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At “Article”, you can read articles on interviews and lectures, and you can enjoy the videos about CLST at “Videos”. If you want to meet and talk directly with the researcher, “Visit” give you some information of such events. You can find more difficult contents to know about our research deeply at “Study”.
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Genome Information Analysis Team _Publication List

Genome Information Analysis Team

1

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.
Science, 347(6225), 1010-1014 (2015).
2

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.

Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B.
Nucleic Acids Res, in press, (2015).
3

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.

Liang, C.; FANTOM Consortium, Forrest, AR., Wagner, GP.
Nat Commun, 6, 6066 (2015).
4

CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

Vitezic, M., Bertin, N., Andersson, R., Lipovich, L., Kawaji, H., Lassmann, T., Sandelin, A., Heutink, P., Goldowitz, D., Ha, T., Zhang, P., Patrizi, A., Fagiolini, M., Forrest, AR., Carninci, P., Saxena, A.
BMC Genomics, 15(1), 1177 (2014).
5

Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer.

Verardo, R., Piazza, S., Klaric, E., Ciani, Y., Bussadori, G., Marzinotto, S., Mariuzzi, L., Cesselli, D., Beltrami, AP., Mano, M., Itoh, M., Kawaji, H., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, AR; Fantom Consortium, Beltrami, CA., Schneider, C.
Stem Cells, 32(11), 2998-3011 (2014).
6

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules.

Grison, A., Zucchelli, S., Urzì, A., Zamparo, I., Lazarevic, D., Pascarella, G., Roncaglia, P., Giorgetti, A., Garcia-Esparcia, P., Vlachouli, C., Simone, R., Persichetti, F., Forrest, AR., Hayashizaki, Y., Carloni, P., Ferrer, I., Lodovichi, C., Plessy, C.; FANTOM Consortium, Carninci, P., Gustincich, S.
BMC Genomics, 15, 729 (2014).
7

A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators.

Hurst, LD., Sachenkova, O., Daub, C., Forrest, AR., Huminiecki, L.; FANTOM consortium.
Genome Biol, 15(7), 413 (2014).
8

A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation.

Tomaru Y, Hasegawa R, Suzuki T, Sato T, Kubosaki A, Suzuki M, Kawaji H, Forrest AR, Hayashizaki Y; FANTOM Consortium, Shin JW, Suzuki H.
Nucleic Acids Research, 42(14), 8905-8913 (2014).
9

CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes

Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest ARR, Suzuki H.
Sci Rep, 4, 5228 (2014).
10

The Evolution of Human Cells in Terms of Protein Innovation

Sardar, AJ; Oates, ME; Fang, H; Forrest, ARR; Kawaji, H; Gough, J; Rackham, OJL
Mol Biol Evol, 31(6), 1364-1374 (2014).
11

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).

Ohmiya, H., Vitezic, M., Frith, M.C., Itoh, M., Carninci, P., Forrest, A.R., Hayashizaki, Y., Lassmann, T.; FANTOM Consortium.
BMC Genomics, 15(269), (2014).
12

Deep transcriptome profiling of mammalian stem cells supports a key regulatory role for retrotransposon in pluripotency maintenance

Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A, Bonetti A, Voineagu I, Bertin N, Kratz A, Noro Y, Wong CH, de Hoon M, Andersson R, Sandelin A, Suzuki H, Wei CL, Koseki H; FANTOM Consortium, Hasegawa Y, Forrest AR, Carninci P.
Nature Genetics, 46(6), 558-566 (2014).
13

Transcription and enhancer profiling in human monocyte subsets.

Schmidl, C., Renner, K., Peter, K., Eder, R., Lassmann, T., Balwierz, P.J., Itoh, M. Nagao-Sato, S., Kawaji, H., Carninci, P., Suzuki, H., Hayashizaki, Y., Andreesen, R., Hume, D.A., Hoffmann, P., Forrest, A.R., Kreutz, M.P., Edinger, M., Rehli, M.; FANTOM consortium.
Blood, 123(17), e90-e99 (2014).
14

Redefinition of the human mast cell transcriptome by deep-CAGE sequencing.

Motakis E, Guhl S, Ishizu Y, Itoh M, Kawaji H, de Hoon M, Lassmann T, Carninci P, Hayashizaki Y, Zuberbier T, Forrest AR, Babina M; FANTOM consortium.
Blood, 123(17), e58-e67 (2014).
15

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.

Rönnerblad, M., Andersson, R., Olofsson, T., Douagi, I., Karimi, M., Lehmann, S., Hoof, I., de Hoon, M., Itoh, M., Nagao-Sato, S., Kawaji, H., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, A.R., Sandelin, A., Ekwall, K., Arner, E., Lennartsson, A., FANTOM consortium.
Blood, 123(17), e79-e89 (2014).
16

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation

Morikawa, H., Ohkura, N., Vandenbon, A., Itoh, M., Nagao-Sato, S., Kawaji, H., Lassmann, T., Carninci, P., Hayashizaki, Y., Forrest, ARR., Standley, DM., Date, H., Sakaguchi, S
Proc Natl Acad Sci U S A, 111(14), 5289-5294 (2014).
17

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

Kawaji, H., Lizio, M., Itoh, M., Kanamori-Katayama, M., Kaiho, A., Nishiyori-Sueki, H., Shin, JW., Kojima-Ishiyama, M., Kawano, M., Murata, M., Ninomiya-Fukuda, N., Ishikawa-Kato, S., Nagao-Sato, S., Noma, S., Hayashizaki, Y., Forrest, ARR., Carninci, P
Genome Res, 24(4), 708-717 (2014).
18

A promoter-level mammalian expression atlas

FANTOM Consortium and the RIKEN PMI and CLST (DGT)
Nature, 507(7493), 462-470 (2014).
19

An atlas of active enhancers across human cell types and tissues

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.
Nature, 507(7493), 455-461 (2014).
20

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU

Severin J, Lizio M, Harshbarger J, Kawaji H, Daub CO, Hayashizaki Y; FANTOM Consortium, Bertin N, Forrest AR.
Nat Biotechnol, 32(3), 217-219 (2014).
21

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.

Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest AR, Carninci P, Biffo S, Stupka E, Gustincich S.
Nature, 491(7424), 454-457 (2012).
22

An atlas of combinatorial transcriptional regulation in mouse and man.

Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y.
Cell, 24(5), 744-752 (2010).
23

Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation.

Forrest AR, Kanamori-Katayama M, Tomaru Y, Lassmann T, Ninomiya N, Takahashi Y, de Hoon MJ, Kubosaki A, Kaiho A, Suzuki M, Yasuda J, Kawai J, Hayashizaki Y, Hume DA, Suzuki H.
Leukemia, 24(2), 460-466 (2010).
24

The regulated retrotransposon transcriptome of mammalian cells.

Faulkner GJ, Kimura Y, Daub CO, Wani S, Plessy C, Irvine KM, Schroder K, Cloonan N, Steptoe AL, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest AR, Suzuki H, Hayashizaki Y, Hume DA, Orlando V, Grimmond SM, Carninci P.
Nat Genet, 41(5), 563-571 (2009).
25

Tiny RNAs associated with transcription start sites in animals.

Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest AR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS.
Nat Genet, 41(5), 572-5778 (2009).
26

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y.
Nat Genet, 41(5), 553-562 (2009).

和文論文

CLST was reorganized into three centers according to the RIKEN 4th Medium-Term Plan from April 1, 2018. For the latest information of Genome Information Analysis Team, please visit the following websites.


> The webpage of Laboratory for Genome Information Analysis, Center for Integrative Medical Sciences [http://www.ims.riken.jp/labo/61/publication.html]