Works by de Hoon, Michiel

Results: 32

Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment.

Published in:

Bioinformatics, 2017, v. 33, n. 23, p. 3696, doi. 10.1093/bioinformatics/btx503

By:

Rapakoulia, Trisevgeni;
Xin Gao;
Yi Huang;
de Hoon, Michiel;
Okada-Hatakeyama, Mariko;
Suzuki, Harukazu;
Arner, Erik

Publication type:

Article

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.

Published in:

Bioinformatics, 2009, v. 25, n. 19, p. 2613, doi. 10.1093/bioinformatics/btp438

By:

Hashimoto, Takehiro;
De Hoon, Michiel J. L.;
Grimmond, Sean M.;
Daub, Carsten O.;
Hayashizaki, Yoshihide;
Faulkner, Geoffrey J.

Publication type:

Article

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Published in:

Bioinformatics, 2009, v. 25, n. 11, p. 1422, doi. 10.1093/bioinformatics/btp163

By:

Peter J. A. Cock;
Tiago 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

Publication type:

Article

The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.

Published in:

BMC Genomic Data, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12863-021-00992-1

By:

Ducoli, Luca;
Agrawal, Saumya;
Hon, Chung-Chau;
Ramilowski, Jordan A.;
Sibler, Eliane;
Tagami, Michihira;
Itoh, Masayoshi;
Kondo, Naoto;
Abugessaisa, Imad;
Hasegawa, Akira;
Kasukawa, Takeya;
Suzuki, Harukazu;
Carninci, Piero;
Shin, Jay W.;
de Hoon, Michiel J. L.;
Detmar, Michael

Publication type:

Article

Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-30702-4

By:

Alhendi, Ahmad M. N.;
Patrikakis, Margaret;
Daub, Carsten O.;
Kawaji, Hideya;
Itoh, Masayoshi;
de Hoon, Michiel;
Carninci, Piero;
Hayashizaki, Yoshihide;
Arner, Erik;
Khachigian, Levon M.

Publication type:

Article

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.

Published in:

Nature Genetics, 2014, v. 46, n. 6, p. 558, doi. 10.1038/ng.2965

By:

Fort, Alexandre;
Hashimoto, Kosuke;
Yamada, Daisuke;
Salimullah, Md;
Keya, Chaman A;
Saxena, Alka;
Bonetti, Alessandro;
Voineagu, Irina;
Bertin, Nicolas;
Kratz, Anton;
Noro, Yukihiko;
Wong, Chee-Hong;
de Hoon, Michiel;
Andersson, Robin;
Sandelin, Albin;
Suzuki, Harukazu;
Wei, Chia-Lin;
Koseki, Haruhiko;
Hasegawa, Yuki;
Forrest, Alistair R R

Publication type:

Article

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Published in:

Nature Genetics, 2009, v. 41, n. 5, p. 553, doi. 10.1038/ng.375

By:

Suzuki, Harukazu;
Forrest, Alistair R R;
van Nimwegen, Erik;
Daub, Carsten O;
Balwierz, Piotr J;
Irvine, Katharine M;
Lassmann, Timo;
Ravasi, Timothy;
Hasegawa, Yuki;
de Hoon, Michiel J L;
Katayama, Shintaro;
Schroder, Kate;
Carninci, Piero;
Tomaru, Yasuhiro;
Kanamori-Katayama, Mutsumi;
Kubosaki, Atsutaka;
Akalin, Altuna;
Ando, Yoshinari;
Arner, Erik;
Asada, Maki

Publication type:

Article

Multiplicity of 5′ Cap Structures Present on Short RNAs.

Published in:

PLoS ONE, 2014, v. 9, n. 7, p. 1, doi. 10.1371/journal.pone.0102895

By:

Abdelhamid, Rehab F.;
Plessy, Charles;
Yamauchi, Yoshio;
Taoka, Masato;
de Hoon, Michiel;
Gingeras, Thomas R.;
Isobe, Toshiaki;
Carninci, Piero

Publication type:

Article

Reconstruction of Monocyte Transcriptional Regulatory Network Accompanies Monocytic Functions in Human Fibroblasts.

Published in:

PLoS ONE, 2012, v. 7, n. 3, p. 1, doi. 10.1371/journal.pone.0033474

By:

Suzuki, Takahiro;
Nakano-Ikegaya, Mika;
Yabukami-Okuda, Haruka;
de Hoon, Michiel;
Severin, Jessica;
Saga-Hatano, Satomi;
Shin, Jay W.;
Kubosaki, Atsutaka;
Simon, Christophe;
Hasegawa, Yuki;
Hayashizaki, Yoshihide;
Suzuki, Harukazu

Publication type:

Article

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection.

Published in:

Cerebellum, 2018, v. 17, n. 3, p. 308, doi. 10.1007/s12311-017-0912-3

By:

Zhang, Peter G. Y.;
Yeung, Joanna;
Gupta, Ishita;
Ramirez, Miguel;
Ha, Thomas;
Swanson, Douglas J.;
Nagao-Sato, Sayaka;
Itoh, Masayoshi;
Kawaji, Hideya;
Lassmann, Timo;
Daub, Carsten O.;
Arner, Erik;
de Hoon, Michiel;
the FANTOM consortium;
Carninci, Piero;
Forrest, Alistair R. R.;
Hayashizaki, Yoshihide;
Goldowitz, Dan

Publication type:

Article

Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.

Published in:

PLoS Genetics, 2017, v. 13, n. 3, p. 1, doi. 10.1371/journal.pgen.1006641

By:

Baillie, J. Kenneth;
Arner, Erik;
Daub, Carsten;
De Hoon, Michiel;
Itoh, Masayoshi;
Kawaji, Hideya;
Lassmann, Timo;
Carninci, Piero;
Forrest, Alistair R. R.;
Hayashizaki, Yoshihide;
null, null;
Faulkner, Geoffrey J.;
Wells, Christine A.;
Rehli, Michael;
Pavli, Paul;
Summers, Kim M.;
Hume, David A.

Publication type:

Article

Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species.

Published in:

PLoS Computational Biology, 2005, v. 1, n. 3, p. 212, doi. 10.1371/journal.pcbi.0010025

By:

De Hoon, Michiel J. L.;
Makita, Yuko;
Nakai, Kenta;
Miyano, Satoru;
Murray, Diana

Publication type:

Article

HER2-encoded mir-4728 forms a receptor-independent circuit with miR-21-5p through the non-canonical poly(A) polymerase PAPD5.

Published in:

Scientific Reports, 2016, p. 35664, doi. 10.1038/srep35664

By:

Newie, Inga;
Søkilde, Rolf;
Persson, Helena;
Jacomasso, Thiago;
Gorbatenko, Andrej;
Borg, Åke;
de Hoon, Michiel;
Pedersen, Stine F.;
Rovira, Carlos

Publication type:

Article

LETR1 is a lymphatic endothelial-specific lncRNA governing cell proliferation and migration through KLF4 and SEMA3C.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21217-0

By:

Ducoli, Luca;
Agrawal, Saumya;
Sibler, Eliane;
Kouno, Tsukasa;
Tacconi, Carlotta;
Hon, Chung-Chao;
Berger, Simone D.;
Müllhaupt, Daniela;
He, Yuliang;
Kim, Jihye;
D'Addio, Marco;
Dieterich, Lothar C.;
Carninci, Piero;
de Hoon, Michiel J. L.;
Shin, Jay W.;
Detmar, Michael

Publication type:

Article

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase.

Published in:

Database: The Journal of Biological Databases & Curation, 2016, v. 2016, p. 1, doi. 10.1093/database/baw144

By:

Ienasescu, Hans;
Kang Li;
Andersson, Robin;
Vitezic, Morana;
Rennie, Sarah;
Yun Chen;
Vitting-Seerup, Kristoffer;
Lagoni, Emil;
Boyd, Mette;
Bornholdt, Jette;
de Hoon, Michiel J. L.;
Hideya Kawaji;
Lassmann, Timo;
Yoshihide Hayashizaki;
Forrest, Alistair R. R.;
Carninci, Piero;
Sandelin, Albin

Publication type:

Article

Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-665

By:

Harbers, Matthias;
Sachi Kato;
de Hoon, Michiel;
Hayashizaki, Yoshihide;
Carninci, Piero;
Plessy, Charles

Publication type:

Article

A field guide to cultivating computational biology.

Published in:

PLoS Biology, 2021, v. 19, n. 10, p. 1, doi. 10.1371/journal.pbio.3001419

By:

Way, Gregory P.;
Greene, Casey S.;
Carninci, Piero;
Carvalho, Benilton S.;
de Hoon, Michiel;
Finley, Stacey;
Gosline, Sara J. C.;
Lȇ Cao, Kim-Anh;
Lee, Jerry S. H.;
Marchionni, Luigi;
Robine, Nicolas;
Sindi, Suzanne S.;
Theis, Fabian J.;
Yang, Jean Y. H.;
Carpenter, Anne E.;
Fertig, Elana J.

Publication type:

Article

Paradigm shifts in genomics through the FANTOM projects.

Published in:

Mammalian Genome, 2015, v. 26, n. 9/10, p. 391, doi. 10.1007/s00335-015-9593-8

By:

de Hoon, Michiel;
Shin, Jay;
Carninci, Piero

Publication type:

Article

Update of the FANTOM web resource: enhancement for studying noncoding genomes.

Published in:

Nucleic Acids Research, 2025, v. 53, n. D1, p. D419, doi. 10.1093/nar/gkae1047

By:

Nobusada, Tomoe;
Yip, Chi Wai;
Agrawal, Saumya;
Severin, Jessica;
Abugessaisa, Imad;
Hasegawa, Akira;
Hon, Chung Chau;
Ide, Satoru;
Koido, Masaru;
Kondo, Atsushi;
Masuya, Hiroshi;
Oki, Shinya;
Tagami, Michihira;
Takada, Toyoyuki;
Terao, Chikashi;
Thalhath, Nishad;
Walker, Scott;
Yasuzawa, Kayoko;
Shin, Jay W;
de Hoon, Michiel J L

Publication type:

Article

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases.

Published in:

Nucleic Acids Research, 2019, v. 47, n. D1, p. D752, doi. 10.1093/nar/gky1099

By:

Lizio, Marina;
Abugessaisa, Imad;
Noguchi, Shuhei;
Kondo, Atsushi;
Hasegawa, Akira;
Hon, Chung Chau;
de Hoon, Michiel;
Severin, Jessica;
Oki, Shinya;
Hayashizaki, Yoshihide;
Carninci, Piero;
Kasukawa, Takeya;
Kawaji, Hideya

Publication type:

Article

Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays.

Published in:

PLoS ONE, 2016, v. 11, n. 2, p. 1, doi. 10.1371/journal.pone.0146950

By:

Kimura, Yasumasa;
Soma, Takahiro;
Kasahara, Naoko;
Delobel, Diane;
Hanami, Takeshi;
Tanaka, Yuki;
de Hoon, Michiel J. L.;
Hayashizaki, Yoshihide;
Usui, Kengo;
Harbers, Matthias

Publication type:

Article

Deep-sequencing of human argonaute-associated small RNAs provides insight into miRNA sorting and reveals argonaute association with RNA fragments of diverse origin.

Published in:

RNA Biology, 2011, v. 8, n. 1, p. 158, doi. 10.4161/rna.8.1.14300

By:

Burroughs, Alexander Maxwell;
Ando, Yoshinari;
de Hoon, Michiel Jan Laurens;
Tomaru, Yasuhiro;
Suzuki, Harukazu;
Hayashizaki, Yoshihide;
Daub, Carsten Olivier

Publication type:

Article

Cell type-dependent directional transcription at enhancers.

Published in:

NAR Genomics & Bioinformatics, 2025, v. 7, n. 1, p. 1, doi. 10.1093/nargab/lqaf007

By:

Agrawal, Saumya;
Kanamaru, Emi;
Saito, Yoriko;
Ishikawa, Fumihiko;
de Hoon, Michiel

Publication type:

Article

ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data.

Published in:

NAR Genomics & Bioinformatics, 2023, v. 5, n. 3, p. 1, doi. 10.1093/nargab/lqad075

By:

Severin, Jessica;
Agrawal, Saumya;
Ramilowski, Jordan A;
Deviatiiarov, Ruslan;
Shin, Jay W;
Carninci, Piero;
de Hoon, Michiel

Publication type:

Article

MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis.

Published in:

Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-50210-3

By:

Kulyté, Agné;
Kwok, Kelvin Ho Man;
de Hoon, Michiel;
Carninci, Piero;
Hayashizaki, Yoshihide;
Arner, Peter;
Arner, Erik

Publication type:

Article

Gateways to the FANTOM5 promoter level mammalian expression atlas.

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-014-0560-6

By:

Lizio, Marina;
Harshbarger, Jayson;
Hisashi Shimoji;
Severin, Jessica;
Takeya Kasukawa;
Sahin, Serkan;
Abugessaisa, Imad;
Shiro Fukuda;
Fumi Hori;
Sachi Ishikawa-Kato;
Mungall, Christopher J.;
Arner, Erik;
Baillie, J. Kenneth;
Bertin, Nicolas;
Hidemasa Bono;
de Hoon, Michiel;
Diehl, Alexander D.;
Dimont, Emmanuel;
Freeman, Tom C.;
Kaori Fujieda

Publication type:

Article

Temporal dynamics and transcriptional control using single-cell gene expression analysis.

Published in:

Genome Biology, 2013, v. 14, n. 10, p. 1, doi. 10.1186/gb-2013-14-10-r118

By:

Kouno, Tsukasa;
de Hoon, Michiel;
Mar, Jessica C.;
Tomaru, Yasuhiro;
Kawano, Mitsuoki;
Carninci, Piero;
Suzuki, Harukazu;
Hayashizaki, Yoshihide;
Shin, Jay W.

Publication type:

Article

Site-specific DICER and DROSHA RNA products control the DNA-damage response.

Published in:

Nature, 2012, v. 488, n. 7410, p. 231, doi. 10.1038/nature11179

By:

Francia, Sofia;
Michelini, Flavia;
Saxena, Alka;
Tang, Dave;
de Hoon, Michiel;
Anelli, Viviana;
Mione, Marina;
Carninci, Piero;
d'Adda di Fagagna, Fabrizio

Publication type:

Article

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

Published in:

Nucleic Acids Research, 2016, v. 44, n. 7, p. 3233, doi. 10.1093/nar/gkw162

By:

Laurent, Georges St.;
Vyatkin, Yuri;
Antonets, Denis;
Ri, Maxim;
Yao Qi;
Saik, Olga;
Shtokalo, Dmitry;
de Hoon, Michiel J. L.;
Hideya Kawaji;
Masayoshi Itoh;
Lassmann, Timo;
Arner, Erik;
Forrest, Alistair R. R.;
Nicolas, Estelle;
McCaffrey, Timothy A.;
Carninci, Piero;
Yoshihide Hayashizaki;
Wahlestedt, Claes;
Kapranov, Philipp

Publication type:

Article

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

Published in:

Nucleic Acids Research, 2015, v. 43, n. 14, p. 6969, doi. 10.1093/nar/gkv646

By:

Roy, Sugata;
Schmeier, Sebastian;
Arner, Erik;
Alam, Tanvir;
Parihar, Suraj P.;
Ozturk, Mumin;
Tamgue, Ousman;
Hideya Kawaji;
de Hoon, Michiel J. L.;
Masayoshi Itoh;
Lassmann, Timo;
Carninci, Piero;
Yoshihide Hayashizaki;
Forrest, Alistair R. R.;
Bajic, Vladimir B.;
Guler, Reto;
Brombacher, Frank;
Harukazu Suzuki

Publication type:

Article

Optimization of turn-back primers in isothermal amplification.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 9, p. e59, doi. 10.1093/nar/gkr041

By:

Kimura, Yasumasa;
de Hoon, Michiel J. L.;
Aoki, Shintaro;
Ishizu, Yuri;
Kawai, Yuki;
Kogo, Yasushi;
Daub, Carsten O.;
Lezhava, Alexander;
Arner, Erik;
Hayashizaki, Yoshihide

Publication type:

Article

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information.

Published in:

Nucleic Acids Research, 2008, v. 36, p. D93, doi. 10.1093/nar/gkm910

By:

Sierro, Nicolas;
Makita, Yuko;
de Hoon, Michiel;
Nakai, Kenta

Publication type:

Article