Prediction of Transcriptional Terminators in Bacillus subtilis and Related Species

por de Hoon, Michiel J. L., Makita, Yuko, Nakai, Kenta, Miyano, Satoru
Publicado 2005

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

por Kimura, Yasumasa, Soma, Takahiro, Kasahara, Naoko, Delobel, Diane, Hanami, Takeshi, Tanaka, Yuki, de Hoon, Michiel J. L., Hayashizaki, Yoshihide, Usui, Kengo, Harbers, Matthias
Publicado 2016

Optimization of turn-back primers in isothermal amplification

por Kimura, Yasumasa, de Hoon, Michiel J. L., Aoki, Shintaro, Ishizu, Yuri, Kawai, Yuki, Kogo, Yasushi, Daub, Carsten O., Lezhava, Alexander, Arner, Erik, Hayashizaki, Yoshihide
Publicado 2011

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

por Cock, Peter J. A., Antao, Tiago, Chang, Jeffrey T., Chapman, Brad A., Cox, Cymon J., Dalke, Andrew, Friedberg, Iddo, Hamelryck, Thomas, Kauff, Frank, Wilczynski, Bartek, de Hoon, Michiel J. L.
Publicado 2009

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

por 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
Publicado 2021

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

por Ienasescu, Hans, Li, Kang, Andersson, Robin, Vitezic, Morana, Rennie, Sarah, Chen, Yun, Vitting-Seerup, Kristoffer, Lagoni, Emil, Boyd, Mette, Bornholdt, Jette, de Hoon, Michiel J. L., Kawaji, Hideya, Lassmann, Timo, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Carninci, Piero, Sandelin, Albin
Publicado 2016

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

por 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
Publicado 2021

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

por Roy, Sugata, Schmeier, Sebastian, Arner, Erik, Alam, Tanvir, Parihar, Suraj P., Ozturk, Mumin, Tamgue, Ousman, Kawaji, Hideya, de Hoon, Michiel J. L., Itoh, Masayoshi, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Bajic, Vladimir B., Guler, Reto, Consortium, FANTOM, Brombacher, Frank, Suzuki, Harukazu
Publicado 2015

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

por Laurent, Georges St., Vyatkin, Yuri, Antonets, Denis, Ri, Maxim, Qi, Yao, Saik, Olga, Shtokalo, Dmitry, de Hoon, Michiel J.L., Kawaji, Hideya, Itoh, Masayoshi, Lassmann, Timo, Arner, Erik, Forrest, Alistair R.R., Nicolas, Estelle, McCaffrey, Timothy A., Carninci, Piero, Hayashizaki, Yoshihide, Wahlestedt, Claes, Kapranov, Philipp
Publicado 2016

Comparative transcriptomics of primary cells in vertebrates

por 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, R.R. Forrest, Alistair, Khachigian, Levon M., Hayashizaki, Yoshihide, Carninci, Piero, de Hoon, Michiel J.L.
Publicado 2020

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

por 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., Chatelain, Clément, Carninci, Piero, de Hoon, Michiel J. L., Wasserman, Wyeth W., Bréhélin, Laurent, Lecellier, Charles-Henri
Publicado 2021

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

por 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., Chatelain, Clément, Carninci, Piero, de Hoon, Michiel J. L., Wasserman, Wyeth W., Bréhélin, Laurent, Lecellier, Charles-Henri
Publicado 2022

Recounting the FANTOM CAGE-Associated Transcriptome

por Imada, Eddie Luidy, Sanchez, Diego Fernando, Collado-Torres, Leonardo, Wilks, Christopher, Matam, Tejasvi, Dinalankara, Wikum, Stupnikov, Aleksey, Lobo-Pereira, Francisco, Yip, Chi-Wai, Yasuzawa, Kayoko, Kondo, Naoto, Itoh, Masayoshi, Suzuki, Harukazu, Kasukawa, Takeya, Hon, Chung-Chau, de Hoon, Michiel J.L., Shin, Jay W., Carninci, Piero, Jaffe, Andrew E., Leek, Jeffrey T., Favorov, Alexander, Franco, Gloria R., Langmead, Ben, Marchionni, Luigi
Publicado 2020

Functional annotation of human long noncoding RNAs via molecular phenotyping

por Ramilowski, Jordan A., Yip, Chi Wai, Agrawal, Saumya, Chang, Jen-Chien, Ciani, Yari, Kulakovskiy, Ivan V., Mendez, Mickaël, 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, Josée, 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, López-Redondo, Fernando, Luginbühl, Joachim, Maeda, Shiori, Makeev, Vsevolod J., Marchionni, Luigi, Medvedeva, Yulia A., Minoda, Aki, Müller, Ferenc, Muñoz-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, Sánchez Martinez, Diego Fernando, 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., Guigó, 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
Publicado 2020