Works by Takeya Kasukawa

Results: 35

Iron regulatory pathways differentially expressed during Madurella mycetomatis grain development in Galleria mellonella.

Published in:

Nature Communications, 2025, v. 16, n. 1, p. 1, doi. 10.1038/s41467-025-60875-2

By:

Abugessaisa, Imad;
Konings, Mickey;
Manabe, Ri-Ichiroh;
Murphy, Cathal M.;
Kawashima, Tsugumi;
Hasegawa, Akira;
Takahashi, Chitose;
Tagami, Michihira;
Okazaki, Yasushi;
Eadie, Kimberly;
Lim, Wilson;
Doyle, Sean;
Verbon, Annelies;
Fahal, Ahmed H.;
Kasukawa, Takeya;
van de Sande, Wendy W. J.

Publication type:

Article

Prediction of transcription factors associated with DNA demethylation during human cellular development.

Published in:

Chromosome Research, 2022, v. 30, n. 1, p. 109, doi. 10.1007/s10577-022-09685-6

By:

Miyajima, Yurina;
Noguchi, Shuhei;
Tanaka, Yuki;
Li, Jing-Ru;
Nishimura, Hajime;
Kishima, Mami;
Lim, Joanne;
Furuhata, Erina;
Suzuki, Takahiro;
Kasukawa, Takeya;
Suzuki, Harukazu

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

MaXML: Mouse Annotation XML.

Published in:

In Silico Biology, 2004, v. 4, n. 1, p. 7

By:

Kasukawa, Takeya;
Bono, Hidemasa;
Hayashizaki, Yoshihide;
Okazaki, Yasushi;
Matsuda, Hideo

Publication type:

Article

Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution.

Published in:

2007

By:

Carninci, Piero;
Sandelin, Albin;
Lenhard, Boris;
Katayama, Shintaro;
Shimokawa, Kazuro;
Ponjavic, Jasmina;
Semple, Colin A. M.;
Taylor, Martin S.;
Engström G, Pär G.;
Frith, Martin C.;
Forrest, Alistair R. R.;
Alkema, Wynand B.;
Tan, Sin Lam;
Plessy, Charles;
Kodzius, Rimantas;
Ravasi, Timothy;
Kasukawa, Takeya;
Fukuda, Shiro;
Kanamori-Katayama, Mutsumi;
Kitazume, Yayoi

Publication type:

Correction Notice

Genome-wide analysis of mammalian promoter architecture and evolution.

Published in:

Nature Genetics, 2006, v. 38, n. 6, p. 626, doi. 10.1038/ng1789

By:

Carninci, Piero;
Sandelin, Albin;
Lenhard, Boris;
Katayama, Shintaro;
Shimokawa, Kazuro;
Ponjavic, Jasmina;
Semple, Colin A. M.;
Taylor, Martin S.;
Engström, Pär G.;
Frith, Martin C.;
Forrest, Alistair R. R.;
Alkema, Wynand B.;
Sin Lam Tan;
Plessy, Charles;
Kodzius, Rimantas;
Ravasi, Timothy;
Kasukawa, Takeya;
Fukuda, Shiro;
Kanamori-Katayama, Mutsumi;
Kitazume, Yayoi

Publication type:

Article

STAP cells are derived from ES cells.

Published in:

Nature, 2015, v. 525, n. 7570, p. E4, doi. 10.1038/nature15366

By:

Konno, Daijiro;
Kasukawa, Takeya;
Hashimoto, Kosuke;
Itoh, Takehiko;
Suetsugu, Taeko;
Miura, Ikuo;
Wakana, Shigeharu;
Carninci, Piero;
Matsuzaki, Fumio

Publication type:

Article

OVCH1 Antisense RNA 1 is differentially expressed between non-frail and frail old adults.

Published in:

GeroScience, 2024, v. 46, n. 2, p. 2063, doi. 10.1007/s11357-023-00961-9

By:

Abugessaisa, Imad;
Manabe, Ri-Ichiroh;
Kawashima, Tsugumi;
Tagami, Michihira;
Takahashi, Chitose;
Okazaki, Yasushi;
Bandinelli, Stefania;
Kasukawa, Takeya;
Ferrucci, Luigi

Publication type:

Article

Author Correction: IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells.

Published in:

NPJ Systems Biology & Applications, 2022, v. 8, n. 1, p. 1, doi. 10.1038/s41540-022-00239-4

By:

Ando, Minami;
Magi, Shigeyuki;
Seki, Masahide;
Suzuki, Yutaka;
Kasukawa, Takeya;
Lefaudeux, Diane;
Hoffmann, Alexander;
Okada, Mariko

Publication type:

Article

IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells.

Published in:

NPJ Systems Biology & Applications, 2021, v. 7, n. 1, p. 1, doi. 10.1038/s41540-021-00204-7

By:

Ando, Minami;
Magi, Shigeyuki;
Seki, Masahide;
Suzuki, Yutaka;
Kasukawa, Takeya;
Lefaudeux, Diane;
Hoffmann, Alexander;
Okada, Mariko

Publication type:

Article

Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Published in:

2022

By:

Grapotte, Mathys;
Saraswat, Manu;
Bessière, Chloé;
Menichelli, Christophe;
Ramilowski, Jordan A.;
Severin, Jessica;
Hayashizaki, Yoshihide;
Itoh, Masayoshi;
Tagami, Michihira;
Murata, Mitsuyoshi;
Kojima-Ishiyama, Miki;
Noma, Shohei;
Noguchi, Shuhei;
Kasukawa, Takeya;
Hasegawa, Akira;
Suzuki, Harukazu;
Nishiyori-Sueki, Hiromi;
Frith, Martin C.;
FANTOM consortium;
Abugessaisa, Imad

Publication type:

Correction Notice

Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space.

Published in:

PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0045373

By:

Okamura-Oho, Yuko;
Shimokawa, Kazuro;
Takemoto, Satoko;
Hirakiyama, Asami;
Nakamura, Sakiko;
Tsujimura, Yuki;
Nishimura, Masaomi;
Kasukawa, Takeya;
Masumoto, Koh-Hei;
Nikaido, Itoshi;
Shigeyoshi, Yasufumi;
Ueda, Hiroki R.;
Gang Song;
Gee, James;
Himeno, Ryutaro;
Yokota, Hideo;
Hayasaka, Satoru

Publication type:

Article

Quantitative Expression Profile of Distinct Functional Regions in the Adult Mouse Brain.

Published in:

PLoS ONE, 2011, v. 6, n. 8, p. 1, doi. 10.1371/journal.pone.0023228

By:

Kasukawa, Takeya;
Masumoto, Koh-hei;
Nikaido, Itoshi;
Nagano, Mamoru;
Uno, Kenichiro D.;
Tsujino, Kaori;
Hanashima, Carina;
Shigeyoshi, Yasufumi;
Ueda, Hiroki R.

Publication type:

Article

Single-Cell RNA-Seq Reveals LRRC75A-Expressing Cell Population Involved in VEGF Secretion of Multipotent Mesenchymal Stromal/Stem Cells Under Ischemia.

Published in:

Stem Cells Translational Medicine, 2023, v. 12, n. 6, p. 379, doi. 10.1093/stcltm/szad029

By:

Miura, Takumi;
Kouno, Tsukasa;
Takano, Megumi;
Kuroda, Takuya;
Yamamoto, Yumiko;
Kusakawa, Shinji;
Morioka, Masaki Suimye;
Sugawara, Tohru;
Hirai, Takamasa;
Yasuda, Satoshi;
Sawada, Rumi;
Matsuyama, Satoko;
Kawaji, Hideya;
Kasukawa, Takeya;
Itoh, Masayoshi;
Matsuyama, Akifumi;
Shin, Jay W;
Umezawa, Akihiro;
Kawai, Jun;
Sato, Yoji

Publication type:

Article

ROR2 expression predicts human induced pluripotent stem cell differentiation into neural stem/progenitor cells and GABAergic neurons.

Published in:

Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-023-51082-4

By:

Kuroda, Takuya;
Yasuda, Satoshi;
Matsuyama, Satoko;
Miura, Takumi;
Sawada, Rumi;
Matsuyama, Akifumi;
Yamamoto, Yumiko;
Morioka, Masaki Suimye;
Kawaji, Hideya;
Kasukawa, Takeya;
Itoh, Masayoshi;
Akutsu, Hidenori;
Kawai, Jun;
Sato, Yoji

Publication type:

Article

Widespread 3′UTR capped RNAs derive from G-rich regions in proximity to AGO2 binding sites.

Published in:

BMC Biology, 2024, v. 22, n. 1, p. 1, doi. 10.1186/s12915-024-02032-7

By:

Haberman, Nejc;
Digby, Holly;
Faraway, Rupert;
Cheung, Rebecca;
Chakrabarti, Anob M.;
Jobbins, Andrew M.;
Parr, Callum;
Yasuzawa, Kayoko;
Kasukawa, Takeya;
Yip, Chi Wai;
Kato, Masaki;
Takahashi, Hazuki;
Carninci, Piero;
Vernia, Santiago;
Ule, Jernej;
Sibley, Christopher R.;
Martinez-Sanchez, Aida;
Lenhard, Boris

Publication type:

Article

Systematic analysis of transcription start sites in avian development.

Published in:

PLoS Biology, 2017, v. 15, n. 9, p. 1, doi. 10.1371/journal.pbio.2002887

By:

Lizio, Marina;
Deviatiiarov, Ruslan;
Nagai, Hiroki;
Galan, Laura;
Arner, Erik;
Itoh, Masayoshi;
Lassmann, Timo;
Kasukawa, Takeya;
Hasegawa, Akira;
Ros, Marian A.;
Hayashizaki, Yoshihide;
Carninci, Piero;
Forrest, Alistair R. R.;
Kawaji, Hideya;
Gusev, Oleg;
Sheng, Guojun

Publication type:

Article

Systematic Functional Annotation Workflow for Insects.

Published in:

Insects (2075-4450), 2022, v. 13, n. 7, p. 586, doi. 10.3390/insects13070586

By:

Bono, Hidemasa;
Sakamoto, Takuma;
Kasukawa, Takeya;
Tabunoki, Hiroko

Publication type:

Article

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-018-08126-5

By:

Kouno, Tsukasa;
Moody, Jonathan;
Kwon, Andrew Tae-Jun;
Shibayama, Youtaro;
Kato, Sachi;
Huang, Yi;
Böttcher, Michael;
Motakis, Efthymios;
Mendez, Mickaël;
Severin, Jessica;
Luginbühl, Joachim;
Abugessaisa, Imad;
Hasegawa, Akira;
Takizawa, Satoshi;
Arakawa, Takahiro;
Furuno, Masaaki;
Ramalingam, Naveen;
West, Jay;
Suzuki, Harukazu;
Kasukawa, Takeya

Publication type:

Article

Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags

Published in:

FEBS Letters, 2004, v. 559, n. 1-3, p. 22, doi. 10.1016/S0014-5793(04)00018-3

By:

Kodzius, Rimantas;
Matsumura, Yonehiro;
Kasukawa, Takeya;
Shimokawa, Kazuro;
Fukuda, Shiro;
Shiraki, Toshiyuki;
Nakamura, Mari;
Arakawa, Takahiro;
Sasaki, Daisuke;
Kawai, Jun;
Harbers, Matthias;
Carninci, Piero;
Hayashizaki, Yoshihide

Publication type:

Article

Successful Diagnosis of Sengers Syndrome Using a Comprehensive Genomic Analysis.

Published in:

2025

By:

Nakamura, Kohta;
Yatsuka, Yukiko;
Naito, Sachie;
Hasegawa, Akira;
Kasukawa, Takeya;
Kondo, Atsushi;
Kishita, Yoshihito;
Sugiyama, Yohei;
Onuki, Takanori;
Ebihara, Tomohiro;
Tsuruoka, Tomoko;
Fushimi, Takuya;
Ohtake, Akira;
Murayama, Kei;
Imai‐Okazaki, Atsuko;
Okazaki, Yasushi

Publication type:

Case Study

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23143-7

By:

Grapotte, Mathys;
Saraswat, Manu;
Bessière, Chloé;
Menichelli, Christophe;
Ramilowski, Jordan A.;
Severin, Jessica;
Hayashizaki, Yoshihide;
Itoh, Masayoshi;
Tagami, Michihira;
Murata, Mitsuyoshi;
Kojima-Ishiyama, Miki;
Noma, Shohei;
Noguchi, Shuhei;
Kasukawa, Takeya;
Hasegawa, Akira;
Suzuki, Harukazu;
Nishiyori-Sueki, Hiromi;
Frith, Martin C.;
FANTOM consortium;
Abugessaisa, Imad

Publication type:

Article

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Published in:

Database: The Journal of Biological Databases & Curation, 2016, v. 2016, p. 1, doi. 10.1093/database/baw105

By:

Abugessaisa, Imad;
Hisashi Shimoji;
Serkan Sahin;
Atsushi Kondo;
Harshbarger, Jayson;
Lizio, Marina;
Yoshihide Hayashizaki;
Carninci, Piero;
Forrest, Alistair;
Takeya Kasukawa;
Hideya Kawaji

Publication type:

Article

EpiFactors: a comprehensive database of human epigenetic factors and complexes.

Published in:

Database: The Journal of Biological Databases & Curation, 2015, v. 2015, p. 1, doi. 10.1093/database/bav067

By:

Medvedeva, Yulia A.;
Lennartsson, Andreas;
Ehsani, Rezvan;
Kulakovskiy, Ivan V.;
Vorontsov, Ilya E.;
Panahandeh, Pouda;
Khimulya, Grigory;
Takeya Kasukawa;
Drabløs, Finn

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

Self-patterning of rostral-caudal neuroectoderm requires dual role of Fgf signaling for localized Wnt antagonism.

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01105-2

By:

Nozomu Takata;
Eriko Sakakura;
Mototsugu Eiraku;
Takeya Kasukawa;
Yoshiki Sasai

Publication type:

Article

Cell-cycle-independent transitions in temporal identity of mammalian neural progenitor cells.

Published in:

Nature Communications, 2016, v. 7, n. 4, p. 11349, doi. 10.1038/ncomms11349

By:

Okamoto, Mayumi;
Miyata, Takaki;
Konno, Daijiro;
Ueda, Hiroki R.;
Kasukawa, Takeya;
Hashimoto, Mitsuhiro;
Matsuzaki, Fumio;
Kawaguchi, Ayano

Publication type:

Article

Thyrotrophin in the pars tuberalis triggers photoperiodic response.

Published in:

Nature, 2008, v. 452, n. 7185, p. 317, doi. 10.1038/nature06738

By:

Nakao, Nobuhiro;
Ono, Hiroko;
Yamamura, Takashi;
Anraku, Tsubasa;
Takagi, Tsuyoshi;
Higashi, Kumiko;
Yasuo, Shinobu;
Katou, Yasuhiro;
Kageyama, Saburo;
Uno, Yumiko;
Kasukawa, Takeya;
Iigo, Masayuki;
Sharp, Peter J.;
Iwasawa, Atsushi;
Suzuki, Yutaka;
Sugano, Sumio;
Niimi, Teruyuki;
Mizutani, Makoto;
Namikawa, Takao;
Ebihara, Shizufumi

Publication type:

Article

FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 1, p. 116, doi. 10.1093/nar/30.1.116

By:

Bono, Hidemasa;
Kasukawa, Takeya;
Furuno, Masaaki;
Hayashizaki, Yoshihide;
Okazaki, Yasushi

Publication type:

Article

READ: RIKEN Expression Array Database.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 1, p. 211, doi. 10.1093/nar/30.1.211

By:

Bono, Hidemasa;
Kasukawa, Takeya;
Hayashizaki, Yoshihide;
Okazaki, Yasushi

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

Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks.

Published in:

Nature Cell Biology, 2008, v. 10, n. 10, p. 1154, doi. 10.1038/ncb1775

By:

Ukai-Tadenuma, Maki;
Kasukawa, Takeya;
Ueda, Hiroki R.

Publication type:

Article

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

Published in:

Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d632, doi. 10.1093/nar/gkj034

By:

Kawaji, Hideya;
Kasukawa, Takeya;
Fukuda, Shiro;
Katayama, Shintaro;
Kai, Chikatoshi;
Kawai, Jun;
Carninci, Piero;
Hayashizaki, Yoshihide

Publication type:

Article

Differential Use of Signal Peptides and<br /> Membrane Domains Is a Common Occurrence in the Protein Output of Transcriptional Units.

Published in:

PLoS Genetics, 2006, v. 2, n. 4, p. e46, doi. 10.1371/journal.pgen.0020046

By:

Davis, Melissa J.;
Hanson, Kelly A.;
Clark, Francis;
Fink, J. Lynn;
Fasheng Zhang;
Kasukawa, Takeya;
Kai, Chikatoshi;
Kawai, Jun;
Carninci, Piero;
Hayashizaki, Yoshihide;
Teasdale, Rohan D.

Publication type:

Article

Transcript Annotation in FANTOM3:<br /> Mouse Gene Catalog Based on Physical<br /> cDNAs.

Published in:

PLoS Genetics, 2006, v. 2, n. 4, p. e62, doi. 10.1371/journal.pgen.0020062

By:

Maeda, Norihiro;
Kasukawa, Takeya;
Oyama, Rieko;
Gough, Julian;
Frith, Martin;
Engström, Pär G.;
Lenhard, Boris;
Aturaliya, Rajith N.;
Batalov, Serge;
Beisel, Kirk W.;
Bult, Carol J.;
Fletcher, Colin F.;
Forrest, Alistair R. R.;
Furuno, Masaaki;
Hill, David;
Itoh, Masayoshi;
Kanamori-Katayama, Mutsumi;
Katayama, Shintaro;
Katoh, Masaru;
Kawashima, Tsugumi

Publication type:

Article