CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing von Carbonell-Sala, Sílvia, Perteghella, Tamara, Lagarde, Julien, Nishiyori, Hiromi, Palumbo, Emilio, Arnan, Carme, Takahashi, Hazuki, Carninci, Piero, Uszczynska-Ratajczak, Barbara, Guigó, Roderic

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Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation von Sharma, Harshita, Valentine, Matthew N. Z., Toki, Naoko, Sueki, Hiromi Nishiyori, Gustincich, Stefano, Takahashi, Hazuki, Carninci, Piero

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Low Quantity Single Strand CAGE (LQ-ssCAGE) Maps Regulatory Enhancers and Promoters von Takahashi, Hazuki, Nishiyori-Sueki, Hiromi, Ramilowski, Jordan A., Itoh, Masayoshi, Carninci, Piero

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Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites von Morioka, Masaki Suimye, Kawaji, Hideya, Nishiyori-Sueki, Hiromi, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Carninci, Piero, Itoh, Masayoshi

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Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE von Valen, Eivind, Pascarella, Giovanni, Chalk, Alistair, Maeda, Norihiro, Kojima, Miki, Kawazu, Chika, Murata, Mitsuyoshi, Nishiyori, Hiromi, Lazarevic, Dejan, Motti, Dario, Marstrand, Troels Torben, Tang, Man-Hung Eric, Zhao, Xiaobei, Krogh, Anders, Winther, Ole, Arakawa, Takahiro, Kawai, Jun, Wells, Christine, Daub, Carsten, Harbers, Matthias, Hayashizaki, Yoshihide, Gustincich, Stefano, Sandelin, Albin, Carninci, Piero

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Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing von Kawaji, Hideya, Lizio, Marina, Itoh, Masayoshi, Kanamori-Katayama, Mutsumi, Kaiho, Ai, Nishiyori-Sueki, Hiromi, Shin, Jay W, Kojima-Ishiyama, Miki, Kawano, Mitsuoki, Murata, Mitsuyoshi, Ninomiya-Fukuda, Noriko, Ishikawa-Kato, Sachi, Nagao-Sato, Sayaka, Noma, Shohei, Hayashizaki, Yoshihide, Forrest, Alistair R R, Carninci, Piero

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High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance von Yoshida, Yuki, Shaikhutdinov, Nurislam, Kozlova, Olga, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Nishiyori-Sueki, Hiromi, Kojima-Ishiyama, Miki, Noma, Shohei, Cherkasov, Alexander, Gazizova, Guzel, Nasibullina, Aigul, Deviatiiarov, Ruslan, Shagimardanova, Elena, Ryabova, Alina, Yamaguchi, Katsushi, Bino, Takahiro, Shigenobu, Shuji, Tokumoto, Shoko, Miyata, Yugo, Cornette, Richard, Yamada, Takahiro G, Funahashi, Akira, Tomita, Masaru, Gusev, Oleg, Kikawada, Takahiro

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Ancient divergence of animal protein tyrosine kinase genes demonstrated by a gene family tree including choanoflagellate genes von Suga, Hiroshi, Sasaki, Go, Kuma, Kei-ichi, Nishiyori, Hiromi, Hirose, Nozomi, Su, Zhi-Hui, Iwabe, Naoyuki, Miyata, Takashi

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Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer von Maeda, Norihiro, Nishiyori, Hiromi, Nakamura, Mari, Kawazu, Chika, Murata, Mitsuyoshi, Sano, Hiromi, Hayashida, Kengo, Fukuda, Shiro, Tagami, Michihira, Hasegawa, Akira, Murakami, Kayoko, Schroder, Kate, Irvine, Katharine, Hume, David A, Hayashizaki, Yoshihide, Carninci, Piero, Suzuki, Harukazu

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Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells von Arner, Erik, Daub, Carsten O., Vitting-Seerup, Kristoffer, Andersson, Robin, Lilje, Berit, Drabløs, Finn, Lennartsson, Andreas, Rönnerblad, Michelle, Hrydziuszko, Olga, Vitezic, Morana, Freeman, Tom C., Alhendi, Ahmad M. N., Arner, Peter, Axton, Richard, Baillie, J. Kenneth, Bodega, Beatrice, Briggs, James, Brombacher, Frank, Davis, Margaret, Detmar, Michael, Ehrlund, Anna, Endoh, Mitsuhiro, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Faulkner, Geoffrey J., Ferrai, Carmelo, Fisher, Malcolm E., Forrester, Lesley, Goldowitz, Daniel, Guler, Reto, Hara, Mitsuko, Herlyn, Meenhard, Ikawa, Tomokatsu, Kai, Chieko, Kawamoto, Hiroshi, Klinken, S. Peter, Kojima, Soichi, Koseki, Haruhiko, Klein, Sarah, Mejhert, Niklas, Miyaguchi, Ken, Mizuno, Yosuke, Morimoto, Mitsuru, Morris, Kelly J., Nakachi, Yutaka, Ogishima, Soichi, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry, Passier, Robert, Patrikakis, Margaret, Pombo, Ana, Qin, Xian-Yang, Roy, Sugata, Sato, Hiroki, Savvi, Suzana, Saxena, Alka, Schwegmann, Anita, Swoboda, Rolf, Tanaka, Hiroshi, Tomoiu, Andru, Winteringham, Louise N., Wolvetang, Ernst, Yanagi-Mizuochi, Chiyo, Yoneda, Misako, Zabierowski, Susan, Zhang, Peter, Abugessaisa, Imad, Bertin, Nicolas, Diehl, Alexander D., Fukuda, Shiro, Furuno, Masaaki, Harshbarger, Jayson, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Ishizu, Yuri, Itoh, Masayoshi, Kawashima, Tsugumi, Kojima, Miki, Kondo, Naoto, Lizio, Marina, Meehan, Terrence F., Mungall, Christopher J., Murata, Mitsuyoshi, Nishiyori-Sueki, Hiromi, Sahin, Serkan, Nagao-Sato, Sayaka, Severin, Jessica, Kawai, Jun, Kasukawa, Takeya, Lassmann, Timo, Suzuki, Harukazu, Kawaji, Hideya, Wells, Christine, Hume, David A., Sandelin, Albin, Hayashizaki, Yoshihide

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CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing von Carbonell Sala, Silvia, Perteghella, Tamara, Lagarde, Julien, Nishiyori, Hiromi, Palumbo, Emilio, Arnan Ros, Carme, Takahashi, Hazuki, Carninci, Piero, Uszczynska-Ratajczak, Barbara, Guigó Serra, Roderic

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CAGE: cap analysis of gene expression von Harbers, Matthias, Hayashizaki, Yoshihide, Carninci, Piero, Kodzius, Rimantas, Kojima, Miki, Nishiyori, Hiromi, Nakamura, Mari, Fukuda, Shiro, Tagami, Michihira, Sasaki, Daisuke, Imamura, Kengo, Kai, Chikatoshi

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FANTOM5 CAGE profiles of human and mouse samples von Noguchi, Shuhei, Arakawa, Takahiro, Fukuda, Shiro, Furuno, Masaaki, Hasegawa, Akira, Hori, Fumi, Kawashima, Tsugumi, Kojima, Miki, Kubosaki, Atsutaka, Manabe, Ri-ichiroh, Nakazato, Kenichi, Nishiyori-Sueki, Hiromi, Saijyo, Eri, Simon, Christophe, Suzuki, Naoko, Tagami, Michihira, Yoshida, Shigehiro, Axton, Richard A., Babina, Magda, Beckhouse, Anthony G., Bodega, Beatrice, Carlisle, Ailsa J., Clevers, Hans C., Davis, Carrie A., Detmar, Michael, Edge, Albert S.B., Ehrlund, Anna, Ekwall, Karl, Enomoto, Hideki, Eslami, Afsaneh, Fujita, Rie, Goldowitz, Daniel, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Hasegawa, Yuki, Hitchens, Kelly J., Hume, David A., Kawamura, Yuki I., Khachigian, Levon M., Klein, Sarah, Klinken, S. Peter, Knox, Alan J., Kojima, Soichi, Koseki, Haruhiko, Koyasu, Shigeo, Lee, Weonju, Lennartsson, Andreas, Mackay-sim, Alan, Mejhert, Niklas, Mizuno, Yosuke, Moro, Kazuyo, Morris, Kelly J., Mummery, Christine L., Nakachi, Yutaka, Nakahara, Fumio, Ogishima, Soichi, Ohkura, Naganari, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Passier, Robert, Pombo, Ana, Pradhan-Bhatt, Swati, Qin, Xian-Yang, Rizzu, Patrizia, Roy, Sugata, Sajantila, Antti, Sakaguchi, Shimon, Satoh, Hironori, Saxena, Alka, Schmidl, Christian, Schulze-Tanzil, Gundula G., Shin, Jay W., Summers, Kim M., Takai, Jun, Tatsukawa, Hideki, Tomoiu, Andru, Toyoda, Hiroo, van de Wetering, Marc, Verardo, Roberto, Vijayan, Dipti, Yamaguchi, Yoko, Yoneda, Misako, Yonekura, Yohei, Harshbarger, Jayson, Lassmann, Timo, Sahin, Serkan, Sengstag, Thierry, Severin, Jessica, Shimoji, Hisashi, Suzuki, Masanori, Itoh, Masayoshi, Daub, Carsten O., Kasukawa, Takeya, Carninci, Piero, Forrest, Alistair R.R., Hayashizaki, Yoshihide

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Tiny RNAs associated with transcription start sites in animals von Grimmond, Sean M, Glazov, Evgeny A, Arakawa, Takahiro, Fukuda, Shiro, Kubosaki, Atsutaka, Schroder, Kate, Hume, David A, Mattick, John S, Daub, Carsten O, Kawazu, Chika, Hayashida, Kengo, Simons, Cas, Cloonan, Nicole, Murata, Mitsuyoshi, Forrest, Alistair R R, Suzuki, Harukazu, Kawai, Jun, Hayashizaki, Yoshihide, Stephen, Stuart, Carninci, Piero, Lassmann, Timo, Orlando, Valerio, Nishiyori, Hiromi, Faulkner, Geoffrey J, Irvine, Katharine, Taft, Ryan J, Nakamura, Mari

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Detecting Expressed Genes Using CAGE von Murata, Mitsuyoshi, Nishiyori-Sueki, Hiromi, Kojima-Ishiyama, Miki, Carninci, Piero, Hayashizaki, Yoshihide, Itoh, Masayoshi

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Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs von de Hoon, Michiel, Bonetti, Alessandro, Plessy, Charles, Ando, Yoshinari, Hon, Chung-Chau, Ishizu, Yuri, Itoh, Masayoshi, Kato, Sachi, Lin, Dongyan, Maekawa, Sho, Murata, Mitsuyoshi, Nishiyori, Hiromi, Shin, Jay W, Stolte, Jens, Suzuki, Ana Maria, Tagami, Michihira, Takahashi, Hazuki, Thongjuea, Supat, Forrest, Alistair R R, Hayashizaki, Yoshihide, Kere, Juha, Carninci, Piero

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Deep Cap Analysis of Gene Expression von Kurosawa, Junpei, Nishiyori, Hiromi, Hayashizaki, Yoshihide

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

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Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types von 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, Josée, Petri, Andreas, Nishiyori-Sueki, Hiromi, Tagami, Michihira, Itoh, Masayoshi, López-Redondo, Fernando, Kouno, Tsukasa, Chang, Jen-Chien, Luginbühl, 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.

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miRNA profiling of bilateral rat hippocampal CA3 by deep sequencing von Shinohara, Yoshiaki, Yahagi, Kazuko, Kawano, Mitsuoki, Nishiyori, Hiromi, Kawazu, Chika, Suzuki, Naoko, Manabe, Ri-ichiroh, Hirase, Hajime

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