Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations. - Michiel J. L. de Hoon; Seiya Imoto; Satoru Miyano (Discovery Science, 2002)

Statistical analysis of a small set of time-ordered gene expression data using linear splines. - Michiel J. L. de Hoon; Seiya Imoto; Satoru Miyano (Bioinform., 2002)

Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations. - Michiel J. L. de Hoon; Seiya Imoto; Kazuo Kobayashi; Naotake Ogasawara; Satoru Miyano (Pacific Symposium on Biocomputing, 2003)

Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. - Michiel J. L. de Hoon; Yuko Makita; Seiya Imoto; Kazuo Kobayashi; Naotake Ogasawara; Kenta Nakai; Satoru Miyano (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information. - Michiel J. L. de Hoon; Seiya Imoto; Kazuo Kobayashi; Naotake Ogasawara; Satoru Miyano (Pacific Symposium on Biocomputing, 2004)

Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis. - Yuko Makita; Michiel J. L. de Hoon; Naotake Ogasawara; Satoru Miyano; Kenta Nakai (Pacific Symposium on Biocomputing, 2005)

Comparative Systems Biology of the Sporulation Initiation Network in Prokaryotes. - Michiel J. L. de Hoon; Dennis Vitkup (Systems Biology and Regulatory Genomics, 2005)

Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species. - Michiel J. L. de Hoon; Yuko Makita; Kenta Nakai; Satoru Miyano (PLoS Comput. Biol., 2005)

Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. - Yuko Makita; Michiel J. L. de Hoon; Antoine Danchin (BMC Bioinform., 2007)

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. - Nicolas Sierro; Yuko Makita; Michiel J. L. de Hoon; Kenta Nakai (Nucleic Acids Res., 2008)

Biopython: freely available Python tools for computational molecular biology and bioinformatics. - Peter J. A. Cock; Tiago Rodrigues Antao; Jeffrey T. Chang; Brad A. Chapman; Cymon J. Cox; Andrew Dalke; Iddo Friedberg; Thomas Hamelryck; Frank Kauff; Bartek Wilczynski; Michiel J. L. de Hoon (Bioinform., 2009)

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite. - Takehiro Hashimoto; Michiel J. L. de Hoon; Sean M. Grimmond; Carsten O. Daub; Yoshihide Hayashizaki; Geoffrey J. Faulkner (Bioinform., 2009)

Optimization of turn-back primers in isothermal amplification. - Yasumasa Kimura; Michiel J. L. de Hoon; Shintaro Aoki; Yuri Ishizu; Carsten O. Daub; Alexander Lezhava; Erik Arner; Yoshihide Hayashizaki; Yuki Kawai; Yasushi Kogo (BIBM Workshops, 2011)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. - Hans Ienasescu; Kang Li; Robin Andersson; Morana Vitezic; Sarah Rennie; Yun Chen; Kristoffer Vitting-Seerup; Emil Lagoni; Mette Boyd; Jette Bornholdt; Michiel J. L. de Hoon; Hideya Kawaji; et al. (Database J. Biol. Databases Curation, 2016)

Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment. - Trisevgeni Rapakoulia; Xin Gao 001; Yi Huang; Michiel J. L. de Hoon; Mariko Okada-Hatakeyama; Harukazu Suzuki; Erik Arner (Bioinform., 2017)

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. - Marina Lizio; Imad Abugessaisa; Shuhei Noguchi; Atsushi Kondo; Akira Hasegawa; Chung-Chau Hon; Michiel J. L. de Hoon; Jessica Severin; Shinya Oki; Yoshihide Hayashizaki; Piero Carninci; Takeya Kasukawa; et al. (Nucleic Acids Res., 2019)

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. - Imad Abugessaisa; Jordan A. Ramilowski; Marina Lizio; Jesicca Severin; Akira Hasegawa; Jayson Harshbarger; Atsushi Kondo; Shuhei Noguchi; Chi Wai Yip; Jasmine Li Ching Ooi; Michihira Tagami; Fumi Hori; et al. (Nucleic Acids Res., 2021)