Members

Michiel De hoon Mr Michiel De hoon, PhD
Research Scientist - LSA Bioinformatics Core Facility
Phone: 045-5039218-3113
Email:

Link to OSC Main Activities: FANTOM Genome Network Functional RNA LSA


Research Interest:
  • Novel types of RNA, in particular their function and biological role in the cell.
  • General features of transcription and gene regulation, as inferred from genome-wide data.
  • Molecular mechanisms of gene regulation.

 


Bibekanand Mallick, Zhumur Ghosh (Editors): Regulatory RNAs: Basics, Methods and Applications. (2012). Springer-Verlag. Book contributor.

Piero Carninci: Cap Analysis Gene Expression (CAGE): The Science of Decoding Genes Transcription. (2009). Pan Stanford. Book contributor.

藤渕航,編堀本勝久: マイクロアレイデータ統計解析プロトコール (Protocols of statistical analysis of microarray data). (2008). 羊土社版 (Yodosha). Book contributor.

宮野悟(委員長),江 口至洋(副委員長), 金久實,高木利久,中 井謙太: バイオインフォマティクス事典 (Encyclopedia of Bioinformatics). (2006). 日本バイオインフォマティクス学会 (JSBi). Book contributor.



Curriculum Vitae:

Education

Ph.D. Physics, University of California, Berkeley. May 2001.

M.Sc. Applied Physics, with honors. Delft University of Technology, Netherlands. September 1995.

Experience

Research Scientist, RIKEN Omics Science Center, RIKEN Yokohama Institute, Bioinformatics team (since May 2007).

Postdoctoral Researcher, Center for Computational Biology and Bioinformatics, Columbia University, New York (May 2005 – March 2007).

Postdoctoral Research and Assistant Professor, Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo (August 2001 – May 2005).


Bibliography:

Site-specific DICER and DROSHA RNA products control the DNA-damage response.
Nature 2012 May 23; Francia S, Michelini F, Saxena A, Tang D, de Hoon M, Anelli V, Mione M, Carninci P, di Fagagna FD
Effect of Thiazole Orange Doubly Labeled Thymidine on DNA Duplex Formation.
Biochemistry 2012 Jul 25; Kimura Y, Hanami T, Tanaka Y, de Hoon MJ, Soma T, Harbers M, Lezhava A, Hayashizaki Y, Usui K
Reconstruction of Monocyte Transcriptional Regulatory Network Accompanies Monocytic Functions in Human Fibroblasts
PLoS One 2012-03-13 Suzuki T, Ikegaya (Nakano) M, Okuda-Yabukami H, De Hoon M, Severin J, Shin J, Kubosaki A, Simon C, Hasegawa Y, Hayashizaki Y, Suzuki H
Targeted methods to improve small RNA profiles generated by deep sequencing
Regulatory RNAs: Basics, Methods and Applications() 2012-01-01 Ando Y, Burroughs A, Kawano M, De Hoon M, Hayashizaki Y
Optimization of turn-back primers in isothermal amplification.
Nucleic Acids Res 2011 Feb 9; Kimura Y, de Hoon MJ, Aoki S, Ishizu Y, Kawai Y, Kogo Y, Daub CO, Lezhava A, Arner E, Hayashizaki Y
Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin.
RNA Biol 2011 Jan 1;8(1) Burroughs AM, Ando Y, Hoon ML, Tomaru Y, Suzuki H, Hayashizaki Y, Daub CO
A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness.
Genome Res 2010 Oct;20(10):1398-410 Burroughs AM, Ando Y, de Hoon MJ, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y, Daub CO
Hierarchical evolution of the bacterial sporulation network.
Curr Biol 2010 Sep 14;20(17):R735-45 de Hoon MJ, Eichenberger P, Vitkup D
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries.
Genome Res 2010 Feb;20(2):257-64 de Hoon MJ, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, Kawano M, Kishima M, Lassmann T, Faulkner GJ, Mattick JS, Daub CO, Carninci P, Kawai J, Suzuki H, Hayashizaki Y
Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation.
Leukemia 2010 Feb;24(2):460-6 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
Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.
Bioinformatics 2009 Oct 1;25(19):2613-4 Hashimoto T, de Hoon MJ, Grimmond SM, Daub CO, Hayashizaki Y, Faulkner GJ
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Nat Genet 2009 May;41(5):553-62 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, 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
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.
Genome Biol 2009;10(4):R39 Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR
Biopython: freely available Python tools for computational molecular biology and bioinformatics.
Bioinformatics 2009 Jun 1;25(11):1422-3 Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ
Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference.
Biotechniques 2008 Apr;44(5):627-8, 630, 632 de Hoon M, Hayashizaki Y
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information.
Nucleic Acids Res 2008 Jan;36(Database issue):D93-6 Sierro N, Makita Y, de Hoon M, Nakai K
Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts.
PLoS One 2012;7(3):e33474 Suzuki T, Nakano-Ikegaya M, Yabukami-Okuda H, de Hoon M, Severin J, Saga-Hatano S, Shin JW, Kubosaki A, Simon C, Hasegawa Y, Hayashizaki Y, Suzuki H
Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes.
BMC Bioinformatics 2007 Feb 8;8:47 Makita Y, de Hoon MJ, Danchin A
Prediction of transcriptional terminators in Bacillus subtilis and related species.
PLoS Comput Biol 2005 Aug;1(3):e25 de Hoon MJ, Makita Y, Nakai K, Miyano S
Bayesian joint prediction of associated transcription factors in Bacillus subtilis.
Pac Symp Biocomput 2005;:507-18 Makita Y, De Hoon MJ, Ogasawara N, Miyano S, Nakai K
Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.
Bioinformatics 2004 Aug 4;20 Suppl 1:i101-8 de Hoon MJ, Makita Y, Imoto S, Kobayashi K, Ogasawara N, Nakai K, Miyano S
Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information.
Pac Symp Biocomput 2004;:276-87 De Hoon MJ, Imoto S, Kobayashi K, Ogasawara N, Miyano S
Open source clustering software.
Bioinformatics 2004 Jun 12;20(9):1453-4 de Hoon MJ, Imoto S, Nolan J, Miyano S
Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations.
Pac Symp Biocomput 2003;:17-28 de Hoon MJ, Imoto S, Kobayashi K, Ogasawara N, Miyano S
Statistical analysis of a small set of time-ordered gene expression data using linear splines.
Bioinformatics 2002 Nov;18(11):1477-85 De Hoon MJ, Imoto S, Miyano S