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Update of the FANTOM web resource: enhancement for studying noncoding genomes 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.; Carninci, Piero; Kawaji, Hideya; Kasukawa, Takeya Share Save
ROR2 expression predicts human induced pluripotent stem cell differentiation into neural stem/progenitor cells and GABAergic neurons 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 Share Save
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Single-Cell RNA-Seq Reveals LRRC75A-Expressing Cell Population Involved in VEGF Secretion of Multipotent Mesenchymal Stromal/Stem Cells Under Ischemia 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 Share Save
Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types Yip, Chi Wai; Hon, Chung-Chau; Yasuzawa, Kayoko; Sivaraman, Divya M.; Ramilowski, Jordan A.; Shibayama, Youtaro; Agrawal, Saumya; Prabhu, Anika V.; Parr, Callum; Severin, Jessica; Lan, Yan Jun; Dostie, Josee; Petri, Andreas; Nishiyori-Sueki, Hiromi; Tagami, Michihira; Itoh, Masayoshi; Lopez-Redondo, Fernando; Kouno, Tsukasa; Chang, Jen-Chien; Luginbuhl, Joachim; Kato, Masaki; Murata, Mitsuyoshi; Yip, Wing Hin; Shu, Xufeng; Abugessaisa, Imad; Hasegawa, Akira; Suzuki, Harukazu; Kauppinen, Sakari; Yagi, Ken; Okazaki, Yasushi; Kasukawa, Takeya; de Hoon, Michiel; Carninci, Piero; Shin, Jay W. Share Save
IκBα is required for full transcriptional induction of some NFκB-regulated genes in response to TNF in MCF-7 cells (vol 7, 42, 2021) Ando, Minami; Magi, Shigeyuki; Seki, Masahide; Suzuki, Yutaka; Kasukawa, Takeya; Lefaudeux, Diane; Hoffmann, Alexander; Okada, Mariko Share Save
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (vol 12, 3279, 2021) Grapotte, Mathys; Saraswat, Manu; Bessiere, Chloe; 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.; Chatelain, Clement; Carninci, Piero; de Hoon, Michiel J. L.; Wasserman, Wyeth W.; Brehelin, Laurent; Lecellier, Charles-Henri Share Save
Inducing human retinal pigment epithelium-like cells from somatic tissue Woogeng, Ivo Ngundu; Kaczkowski, Bogumil; Abugessaisa, Imad; Hu, Haiming; Tachibana, Akihiro; Sahara, Yoshiki; Hon, Chung-Chau; Hasegawa, Akira; Sakai, Noriko; Nishida, Mitsuhiro; Sanyal, Hashimita; Sho, Junki; Kajita, Keisuke; Kasukawa, Takeya; Takasato, Minoru; Carninci, Piero; Maeda, Akiko; Mandai, Michiko; Arner, Erik; Takahashi, Masayo; Kime, Cody Share Save
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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network Grapotte, Mathys; Saraswat, Manu; Bessiere, Chloe; Menichelli, Christophe; Ramilowski, Jordan A.; Severin, Jessica; Hayashizaki, Yoshihide; Itoh, Masayoshi; Tagami, Michihira; Murata, Mitsuyoshi; Kojima-Ishiyamas, Miki; Noma, Shohei; Noguchi, Shuhei; Kasukawa, Takeya; Hasegawa, Akira; Suzuki, Harukazu; Nishiyori-Sueki, Hiromi; Frith, Martin C.; Chatelain, Clement; Carninci, Piero; de Hoom, Michiel J. L.; Wasserman, Wyeth W.; Brehelin, Laurent; Lecellieree, Charles-Henri Share Save
RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (vol 11, 1018, 2020) Bonetti, Alessandro; Agostini, Federico; Suzuki, Ana Maria; Hashimoto, Kosuke; Pascarella, Giovanni; Gimenez, Juliette; Roos, Leonie; Nash, Alex J.; Ghilotti, Marco; Cameron, Christopher J. F.; Valentine, Matthew; Medvedeva, Yulia A.; Noguchi, Shuhei; Agirre, Eneritz; Kashi, Kaori; Samudyata; Luginbuehl, Joachim; Cazzoli, Riccardo; Agrawal, Saumya; Luscombe, Nicholas M.; Blanchette, Mathieu; Kasukawa, Takeya; de Hoon, Michiel; Arner, Erik; Lenhard, Boris; Plessy, Charles; Castelo-Branco, Goncalo; Orlando, Valerio; Carninci, Piero Share Save
Automatic identification of small molecules that promote cell conversion and reprogramming Napolitano, Francesco; Rapakoulia, Trisevgeni; Annunziata, Patrizia; Hasegawa, Akira; Cardon, Melissa; Napolitano, Sara; Vaccaro, Lorenzo; Iuliano, Antonella; Wanderlingh, Luca Giorgio; Kasukawa, Takeya; Medina, Diego L.; Cacchiarelli, Davide; Gao, Xin; di Bernardo, Diego; Arner, Erik Share Save
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs Abugessaisa, Imad; Ramilowski, Jordan A.; Lizio, Marina; Severin, Jesicca; Hasegawa, Akira; Harshbarger, Jayson; Kondo, Atsushi; Noguchi, Shuhei; Yip, Chi Wai; Ooi, Jasmine Li Ching; Tagami, Michihira; Hori, Fumi; Agrawal, Saumya; Hon, Chung Chau; Cardon, Melissa; Ikeda, Shuya; Ono, Hiromasa; Bono, Hidemasa; Kato, Masaki; Hashimoto, Kosuke; Bonetti, Alessandro; Kobayashi, Norio; Shin, Jay; de Hoon, Michiel; Hayashizakil, Yoshihide; Carninci, Piero; Kawaji, Hideya; Kasukawa, Takeya Share Save
Functional annotation of human long noncoding RNAs via molecular phenotyping (vol 30, pg 1060, 2020) Ramilowski, Jordan A.; Yip, Chi Wai; Agrawal, Saumya; Chang, Jen-Chien; Ciani, Yari; Kulakovskiy, Ivan V.; Mendez, Mickael; Ooi, Jasmine Li Ching; Ouyang, John F.; Parkinson, Nick; Petri, Andreas; Roos, Leonie; Severin, Jessica; Yasuzawa, Kayoko; Abugessaisa, Imad; Akalin, Altuna; Antonov, Ivan V.; Arner, Erik; Bonetti, Alessandro; Bono, Hidemasa; Borsari, Beatrice; Brombacher, Frank; Cameron, Christopher J. F.; Cannistraci, Carlo Vittorio; Cardenas, Ryan; Cardon, Melissa; Chang, Howard; Dostie, Josee; Ducoli, Luca; Favorov, Alexander; Fort, Alexandre; Garrido, Diego; Gil, Noa; Gimenez, Juliette; Guler, Reto; Handoko, Lusy; Harshbarger, Jayson; Hasegawa, Akira; Hasegawa, Yuki; Hashimoto, Kosuke; Hayatsu, Norihito; Heutink, Peter; Hirose, Tetsuro; Imada, Eddie L.; Itoh, Masayoshi; Kaczkowski, Bogumil; Kanhere, Aditi; Kawabata, Emily; Kawaji, Hideya; Kawashima, Tsugumi; Kelly, S. Thomas; Kojima, Miki; Kondo, Naoto; Koseki, Haruhiko; Kouno, Tsukasa; Kratz, Anton; Kurowska-Stolarska, Mariola; Kwon, Andrew Tae Jun; Leek, Jeffrey; Lennartsson, Andreas; Lizio, Marina; Lopez-Redondo, Fernando; Luginbuhl, Joachim; Maeda, Shiori; Makeev, Vsevolod J.; Marchionni, Luigi; Medvedeva, Yulia A.; Minoda, Aki; Muller, Ferenc; Munoz-Aguirre, Manuel; Murata, Mitsuyoshi; Nishiyori, Hiromi; Nitta, Kazuhiro R.; Noguchi, Shuhei; Noro, Yukihiko; Nurtdinov, Ramil; Okazaki, Yasushi; Orlando, Valerio; Paquette, Denis; Parr, Callum J. C.; Rackham, Owen J. L.; Rizzu, Patrizia; Martinez, Diego Fernando Sanchez; Sandelin, Albin; Sanjana, Pillay; Semple, Colin A. M.; Shibayama, Youtaro; Sivaraman, Divya M.; Suzuki, Takahiro; Szumowski, Suzannah C.; Tagami, Michihira; Taylor, Martin S.; Terao, Chikashi; Thodberg, Malte; Thongjuea, Supat; Tripathi, Vidisha; Ulitsky, Igor; Verardo, Roberto; Vorontsov, Ilya E.; Yamamoto, Chinatsu; Young, Robert S.; Baillie, J. Kenneth; Forrest, Alistair R. R.; Guigo, Roderic; Hoffman, Michael M.; Hon, Chung Chau; Kasukawa, Takeya; Kauppinen, Sakari; Kere, Juha; Lenhard, Boris; Schneider, Claudio; Suzuki, Harukazu; Yagi, Ken; de Hoon, Michiel J. L.; Shin, Jay W.; Carninci, Piero Share Save
Functional annotation of human long noncoding RNAs via molecular phenotyping Ramilowski, Jordan A.; Yip, Chi Wai; Agrawal, Saumya; Chang, Jen-Chien; Ciani, Yari; Kulakovskiy, Ivan V.; Mendez, Mickael; Ooi, Jasmine Li Ching; Ouyang, John F.; Parkinson, Nick; Petri, Andreas; Roos, Leonie; Severin, Jessica; Yasuzawa, Kayoko; Abugessaisa, Imad; Akalin, Altuna; Antonov, Ivan V.; Arner, Erik; Bonetti, Alessandro; Bono, Hidemasa; Borsari, Beatrice; Brombacher, Frank; Cameron, Chris J. F.; Cannistraci, Carlo Vittorio; Cardenas, Ryan; Cardon, Melissa; Chang, Howard; Dostie, Josee; Ducoli, Luca; Favorov, Alexander; Fort, Alexandre; Garrido, Diego; Gil, Noa; Gimenez, Juliette; Guler, Reto; Handoko, Lusy; Harshbarger, Jayson; Hasegawa, Akira; Hasegawa, Yuki; Hashimoto, Kosuke; Hayatsu, Norihito; Heutink, Peter; Hirose, Tetsuro; Imada, Eddie L.; Itoh, Masayoshi; Kaczkowski, Bogumil; Kanhere, Aditi; Kawabata, Emily; Kawaji, Hideya; Kawashima, Tsugumi; Kelly, S. Thomas; Kojima, Miki; Kondo, Naoto; Koseki, Haruhiko; Kouno, Tsukasa; Kratz, Anton; Kurowska-Stolarska, Mariola; Kwon, Andrew Tae Jun; Leek, Jeffrey; Lennartsson, Andreas; Lizio, Marina; Lopez-Redondo, Fernando; Luginbuhl, Joachim; Maeda, Shiori; Makeev, Vsevolod J.; Marchionni, Luigi; Medvedeva, Yulia A.; Minoda, Aki; Mueller, Ferenc; Munoz-Aguirre, Manuel; Murata, Mitsuyoshi; Nishiyori, Hiromi; Nitta, Kazuhiro R.; Noguchi, Shuhei; Noro, Yukihiko; Nurtdinov, Ramil; Okazaki, Yasushi; Orlando, Valerio; Paquette, Denis; Parr, Callum J. C.; Rackham, Owen J. L.; Rizzu, Patrizia; Martinez, Diego Fernando Sanchez; Sandelin, Albin; Sanjana, Pillay; Semple, Colin A. M.; Shibayama, Youtaro; Sivaraman, Divya M.; Suzuki, Takahiro; Szumowski, Suzannah C.; Tagami, Michihira; Taylor, Martin S.; Terao, Chikashi; Thodberg, Malte; Thongjuea, Supat; Tripathi, Vidisha; Ulitsky, Igor; Verardo, Roberto; Vorontsov, Ilya E.; Yamamoto, Chinatsu; Young, Robert S.; Baillie, J. Kenneth; Forrest, Alistair R. R.; Guigo, Roderic; Hoffman, Michael M.; Hon, Chung Chau; Kasukawa, Takeya; Kauppinen, Sakari; Kere, Juha; Lenhard, Boris; Schneider, Claudio; Suzuki, Harukazu; Yagi, Ken; de Hoon, Michiel J. L.; Shin, Jay W.; Carninci, Piero Share Save
Comparative transcriptomics of primary cells in vertebrates Alam, Tanvir; Agrawal, Saumya; Severin, Jessica; Young, Robert S.; Andersson, Robin; Arner, Erik; Hasegawa, Akira; Lizio, Marina; Ramilowski, Jordan A.; Abugessaisa, Imad; Ishizu, Yuri; Noma, Shohei; Tarui, Hiroshi; Taylor, Martin S.; Lassmann, Timo; Itoh, Masayoshi; Kasukawa, Takeya; Kawaji, Hideya; Marchionni, Luigi; Sheng, Guojun; Forrest, Alistair R. R.; Khachigian, Levon M.; Hayashizaki, Yoshihide; Carninci, Piero; de Hoon, Michiel J. L. Share Save
The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression Michida, Hiroki; Imoto, Hiroaki; Shinohara, Hisaaki; Yumoto, Noriko; Seki, Masahide; Umeda, Mana; Hayashi, Tetsutaro; Nikaido, Itoshi; Kasukawa, Takeya; Suzuki, Yutaka; Okada-Hatakeyama, Mariko Share Save
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