Laboratory for Applied Computational Genomics

Publications List

 

  1. Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection.
    Zhang PGY, Yeung J, Gupta I, Ramirez M, Ha T, Swanson DJ, Nagao-Sato S, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, De Hoon M,; FANTOM consortium, Carninci P, Forrest ARR, Hayashizaki Y, Goldowitz D.
    Cerebellum. , 2018 Jan 6:[Epub ahead of print] (2018)
  2. Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment.
    Rapakoulia T, Gao X, Huang Y, De Hoon M, Okada-Hatakeyama M, Suzuki H, Arner E.
    Bioinformatics., 33(23):3696-3700 (2017)
  3. An integrated expression atlas of miRNAs and their promoters in human and mouse.
    de Rie D, Abugessaisa I, Alam T, Arner E, Arner P, Ashoor H, Åström G, Babina M, Bertin N, Burroughs AM, Carlisle AJ, Daub CO, Detmar M, Deviatiiarov R, Fort A, Gebhard C, Goldowitz D, Guhl S, Ha TJ, Harshbarger J, Hasegawa A, Hashimoto K, Herlyn M, Heutink P, Hitchens KJ, Hon CC, Huang E, Ishizu Y, Kai C, Kasukawa T, Klinken P, Lassmann T, Lecellier CH, Lee W, Lizio M, Makeev V, Mathelier A, Medvedeva YA, Mejhert N, Mungall CJ, Noma S, Ohshima M, Okada-Hatakeyama M, Persson H, Rizzu P, Roudnicky F, Sætrom P, Sato H, Severin J, Shin JW, Swoboda RK, Tarui H, Toyoda H, Vitting-Seerup K, Winteringham L, Yamaguchi Y, Yasuzawa K, Yoneda M, Yumoto N, Zabierowski S, Zhang PG, Wells CA, Summers KM, Kawaji H, Sandelin A, Rehli M,; FANTOM Consortium, Hayashizaki Y, Carninci P, Forrest ARR, De Hoon MJL.
    Nat Biotechnol., 35(9):872-878 (2017)
  4. An atlas of human long non-coding RNAs with accurate 5' ends.
    Hon CC, Ramilowski JA, Harshbarger J, Bertin N, Rackham OJ, Gough J, Denisenko E, Schmeier S, Poulsen TM, Severin J, Lizio M, Kawaji H, Kasukawa T, Itoh M, Burroughs AM, Noma S, Djebali S, Alam T, Medvedeva YA, Testa AC, Lipovich L, Yip CW, Abugessaisa I, Mendez M, Hasegawa A, Tang D, Lassmann T, Heutink P, Babina M, Wells CA, Kojima S, Nakamura Y, Suzuki H, Daub CO, De Hoon MJ, Arner E, Hayashizaki Y, Carninci P, Forrest AR.
    Nature., 543(7644):199-204 (2017)
  5. Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.
    Baillie JK, Arner E, Daub C, De Hoon M, Itoh M, Kawaji H, Lassmann T, Carninci P, Forrest AR, Hayashizaki Y; FANTOM Consortium, Faulkner GJ, Wells CA, Rehli M, Pavli P, Summers KM, Hume DA.
    PLoS Genet. , 13(3):e1006641 (2017)
  6. HER2-encoded mir-4728 forms a receptor-independent circuit with miR-21-5p through the non-canonical poly(A) polymerase PAPD5.
    Newie I, Søkilde R, Persson H, Jacomasso T, Gorbatenko A, Borg Å, De Hoon M, Pedersen SF, Rovira C.
    Sci Rep., 6:35564 (2016)
  7. Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.
    St Laurent G, Vyatkin Y, Antonets D, Ri M, Qi Y, Saik O, Shtokalo D, De Hoon MJ, Kawaji H, Itoh M, Lassmann T, Arner E, Forrest AR; FANTOM consortium, Nicolas E, McCaffrey TA, Carninci P, Hayashizaki Y, Wahlestedt C, Kapranov P.
    Nucleic Acids Res., 44(7):3233-52 (2016)
  8. Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays.
    Kimura Y, Soma T, Kasahara N, Delobel D, Hanami T, Tanaka Y, De Hoon MJ, Hayashizaki Y, Usui K, Harbers M.
    PLoS One., 11(2):e0146950 (2016)
  9. Paradigm shifts in genomics through the FANTOM projects.
    De Hoon M, Shin JW, Carninci P.
    Mamm Genome., 26(9-10):391-402 (2015)
  10. Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.
    Roy S, Schmeier S, Arner E, Alam T, Parihar SP, Ozturk M, Tamgue O, Kawaji H, De Hoon MJ, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Bajic VB, Guler R; Fantom Consortium, Brombacher F, Suzuki H.
    Nucleic Acids Res., 43(14):6969-82 (2015)
  11. Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection.
    Roy S, Guler R, Parihar SP, Schmeier S, Kaczkowski B, Nishimura H, Shin JW, Negishi Y, Ozturk M, Hurdayal R, Kubosaki A, Kimura Y, De Hoon MJ, Hayashizaki Y, Brombacher F, Suzuki H.
    J Immunol., 194(12):6035-44 (2015)
  12. Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles.
    Persson H, Kwon AT, Ramilowski JA, Silberberg G, Söderhäll C, Orsmark-Pietras C, Nordlund B, Konradsen JR, De Hoon MJ, Melén E, Hayashizaki Y, Hedlin G, Kere J, Daub CO.
    J Allergy Clin Immunol., 136(3):638-48 (2015)
  13. Gateways to the FANTOM5 promoter level mammalian expression atlas.
    Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, De Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H; FANTOM consortium.
    Genome Biol., 16:22 (2015)
  14. 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):1010-4 (2015)
  15. Multiplicity of 5' cap structures present on short RNAs.
    Abdelhamid RF, Plessy C, Yamauchi Y, Taoka M, De Hoon M, Gingeras TR, Isobe T, Carninci P.
    PLoS One., 9(7):e102895 (2014)
  16. PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.
    Boele J, Persson H, Shin JW, Ishizu Y, Newie IS, Søkilde R, Hawkins SM, Coarfa C, Ikeda K, Takayama K, Horie-Inoue K, Ando Y, Burroughs AM, Sasaki C, Suzuki C, Sakai M, Aoki S, Ogawa A, Hasegawa A, Lizio M, Kaida K, Teusink B, Carninci P, Suzuki H, Inoue S, Gunaratne PH, Rovira C, Hayashizaki Y, De Hoon MJ.
    Proc Natl Acad Sci U S A. , 111(31):11467-72 (2014)
  17. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons 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.
    Nat Genet., 46(6):558-66 (2014)
  18. Systemic identification of estrogen-regulated genes in breast cancer cells through cap analysis of gene expression mapping.
    Yamaga R, Ikeda K, Boele J, Horie-Inoue K, Takayama K, Urano T, Kaida K, Carninci P, Kawai J, Hayashizaki Y, Ouchi Y, De Hoon M, Inoue S.
    Biochem Biophys Res Commun., 447(3):531-6 (2014)
  19. Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.
    Davis MR, Andersson R, Severin J, De Hoon M, Bertin N, Baillie JK, Kawaji H, Sandelin A, Forrest AR, Summers KM; FANTOM Consortium.
    Mol Genet Metab., 112(1):73-83 (2014)
  20. 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):e58-67 (2014)
  21. 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 AR, Sandelin A, Ekwall K, Arner E, Lennartsson A; FANTOM consortium.
    Blood., 123(17):e79-89 (2014)
  22. A promoter-level mammalian expression atlas.
    FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, 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, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, 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, Furino 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, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya 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, 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, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado 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, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.
    Nature., 507(7493):462-70 (2014)
  23. Temporal dynamics and transcriptional control using single-cell gene expression analysis.
    Kouno T, De Hoon M, Mar JC, Tomaru Y, Kawano M, Carninci P, Suzuki H, Hayashizaki Y, Shin JW.
    Genome Biol., 14(10):R118 (2013)
  24. Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation.
    Harbers M, Kato S, De Hoon M, Hayashizaki Y, Carninci P, Plessy C.
    BMC Genomics., 14:665 (2013)
  25. Identification of ZNF395 as a novel modulator of adipogenesis.
    Hasegawa R, Tomaru Y, De Hoon M, Suzuki H, Hayashizaki Y, Shin JW.
    Exp Cell Res., 319(3):68-76 (2013)
  26. Effect of thiazole orange doubly labeled thymidine on DNA duplex formation.
    Kimura Y, Hanami T, Tanaka Y, De Hoon MJ, Soma T, Harbers M, Lezhava A, Hayashizaki Y, Usui K.
    Biochemistry., 51(31):6056-67 (2012)
  27. Site-specific DICER and DROSHA RNA products control the DNA-damage response.
    Francia S, Michelini F, Saxena A, Tang D, De Hoon M, Anelli V, Mione M, Carninci P, d'Adda di Fagagna F.
    Nature., 488(7410):231-5 (2012)
  28. Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts.
    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.
    PLoS One., 7(3):e33474 (2012)
  29. Optimization of turn-back primers in isothermal amplification.
    Kimura Y, De Hoon MJ, Aoki S, Ishizu Y, Kawai Y, Kogo Y, Daub CO, Lezhava A, Arner E, Hayashizaki Y.
    Nucleic Acids Res., 39(9):e59 (2011)
  30. Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin.
    Burroughs AM, Ando Y, De Hoon MJ, Tomaru Y, Suzuki H, Hayashizaki Y, Daub CO.
    RNA Biol., 8(1):158-77 (2011)
  31. Hierarchical evolution of the bacterial sporulation network.
    De Hoon MJ, Eichenberger P, Vitkup D.
    Curr Biol., 20(17):R735-45 (2010)
  32. A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness.
    Burroughs AM, Ando Y, De Hoon MJ, Tomaru Y, Nishibu T, Ukekawa R, Funakoshi T, Kurokawa T, Suzuki H, Hayashizaki Y, Daub CO.
    Genome Res., 20(10):1398-410 (2010)
  33. Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries.
    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.
    Genome Res., 20(2):257-64 (2010)
  34. 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):460-6 (2010)
  35. Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.
    Hashimoto T, De Hoon MJ, Grimmond SM, Daub CO, Hayashizaki Y, Faulkner GJ.
    Bioinformatics., 25(19):2613-4 (2009)
  36. 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):553-62 (2009)
  37. FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.
    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.
    Genome Biol. , 10(4):R39 (2009)
  38. Biopython: freely available Python tools for computational molecular biology and bioinformatics.
    Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, De Hoon MJ.
    Bioinformatics., 25(11):1422-3 (2009)
  39. Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference.
    De Hoon M, Hayashizaki Y.
    Biotechniques., 44(5):627-8, 630, 632 (2008)
  40. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information.
    Sierro N, Makita Y, De Hoon M, Nakai K.
    Nucleic Acids Res., 36(Database issue):D93-6 (2008)
  41. Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes.
    Makita Y, De Hoon MJ, Danchin A.
    BMC Bioinformatics., 8:47 (2007)
  42. Prediction of transcriptional terminators in Bacillus subtilis and related species.
    De Hoon MJ, Makita Y, Nakai K, Miyano S.
    PLoS Comput Biol., 1(3):e25 (2005)
  43. Bayesian joint prediction of associated transcription factors in Bacillus subtilis.
    Makita Y, De Hoon MJ, Ogasawara N, Miyano S, Nakai K.
    Pac Symp Biocomput., 2005:507-18 (2005)
  44. Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.
    De Hoon MJ, Makita Y, Imoto S, Kobayashi K, Ogasawara N, Nakai K, Miyano S.
    Bioinformatics., 20 Suppl 1:i101-8 (2004)
  45. Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information.
    De Hoon MJ, Imoto S, Kobayashi K, Ogasawara N, Miyano S.
    Pac Symp Biocomput., 2004:276-87 (2004)
  46. Open source clustering software.
    De Hoon MJ, Imoto S, Nolan J, Miyano S.
    Bioinformatics., 20(9):1453-4 (2004)
  47. Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations.
    De Hoon MJ, Imoto S, Kobayashi K, Ogasawara N, Miyano S.
    Pac Symp Biocomput., 2003:17-28 (2003)
  48. Statistical analysis of a small set of time-ordered gene expression data using linear splines.
    De Hoon MJ, Imoto S, Miyano S.
    Bioinformatics., 18(11):1477-85 (2002)