s disease. BMC Syst Biol. 6:52.
12. Böck M, Ogishima S, Tanaka H, Kramer S, Kaderali L. (2012) Hub-centered gene network reconstruction using automatic relevance determination. PLoS One. 7(5):e35077.
13. Sekiya I†, Ojima M, Suzuki S, Yamaga M, Horie M, Koga H, Tsuji K, Miyaguchi K, Ogishima S, Tanaka H, Muneta T. (2011) Human mesenchymal stem cells in synovial fluid increase in the knee with degenerated cartilage and osteoarthritis. J Orthop Res. 30(6):943-9.
14. Katayama T†, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernández JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T. (2011) The 2nd DBCLS BioHackathon: interoperable bioinformatics web services for integrated applications. J Biomed Semantics. 2:4.
15. Tanaka H, Ogishima S. (2011) Omics-based identification of pathophysiological processes. Methods Mol Biol. 719:499-509.
16. Shiwaku H, Yoshimura N, Tamura T, Sone M, Ogishima S, Watase K, Tagawa K, Okazawa H†. (2010) Suppression of the novel ER protein Maxer by mutant ataxin-1 in Bergman glia contributes to non-cell-autonomous toxicity. EMBO J. 29(14):2446-60.
17. Yoshimura K, Takeuchi K, Nagasaki K, Ogishima S, Tanaka H, Iwase T, Akiyama F, Kuroda Y, Miki Y.† (2009) Prognostic value of matrix Gla protein in breast cancer. Mol Med Report. 2(4):549-53.
18. Ota MS, Kaneko Y, Kondo K, Ogishima S, Tanaka H, Eto K, Kondo T†. (2009) Combined in silico and in vivo analyses reveal role of Hes1 in taste cell differentiation. PLoS Genetics. 5(4): e1000443.
19. Ishiwata, R.R., Morioka, M.S., Ogishima, S.†, Tanaka, H. (2009) BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network. Bioinformatics. 25(4):543-544.
20. Ogishima S, Tanaka H.† (2007) Missing link in the evolution of Hox clusters. Gene 387(1-2):21-30.
21. Endo T†, Ogishima S, Tanaka H. (2003) Standardized phylogenetic tree: a reference to discover functional evolution. J Mol Evol. 57(Suppl 1):S174-81.
22. Ren F, Ogishima S, Tanaka H.† (2003) Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples: a distance-based sequential-linking method. Gene 317(1-2):89-95.
23. Ren F, Ogishima S, Tanaka H.† (2001) Inference and prediction of course of disease by pathologic viruses by estimating molecular evolution of within host virus. Stud Health Technol Inform. 84(Pt 2):979-83.
24. Ren F, Ogishima S, Tanaka H.† (2001) A new algorithm for analysis of within-host HIV-1 evolution. Pac Symp Biocomput 2001:595-605.
25. Ogishima S, Ren F, Tanaka H.† (2001) Reconstruction and analysis of within-host longitudinal HIV-1 evolution by a distance-based sequential-linking algorithm. Chem-Bio Info J. 1(2):73-83.