Current positions
- Team Leader (laboratory head / principal investigator); tenured. Laboratory for Applied Computational Genomics, RIKEN Center for Integrative Medical Sciences
- Visiting Researcher, Machine Learning and Data Science Unit, Okinawa Institute of Science and Technology
Awards
- RIKEN BAIHO (RIKEN Excellent Achievement Award), June 5, 2018
- OSC Award, March 23, 2011, with Harukazu Suzuki (project representative), Alistair Raymond Russell Forrest, Carsten Olivier Daub, Timo Lassmann, Yuki Hasegawa, Piero Carninci, Atsutaka Kubosaki, Yasuhiro Tomaru, Jun Kawai
Publications
Agrawal, S.; Buyan, A.; Severin, J.; Koido, M.; Alam, T.; Abugessaisa, I.; Chang, H.Y.; Dostie, J.; Itoh, M.; Kere, J.; Kondo, N.; Li, Y.; Makeev, V.J.; Mendez, M.; Okazaki, Y.; Ramilowski, J.A.; Sigorskikh, A.I.; Strug, L.J.; Yagi, K.; Yasuzawa, K.; Yip, C.W.; Hon, C.C.; Hoffman, M.M.; Terao, C.; Kulakovskiy, I.V.; Kasukawa, T.; Shin, J.W.; Carninci, P.; De Hoon, M.J.L. “Annotation of nuclear lncRNAs based on chromatin interactions.” PLoS One 19(5): e0295971 (2024).
Severin, J.; Agrawal, S.; Ramilowski, J.R.; Deviatiiarov, R.; Shin, J.W.; Carninci, P.; De Hoon, M. “ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data.” NAR Genomics and Bioinformatics 5(3): lqad075 (2023).
Agrawal, S.; Kanamaru, E.; Saito, Y.; Ishikawa, F.; De Hoon, M. “Unidirectional expression of enhancers with cell type-dependent direction of transcription.” bioRxiv doi: 10.1101/2023.06.27.546647v1 (2023).
“Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs.” Genome Research 32(9):1727-1735 (2022).
Ducoli, L.; Agrawal. S.; Hon, C.C.; Ramilowski, J.A.; Sibler, E.; Tagami, M.; Ito, M.; Kondo ,N.; Abugessaisa, I.; Hasegawa, A.; Kasukawa, T.; Suzuki, H.; Carninci, P.; Shin, J.W.; De Hoon, M.J.L.; Detmar, M.: “The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.” BMC Genomic Data 22, 33 (2021).
Grapotte, M.; Saraswat, M.; Bessière, C.; Menichelli, C.; Ramilowski, J.; Severin, J.; Hayashizaki, Y.; Itoh, M.; Tagami, M.; Murata, M.; Kojima, M.; Noma, S.; Noguchi, S.; Kasukawa, T.; Hasegawa, A.; Suzuki, H.; Nishiyori-Sueki, H.; Frith, M.C.; The FANTOM consortium; Chatelain, C.; Carninci, P.; De Hoon, M.; Wasserman, W.; Bréhélin, L.; Lecellier, C.: “Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.” Nature Communications 12, 3297 (2021).
Way, G.P.; Greene, C.S.; Carninci, P.; Carvalho, B.S.; De Hoon, M.; Finley, S.; Gosline, S.J.; Cao, K.L.; Lee, J.S.; Marchionni, L.; Robine, N.; Sindi, S.S.; Theis, F.J.; Yang, J.Y.; Carpenter, A.E.; Fertig, E.J.: “A field guide to cultivating computational biology.” PLoS Biology 19, e3001419–e3001419 (2021).
Hashimoto, M.; Saito, Y.; Nakagawa, R.; Ogahara, I.; Takagi, S.; Takata, S.; Amitani, H.; Endo, M.; Yuki, H.; Ramilowski, J.A.; Severin, J.; Manabe, R-I.; Watanabe, T.; Ozaki, K.; Kaneko, A.; Kajita, H.; Fujiki, S.; Sato, K.; Honma, T.; Uchida, N.; Fukami, T.; Okazaki, Y.; Ohara, O.; Shultz, L.D.; Yamada, M.; Taniguchi, S.; Vyas, P.; De Hoon, M.; Momozawa, Y.; Ishikawa, F.: “Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia.” Nature Cancer 2: 340–356 (2021).
Abugessaisa, I.; Ramilowski, J.A.; Lizio, M.; Severin, J.; Hasegawa, A.; Harshbarger, J.; Kondo, A.; Noguchi, S.; Yip, C.W.; Ooi, J.L.C.; Tagami, M.; Hori, F.; Agrawal, S.; Hon, C.C.; Cardon, M.; Ikeda, S.; Ono, H.; Bono, H.; Kato, M.; Hashimoto, K.; Bonetti, A.; Kato, M.; Kobayashi, N.; Shin, J.; De Hoon, M.; Hayashizaki, Y.; Carninci, P.; Kawaji, H.; Kasukawa, T.: “FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.” Nucleic Acids Research 49(D1): D892-D898 (2021).
Gažová, I.; Lefevre, L.; Bush, S.J.; Clohisey, S.; Arner, E.; De Hoon, M.; Severin, J.; Van Duin, L.; Andersson, R.; Lengeling, A.; Hume, D.A.; Summers, K.M.: “The transcriptional network that controls growth arrest and macrophage differentiation in the human myeloid leukemia cell line THP-1.” Frontiers in Cell and Developmental Biology 8:498 (2020).
Ramilowski, J.A.; Yip, C.W.; Agrawal, S.; Chang, J.C.; Ciani, Y.; Kulakovskiy, I.V.; Mendez, M.; Ooi, J.L.C.; Ouyang, J.F.; Parkinson, N.; Petri, A.; Roos, L.; Severin, J.; Yasuzawa, K.; Abugessaisa, I.; Akalin, A.; Antonov, I.V.; Arner, E.; Bonetti, A.; Bono, H.; Borsari, B.; Brombacher, F.; Cameron, C.J.F.; Cannistraci, C.V.; Cardenas, R.; Cardon, M.; Chang, H.; Dostie, J.; Ducoli, L.; Favorov, A.; Fort, A.; Garrido, D.; Gil, N.; Gimenez, J.; Guler, R.; Handoko, L.; Harshbarger, J.; Hasegawa, A.; Hasegawa, Y.; Hashimoto, K.; Hayatsu, N.; Heutink, P.; Hirose, T.; Imada, E.L.; Itoh, M.; Kaczkowski, B.; Kanhere, A.; Kawabata, E.; Kawaji, H.; Kawashima, T.; Kelly, S.T.; Kojima, M.; Kondo, N.; Koseki, H.; Kouno, T.; Kratz, A.; Kurowska-Stolarska, M.; Kwon, A.T.J.; Leek, J.; Lennartsson, A.; Lizio, M.; López-Redondo, F.; Luginbühl, J.; Maeda, S.; Makeev, V.J.; Marchionni, L.; Medvedeva, Y.A.; Minoda, A.; Müller, F.; Muñoz-Aguirre, M.; Murata, M.; Nishiyori, H.; Nitta, K.R.; Noguchi, S.; Noro, Y.; Nurtdinov, R.; Okazaki, Y.; Orlando, V.; Paquette, D.; Parr, C.J.C.; Rackham, O.J.L.; Rizzu, P.; Sánchez, Martinez, D.F.; Sandelin, A.; Sanjana, P.; Semple, C.A.M.; Shibayama, Y.; Sivaraman, D.M.; Suzuki, T.; Szumowski, S.C.; Tagami, M.; Taylor, M.S.; Terao, C.; Thodberg, M.; Thongjuea, S.; Tripathi, V.; Ulitsky, I.; Verardo, R.; Vorontsov, I.E.; Yamamoto, C.; Young, R.S.; Baillie, J.K.; Forrest, A.R.R.; Guigó, R.; Hoffman, M.M.; Hon, C.C.; Kasukawa, T.; Kauppinen, S.; Kere, J.; Lenhard, B.; Schneider, C.; Suzuki, H.; Yagi, K.; De Hoon, M.J.L.; Shin, J.W.; Carninci, P.: “Functional annotation of human long noncoding RNAs via molecular phenotyping.” Genome Research 30(7): 1060-1072 (2020).
Alam, T.; Agrawal, S.; Severin, J.; Young, R.S.; Andersson, R.; Arner, E.; Hasegawa, A.; Lizio, M.; Ramilowski, J.A.; Abugessaisa, I.; Ishizu, Y.; Noma, S.; Tarui, H.; Taylor, M.S.; Lassmann, T.; Itoh, M.; Kasukawa, T.; Kawaji, H.; Marchionni, L.; Sheng, G.; Forrest, A.R.R.; Khachigian, L.M.; Hayashizaki, Y.; Carninci, P.; De Hoon, M.J.L.: “Comparative transcriptomics of primary cells in vertebrates.” Genome Research 30(7): 951-961 (2020).
Imada, E.L.; Sanchez, D.F.; Collado-Torres, L.; Wilks, C.; Matam, T.; Dinalankara, W.; Stupnikov, A.; Lobo-Pereira, F.; Yip, C.W.; Yasuzawa, K.; Kondo, N.; Itoh, M.; Suzuki, H.; Kasukawa, T.; Hon, C.C.; De Hoon, M.J.L.; Shin, J.W.; Carninci, P.; Jaffe, A.E.; Leek, J.T.; Favorov, A.; Franco, G.R.; Langmead, B.; Marchionni, L.: “Recounting the FANTOM CAGE-Associated Transcriptome.” Genome Research 30(7): 1073-1081 (2020).
Bonetti, A.; Agostini, F.; Suzuki, A.M.; Hashimoto, K.; Pascarella, G.; Gimenez, J.; Roos, L.; Nash, A.J.; Ghilotti, M.; Cameron, C.J.F.; Valentine, M.; Medvedeva, Y.A.; Noguchi, S.; Agirre, E.; Kashi, K.; Samudyata, Luginbühl, J.; Cazzoli, R.; Agrawal, S.; Luscombe, N.M.; Blanchette, M.; Kasukawa, T.; De Hoon, M.; Arner, E.; Lenhard, B.; Plessy, C.; Castelo-Branco, G.; Orlando, V.; Carninci, P.: “RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions.” Nature Communications 11(1): 1018 (2020).
Kulyté, A.; Kwok, K.H.M.; De Hoon, M.; Carninci, P.; Hayashizaki, Y.; Arner, P.; Arner, E.: “MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis.” Scientific Reports 9(1): 13891 (2019).
Lizio, M.; Abugessaisa, I.; Noguchi, S.; Kondo, A.; Hasegawa, A.; Hon, C.C.; De Hoon, M.; Severin, J.; Oki, S.; Hayashizaki, Y.; Carninci, P.; Kasukawa, T.; Kawaji, H.: “Update of the FANTOM web resource: expansion to provide additional transcriptome atlases”. Nucleic Acids Research 47(D1): D752-D758 (2019).
Guigo, R.; De Hoon, M.: “Recent advances in functional genome analysis.” F1000Research 2018, 7(F1000 Faculty Rev): 1968 (2018).
Lizio, M.; Abugessaisa, I.; Noguchi, S.; Kondo, A.; Hasegawa, A.; Hon, C.C.; De Hoon, M.; Severin, J.; Oki, S.; Hayashizaki, Y.; Carninci, P.; Kasukawa, T.; Kawaji, H.: “Update of the FANTOM web resource: expansion to provide additional transcriptome atlases.” Nucleic Acids Research 47(D1): D752-D758 (2018).
Sakaue, S.; Hirata, J.; Maeda, Y.; Kawakami, E.; Nii, T.; Kishikawa, T.; Ishigaki, K.; Terao, C.; Suzuki, K.; Akiyama, M.; Suita, N.; Masuda, T.; Ogawa, K.; Yamamoto, K.; Saeki, Y.; Matsushita, M.; Yoshimura, M.; Matsuoka, H.; Ikari, K.; Taniguchi, A.; Yamanaka, H.; Kawaji, H.; Lassmann, T.; Itoh, M.; Yoshitomi, H.; Ito, H.; Ohmura, K.; Forrest, A.R.R.; Hayashizaki, Y.; Carninci, P.; Kumanogoh, A.; Kamatani, Y.; De Hoon, M.; Yamamoto, K.; Okada, Y.: “Integration of genetics and miRNA-target gene network identified disease biology implicated in tissue specificity.” Nucleic Acids Research 46(22): 11898-11909 (2018).
Alhendi, A.M.N.; Patrikakis, M.; Daub, C.O.; Kawaji, H.; Itoh, M.; De Hoon, M.; Carninci, P.; Hayashizaki, Y.; Arner, E.; Khachigian, L.M.: “Promoter usage and dynamics in vascular smooth muscle cells exposed to Fibroblast Growth Factor-2 or Interleukin-1β.” Scientific Reports 8(10): 13164 (2018).
Zhang, P.G.Y.; Yeung, J.; Gupta, I.; Ramirez, M.; Ha, T.; Swanson, D.J.; Nagao-Sato, S.; Itoh, M.; Kawaji, H.; Lassmann, T.; Daub, C.O.; Arner, E.; De Hoon, M.; FANTOM consortium, Carninci, P.; Forrest, A.R.R.; Hayashizaki, Y.; Goldowitz, D.: “Discovery of transcription factors novel to mouse cerebellar granule cell development through laser-capture microdissection.” Cerebellum 17(3): 308-325 (2018).
Rapakoulia, T.; Gao, X.; Huang, Y.; De Hoon, M.; Okada-Hatakeyama, M.; Suzuki, H.; Arner, E.: “Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment.”
Bioinformatics 33(23): 3696-3700 (2017).
De Rie, D.; Abugessaisa, I.; Alam, T.; Arner, E.; Arner, P.; Ashoor, H.; Åström, G.; Babina, M.; Bertin, N.; Burroughs, A.M.; Carlisle, A.J.; Daub, C.O.; Detmar, M.; Deviatiiarov, R.; Fort, A.; Gebhard, C.; Goldowitz, D.; Guhl, S.; Ha, T.J.; Harshbarger, J.; Hasegawa, A.; Hashimoto, K.; Herlyn, M.; Heutink, P.; Hitchens, K.J.; Hon, C.C.; Huang, E.; Ishizu, Y.; Kai, C.; Kasukawa, T.; Klinken, P.; Lassmann, T.; Lecellier, C.H.; Lee, W.; Lizio, M.; Makeev, V.; Mathelier, A.; Medvedeva, Y.A.; Mejhert, N.; Mungall, C.J.; Noma, S.; Ohshima, M.; Okada-Hatakeyama, M.; Persson, H.; Rizzu, P.; Roudnicky, F.; Sætrom, P.; Sato, H.; Severin, J.; Shin, J.W.; Swoboda, R.K.; Tarui, H.; Toyoda, H.; Vitting-Seerup, K.; Winteringham, L.; Yamaguchi, Y.; Yasuzawa, K.; Yoneda, M.; Yumoto, N.; Zabierowski, S.; Zhang, P.G.; Wells, C.A.; Summers, K.M.; Kawaji, H.; Sandelin, A.; Rehli, M.; The FANTOM Consortium, Hayashizaki, Y.; Carninci, P.; Forrest, A.R.R.; De Hoon, M.J.L.: “An integrated expression atlas of miRNAs and their promoters in human and mouse.” Nature Biotechnology 35(9): 872-878 (2017).
Hon, C.C.; Ramilowski, J.A.; Harshbarger, J.; Bertin, N.; Rackham, O.J.; Gough, J.; Denisenko, E.; Schmeier, S.; Poulsen, T.M.; Severin, J.; Lizio, M.; Kawaji, H.; Kasukawa, T.; Itoh, M.; Burroughs, A.M.; Noma, S.; Djebali, S.; Alam, T.; Medvedeva Y.A.; Testa, A.C.; Lipovich, L.; Yip, C.W.; Abugessaisa, I.; Mendez, M.; Hasegawa, A.; Tang, D.; Lassmann, T.; Heutink, P.; Babina, M.; Wells, C.A.; Kojima, S.; Nakamura, Y.; Suzuki, H.; Daub, C.O.; De Hoon, M.J.L.; Arner, E.; Hayashizaki, Y.; Carninci, P.; Forrest, A.R.R.: “An atlas of human long non-coding RNAs with accurate 5′ ends.” Nature 543(7644): 199-204 (2017).
Baillie, J.K.; Arner, E.; Daub, C.; De Hoon, M.; Itoh, M.; Kawaji, H.; Lassmann, T.; Carninci, P.; Forrest, A.R.; Hayashizaki, Y.; FANTOM Consortium; Faulkner, G.J.; Wells, C.A.; Rehli, M.; Pavli, P.; Summers, K.M.; Hume, D.A.: “Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.” PLoS Genetics 13(3): e1006641 (2017).
Newie, I.; Søkilde, R.; Persson, H.; Jacomasso, T.; Gorbatenko, A.; Borg, Å.; De Hoon, M.; Pedersen, S.F.; Rovira, C.: “HER2-encoded mir-4728 forms a receptor-independent circuit with miR-21-5p through the non-canonical poly(A) polymerase PAPD5.” Scientific Reports 6: 35664 (2016).
St Laurent, G.; Vyatkin, Y.; Antonets, D.; Ri, M.; Qi, Y.; Saik, O.; Shtokalo, D.; De Hoon, M.J.L.; Kawaji, H.; Itoh, M.; Lassmann, T.; Arner, E.; Forrest, A.R.R.; FANTOM consortium; Nicolas, E.; McCaffrey, T.A.; Carninci, P.; Hayashizaki, Y.; Wahlestedt, C.; Kapranov, P.:
“Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.”
Nucleic Acids Research 44(7): 3233-3252 (2016).
Kimura, Y.; Soma, T.; Kasahara, N.; Delobel, D.; Hanami, T.; Tanaka, Y.; De Hoon, M.J.L.; Hayashizaki, Y.; Usui, K.; Harbers, M.:
“Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays.”
PLoS One 11(2):e0146950 (2016).
De Hoon, M.; Shin, J.W.; Carninci, P.:
“Paradigm shifts in genomics through the FANTOM projects”
Mammalian Genome 26: 391-402 (2015).
Roy, S.; Schmeier, S.; Arner, E.; Alam, T.; Parihar, S.P.; Ozturk, M.; Tamgue, O.; Kawaji, H.; De Hoon, M.J.L.; Itoh, M.; Lassmann, T.; Carninci, P.; Hayashizaki, Y.; Forrest A.R.R.F.; Bajic, V.B.; Guler, R.; Fantom Consortium, Brombacher, F.; Suzuki, H.:
“Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.”
Nucleic Acids Research 43(14): 6969-6982 (2015).
Roy, S.; Guler, R.; Parihar, S.P.; Schmeier, S.; Kaczkowski, B.; Nishimura, H.; Shin, J.W.; Negishi, Y.; Ozturk, M.; Hurdayal, R.; Kubosaki, A.; Kimura, Y.; De Hoon, M.J.L.; Hayashizaki, Y.; Brombacher, F.; Suzuki, H.:
“Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection.”
The Journal of Immunology 194(12): 6035-6044 (2015).
Persson, H.; Kwon, A.T.; Ramilowski, J.A.; Silberberg, G.; Söderhäll, C.; Orsmark-Pietras, C.; Nordlund, B.; Konradsen, J.R.; De Hoon, M.J.L.; Melén, E.; Hayashizaki, Y.; Hedlin, G.; Kere, J.; Daub, C.O.:
“Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles.”
Journal of Allergy and Clinical Immunology 136(3): 638-648 (2015).
Lizio, M.; Harshbarger, J.; Shimoji, H.; Severin, J.; Kasukawa, T.; Sahin, S.; Abugessaisa, I.; Fukuda, S.; Hori, F.; Ishikawa-Kato, S.; Mungall, C.J.; Arner, E.; Baillie, J.K.; Bertin, N.; Bono, H.; De Hoon, M.; Diehl, A.D.; Dimont, E.; Freeman, T.C.; Fujieda, K.; Hide, W.; Kaliyaperumal, R.; Katayama, T.; Lassmann, T.; Meehan, T.F.; Nishikata, K.; Ono, H.; Rehli, M.; Sandelin, A.; Schultes, E.A.; ‘t Hoen, P.A.; Tatum, Z.; Thompson, M.; Toyoda, T.; Wright, D.W.: Daub, C.O.; Itoh, M.; Carninci, P.; Hayashizaki, Y.; Forrest, A.R.R.F.; Kawaji, H.; FANTOM consortium:
“Gateways to the FANTOM5 promoter level mammalian expression atlas.”
Genome Biology 16: 22 (2015).
Arner, E.; Daub, C.O.; Vitting-Seerup, K.; Andersson, R.; Lilje, B.; Drabløs, F.; Lennartsson, A.; Rönnerblad, M.; Hrydziuszko, O.; Vitezic, M.; Freeman, T.C.; Alhendi, A.M.; Arner, P.; Axton, R.; Baillie, J.K.; Beckhouse, A.; Bodega, B.; Briggs, J.; Brombacher, F.; Davis, M.; Detmar, M.; Ehrlund, A.; Endoh, M.; Eslami, A.; Fagiolini, M.; Fairbairn, L.; Faulkner, G.J.; Ferrai, C.; Fisher, M.E.; Forrester, L.; Goldowitz, D.; Guler, R.; Ha, T.; Hara, M.; Herlyn, M.; Ikawa, T.; Kai, C.; Kawamoto, H.; Khachigian, L.M.; Klinken, S.P.; Kojima, S.; Koseki, H.; Klein, S.; Mejhert, N.; Miyaguchi, K.; Mizuno, Y.; Morimoto, M.; Morris, K.J.; Mummery, C.; Nakachi, Y.; Ogishima, S.; Okada-Hatakeyama, M.; Okazaki, Y.; Orlando, V.; Ovchinnikov, D.; Passier, R.; Patrikakis, M.; Pombo, A.; Qin, X.Y.; Roy, S.; Sato, H.; Savvi, S.; Saxena, A.; Schwegmann, A.; Sugiyama, D.; Swoboda, R.; Tanaka, H.; Tomoiu, A.; Winteringham, L.N.; Wolvetang, E.; Yanagi-Mizuochi, C.; Yoneda, M.; Zabierowski, S.; Zhang, P.; Abugessaisa, I.; Bertin, N.; Diehl, A.D.; 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, T.F.; Mungall, C.J.; Murata, M.; Nishiyori-Sueki, H.; Sahin, S.; Nagao-Sato, S.; Severin, J.; De Hoon, M.J.L.; Kawai, J.; Kasukawa, T.; Lassmann, T.; Suzuki, H.; Kawaji, H.; Summers, K.M.; Wells, C.; FANTOM Consortium; Hume, D.A.; Forrest, A.R.; Sandelin, A.; Carninci, P.; Hayashizaki, Y.:
“Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells”
Science 347: 1010-1014 (2015).
Abdelhamid, R.F.; Plessy, C.; Yamauchi, Y.; Taoka, M.; De Hoon, M.; Gingeras, T.R.; Isobe, T.; Carninci, P.:
“Multiplicity of 5′ cap structures present on short RNAs.”
PLoS One 9(7): e102895 (2014).
Boele, J., Persson, H., Shin, J.W., Ishizu, Y., Newie, I.S., Søkilde, R., Hawkins, S.M., Coarfa, C., Ikeda, K., Takayama, K.I., Horie-Inoue, K., Ando, Y., Burroughs, A.M., 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, P.H., Rovira, C., Hayashizaki, Y., De Hoon, M.J.L.:
“PAPD5-mediated 3′ adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease”
Proceedings of the National Academy of Sciences USA 111: 11467-11472 (2014).
Fort, A., Hashimoto, K., Yamada, D., Salimullah, M., Keya, C.A., Saxena, A., Bonetti, A., Voineagu, I., Bertin, N., Kratz, A., Noro, Y., Wong, C.H., De Hoon, M.J.L., Andersson, R., Sandelin, A., Suzuki, H., Wei, C.L., Koseki, H., The FANTOM Consortium, Hasegawa, Y., Forrest, A.R.R., Carninci, P.:
“Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance”
Nature Genetics 46: 558-566 (2014).
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.:
“Systemic identification of estrogen-regulated genes in breast cancer cells through cap analysis of gene expression mapping.”
Biochemical and Biophysical Research Communications 447(3): 531-536 (2014).
Davis, M.R.; Andersson, R.; Severin, J.; De Hoon, M.; Bertin, N.; Baillie, J.K.; Kawaji, H.; Sandelin, A.; Forrest, A.R.R.F.; Summers, K.M.; FANTOM Consortium:
“Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.”
Molecular Genetics and Metabolism 112(1): 73-83 (2014).
Motakis, E.; Guhl, S.; Ishizu, Y.; Itoh, M.; Kawaji, H.; De Hoon, M.; Lassmann, T.; Carninci, P.; Hayashizaki, Y.; Zuberbier, T.; Forrest, A.R.R.F.; Babina, M.; FANTOM consortium:
“Redefinition of the human mast cell transcriptome by deep-CAGE sequencing.”
Blood 123(17): e58-e67 (2014).
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.R.F.; Sandelin, A.; Ekwall, K.; Arner, E.; Lennartsson, A.; FANTOM consortium:
“Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.”
Blood 123(17): e79-e89 (2014).
FANTOM Consortium and the RIKEN PMI and CLST (DGT):
“A promoter-level mammalian expression atlas”
Nature 507: 462-470 (2014)
Kouno, T.; De Hoon, M.; Mar, J.C.; Tomaru, Y.; Kawano, M.; Carninci, P.; Suzuki, H.; Hayashizaki, Y.; Shin, J.W.:
“Temporal dynamics and transcriptional control using single-cell gene expression analysis.”
Genome Biology 14(10): R118 (2013).
Harbers, M.; Kato, S.; De Hoon, M.; Hayashizaki, Y.; Carninci, P.; Plessy, C.:
“Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation.”
BMC Genomics 14: 665 (2013).
Hasegawa, R.; Tomaru, Y.; De Hoon, M.; Suzuki, H.; Hayashizaki, Y.; Shin, J.W.:
“Identification of ZNF395 as a novel modulator of adipogenesis.”
Experimental Cell Research 319(3): 68-76 (2013).
Kimura, Y.; Hanami, T.; Tanaka, Y.; De Hoon, M.J.L.; Soma, T.; Harbers, M.; Lezhava, A.; Hayashizaki, Y.; Usui, K.:
“Effect of thiazole orange doubly labeled thymidine on DNA duplex formation.”
Biochemistry 51(31): 6056-6067 (2012).
Francia, S.; Michelini, F.; Saxena, A.; Tang, D.; De Hoon, M.J.L.; Anelli, V.; Mione, M.; Carninci, P.; d’Adda di Fagagna, F.:
“Site-specific DICER and DROSHA RNA products control the DNA-damage response”
Nature 488: 231-235 (2012)
Suzuki, T.; Nakano-Ikegaya, M.; Yabukami-Okuda, H.; De Hoon, M.; Severin, J.; Saga-Hatano, S.; Shin, J.W.; Kubosaki, A.; Simon, C.; Hasegawa, Y.; Hayashizaki, Y.; Suzuki, H.:
“Reconstruction of monocyte transcriptional regulatory network accompanies monocytic functions in human fibroblasts.”
PLoS One 7(3): e33474 (2012).
Kimura, Y.; De Hoon, M.J.L., Aoki, S.; Ishizu, Y.; Kawai, Y.; Kogo, Y.; Daub, C.O.; Lezhava, A.; Arner, E.; Hayashizaki, Y.:
“Optimization of turn-back primers in isothermal amplification.”
Nucleic Acids Research 39(9): e59 (2011).
Burroughs, A.M.; Ando, Y.; De Hoon, M.J.L.; Tomaru, Y.; Suzuki, H.; Hayashizaki, Y.; Daub, C.O.:
“Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin.”
RNA Biology 8(1): 158-177 (2011).
De Hoon, M.J.L., Eichenberger, P.; Vitkup, D.:
“Hierarchical evolution of the bacterial sporulation network.”
Current Biology 20(17): R735-R745 (2010).
Burroughs, A.M.; Ando, Y.; De Hoon, M.J.L.; Tomaru, Y.; Nishibu, T.; Ukekawa, R.; Funakoshi, T.; Kurokawa, T.; Suzuki, H.; Hayashizaki, Y.; Daub, C.O.:
“A comprehensive survey of 3′ animal miRNA modification events and a possible role for 3′ adenylation in modulating miRNA targeting effectiveness”
Genome Research 20: 1398-1410 (2010).
De Hoon, M.J.L.; Taft, R.J.; Hashimoto, T.; Kanamori-Katayama, M.; Kawaji, H.; Kawano, M.; Kishima, M.; Lassmann, T.; Faulkner, G.J.; Mattick, J.S.; Daub, C.O.; Carninci, P.; Kawai, J.; Suzuki, H.; Hayashizaki, Y.:
“Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries”.
Genome Research 20: 257-264 (2010)
Forrest, A.R.R.F., Kanamori-Katayama, M.; Tomaru, Y.; Lassmann, T.; Ninomiya, N.; Takahashi, Y.; De Hoon, M.J.L.; Kubosaki, A.; Kaiho, A.; Suzuki, M.; Yasuda, J.; Kawai, J.; Hayashizaki, Y.; Hume, D.A.; Suzuki, H.:
“Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation.”
Leukemia 24(2):460-466 (2010).
Hashimoto, T.; De Hoon, M.J.L.; Grimmond, S.M.; Daub, C.O.; Hayashizaki, Y.; Faulkner, G.J.:
“Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.”
Bioinformatics 25(19): 2613-2614 (2009).
The FANTOM Consortium & Riken Omics Science Center:
“The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line”
Nature Genetics 41: 553-562 (2009)
Severin, J.; Waterhouse, A.M.; Kawaji, H.; Lassmann, T.; Van Nimwegen, E.; Balwierz, P.J.; De Hoon, M.J.L.; Hume, D.A.; Carninci, P.; Hayashizaki, Y.; Suzuki, H.; Daub, C.O.; Forrest, A.R.R.F:
“FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.”
Genome Biology 10(4): R39 (2009).
Cock, P.J., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., De Hoon, M.J.L.:
“Biopython: freely available Python tools for computational molecular biology and bioinformatics”
Bioinformatics 25: 1422-1423 (2009).
De Hoon, M. & Hayashizaki, Y.:
“Deep cap analysis gene expression (CAGE): genome-wide identification of promoters, quantification of their expression, and network inference.”
Biotechniques 44(5): 627-8, 630, 632 (2008).
Sierro, N.; Makita, Y.; De Hoon, M.; Nakai, K.:
“DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information.”
Nucleic Acids Research 36(Database issue): D93-D96 (2007).
Makita, Y.; De Hoon, M.J.L.; Danchin, A.:
“Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes.”
BMC Bioinformatics 8: 47 (2007).
De Hoon, M.J.L.; Makita, Y.; Nakai, K.; Miyano, S.:
“Prediction of transcriptional terminators in Bacillus subtilis and related species.”
PLoS Computational Biology 1(3): e25 (2005).
Makita, Y.; De Hoon, M.J.L.; Ogasawara, N.; Miyano, S.; Nakai, K.:
“Bayesian joint prediction of associated transcription factors in Bacillus subtilis.”
Pacific Symposium on Biocomputing 2005: 507-518 (2005).
De Hoon, M.J.L.; Makita, Y.; Imoto, S.; Kobayashi, K.; Ogasawara, N.; Nakai, K.; Miyano S.:
“Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data.”
Bioinformatics 20 Supplement 1: i101-i108 (2004).
De Hoon, M.J.L.; Imoto, S.; Kobayashi, K.; Ogasawara, N.; Miyano S.:
“Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information.”
Pacific Symposium on Biocomputing 2004: 276-287 (2004).
De Hoon, M.J.L.; Imoto, S.; Nolan, J.; Miyano, S.:
“Open source clustering software.”
Bioinformatics 20(9): 1453-1454 (2004).
De Hoon, M.J.L.; Imoto, S.; Kobayashi, K.; Ogasawara, N.; Miyano, S.:
“Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations.”
Pacific Symposium on Biocomputing 2003: 17-28 (2003).
De Hoon, M.J.L.; Imoto, S.; Miyano, S.:
“Statistical analysis of a small set of time-ordered gene expression data using linear splines.”
Bioinformatics 18(11): 1477-1485 (2002).
De Hoon, M.J.L., Lee, E.P.; Barnard, J.J.; Friedman, A.:
“Cold phase fluid model of the longitudinal dynamics of space-charge dominated beams”.
Physics of Plasmas 10 (3): 855-861 (2003).
De Hoon, M.J.L.; Lee, E.P.; Barnard, J.J.:
“Drift Compression of Space Charge Dominated Beams”
Proceedings of the 2001 Particle Accelerator Conference: 729-731 (2001).
De Hoon, M.J.L.; MacLaren, S.A.; Lee, E.P.:
“Simulation of the LBNL scaled final focus experiment”.
Nuclear Instruments and Methods in Physics Research A 464: 278-283 (2001).
MacLaren, S.A.; De Hoon, M.; Faltens, A.; Ghiorso, W.; Seidl, P.:
“Results from the scaled final focus experiment”.
Nuclear Instruments and Methods in Physics Research A 464: 126–133 (2001).
Barnard, J.J.; Ahle, L.E.; Bangerter, R.O.; Bieniosek, F.M.; Celata, C.M.; Faltens, A.; Friedman, A; Grote, D.P.; Haber, I.; Henestroza, E.; Kishek, R.A.; De Hoon, M.J.L.; Karpenko, V.P.; Kwan, J.W.; Lee, E.P.; Logan, B.G.; Lund, S.M.; Meier, W.R.; Molvik, A.W.; Sangster, T.C.; Seidl, P.A.; Sharp, W.M.:
“Planning for an integrated research experiment”.
Nuclear Instruments and Methods in Physics Research A 464: 621–628 (2001).
Celata, C.M.; De Hoon, M.J.L.; Barnard, J.J.:
“Effects of misalignments on space-charge-dominated heavy ion beams in an IRE”.
Proceedings of the 1999 Particle Accelerator Conference: 1803-1805 (1999).
Friedman, A.; Barnard, J.J.; Celata, C.M.; Craig, G.D.; De Hoon, M.J.L.; Faltens, A.; Grote, D.P.; Lee, E.P.; Sharp, W.M.; Sonnendrucker, E.; Haber, I.; Kishek, R.A.:
“Beam Dynamics Studies for Heavy Ion Fusion Drivers”.
Proceedings of the 1999 Particle Accelerator Conference: 1830-1832 (1999).
De Hoon, M.J.L.; Greenspan, E.; Lowenthal, M.D.:
“A Model for Pulsed Activation Accounting for Circulation, Extraction and Makeup.”
Fusion Technology 34 (3): 974–979 (1998).
De Hoon, M.J.L.; Van der Hagen, T.H.J.J.; Schoonewelle, H.; Van Dam, H.: “Why Yule-Walker should not be used for autoregressive modelling.” Annals of Nuclear Energy 23: 1219–1228 (1996).