Genome Information Analysis Team

How can we discriminate healthy and disease status in our body? We will study transcriptional networks and develop innovative analysis technologies based on next generation sequencing data to clarify differences between normal and disease cells, such as cancer. The team will also develop methods to identify biomarkers for early detection of disease, and applications to use genomics data to broadly understand biological function.

Research Fields

Biology & Biochemistry / Molecular Biology & Genetics

Research Subjects

• Mammalian transcriptional networks
• Transcriptome
• Bioinformatics

Publications

1. Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest ARR, Carninci P, Biffo S, Stupka E, Gustincich S: Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature doi:10.1038/nature11508 (2012)
2. Kanamori-Katayama M, Itoh M, Hideya K, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest ARR, Hayashizaki Y. Unamplified Cap Analysis of Gene Expression on a single molecule sequencer. Genome Research doi: 10.1101/gr.115469.110 (2011)
3. Forrest ARR, Kanamori-Katayama M, Tomaru Y, Lassmann T, Ninomiya N, Takahashi Y, de Hoon MJL, Kubosaki A, Kaiho A, Suzuki M, Yasuda J, Kawai J, Hayashizaki Y, Hume DA, Suzuki H. Induction of microRNAs mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation. Leukemia 24: 460-466 (2010)
4. Ravasi T, Cannistraci C, Katayama S, Bajic V, Tan K, Akalin A, Schmeier S, Kamburov A, Kanamori M, Bertin N, Carninci P, Daub C, Forrest A, Gough J, Grimmond S, Han J, Hashimoto T, Hide W, Hofmann O, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson C, Ogawa C, Radovanovic A, Schwartz A, Teasdale R, Tegnér J, Lenhard B, Teichmann S, Hume D, Ideker T, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Suzuki H, Hayashizaki Y. An atlas of combinatorial transcriptional regulation in mouse and man. Cell Mar 5;140(5):744-52 (2010)
5. Suzuki H, Forrest ARR, van Nimwegen E, Daub C, Balwierz P, Irvine K, Lassmann T, Ravasi T, Hasegawa Y, de Hoon J, 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 V, Bauer D, Beckhouse A, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk A, Chiba J, Cloonan N, Dawe A, Dostie J, Engström P, Essack M, Faulkner G, Fink J, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond S, 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 M, 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 C, Maqungo M, Mar J, Matigian N, Matsuda H, Mattick J, 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 A, Semple C, Sera M, Severin J, Shirahige K, Simons C, St. Laurent G, Suzuki M, Suzuki T, Sweet M, Taft R, Takeda S, Takenaka S, Tan K, Taylor M, Teasdale R, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells C, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume D, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami H, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J Hayashizaki Y: The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics doi:10.1038/ng.375 (2009)
6. Severin JM, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJL, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest ARR: FANTOM4 EdgeExpressDB: an integrated database of genes, microRNAs, their promoters, expression dynamics and regulatory interactions. Genome Biology. 10:R39 (2009)
7. Faulkner G, Kimura Y, Daub C, Wani S, Plessy C, Irvine K, Schroder K, Cloonan N, Steptoe A, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest ARR, Suzuki H, Hayashizaki Y, Hume D, Orlando V, Grimmond S, Carninci P: The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics doi:10.1038/ng.368 (2009)
8. Taft R, Glazov E, Cloonan N, Simons C, Stephen S, Faulkner G, Lassmann T, Forrest ARR, Grimmond S, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub C, Hume D, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick J: Tiny RNAs associated with transcription start sites in animals. Nature Genetics doi:10.1038/ng.312 (2009)
9. Takahashi Y, Forrest A, Maeno E, Hashimoto T, Daub C, Yasuda J. MiR-107 and miR-185 can induce cell cycle arrest in human non small cell lung cancer cell lines, PLoS One 4, 2009-08-18
10. Cloonan N, Forrest ARR, Kolle G, Gardiner BA, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM. Stem cell transcriptome profiling via massive-scale mRNA sequencing Nature Methods doi:10.1038/nmeth.1223 (2008)