Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians von Hashimoto, Kosuke, Kouno, Tsukasa, Ikawa, Tomokatsu, Hayatsu, Norihito, Miyajima, Yurina, Yabukami, Haruka, Terooatea, Tommy, Sasaki, Takashi, Suzuki, Takahiro, Valentine, Matthew, Pascarella, Giovanni, Okazaki, Yasushi, Suzuki, Harukazu, Shin, Jay W., Minoda, Aki, Taniuchi, Ichiro, Okano, Hideyuki, Arai, Yasumichi, Hirose, Nobuyoshi, Carninci, Piero

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A predictive computational framework for direct reprogramming between human cell types von Rackham, Owen J L, Firas, Jaber, Fang, Hai, Oates, Matt E, Holmes, Melissa L, Knaupp, Anja S, Suzuki, Harukazu, Nefzger, Christian M, Daub, Carsten O, Shin, Jay W, Petretto, Enrico, Forrest, Alistair R R, Hayashizaki, Yoshihide, Polo, Jose M, Gough, Julian

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Paradigm shifts in genomics through the FANTOM projects von de Hoon, Michiel, Shin, Jay W., Carninci, Piero

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C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution von 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, Lassmann, Timo, Hon, Chung-Chau, Arner, Erik, Carninci, Piero, Plessy, Charles, Shin, Jay W.

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Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality von Sabate‐Soler, Sonia, Nickels, Sarah Louise, Saraiva, Cláudia, Berger, Emanuel, Dubonyte, Ugne, Barmpa, Kyriaki, Lan, Yan Jun, Kouno, Tsukasa, Jarazo, Javier, Robertson, Graham, Sharif, Jafar, Koseki, Haruhiko, Thome, Christian, Shin, Jay W., Cowley, Sally A., Schwamborn, Jens C.

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The Human Cell Atlas von Regev, Aviv, Teichmann, Sarah A, Lander, Eric S, Amit, Ido, Benoist, Christophe, Birney, Ewan, Bodenmiller, Bernd, Campbell, Peter, Carninci, Piero, Clatworthy, Menna, Clevers, Hans, Deplancke, Bart, Dunham, Ian, Eberwine, James, Eils, Roland, Enard, Wolfgang, Farmer, Andrew, Fugger, Lars, Göttgens, Berthold, Hacohen, Nir, Haniffa, Muzlifah, Hemberg, Martin, Kim, Seung, Klenerman, Paul, Kriegstein, Arnold, Lein, Ed, Linnarsson, Sten, Lundberg, Emma, Lundeberg, Joakim, Majumder, Partha, Marioni, John C, Merad, Miriam, Mhlanga, Musa, Nawijn, Martijn, Netea, Mihai, Nolan, Garry, Pe'er, Dana, Phillipakis, Anthony, Ponting, Chris P, Quake, Stephen, Reik, Wolf, Rozenblatt-Rosen, Orit, Sanes, Joshua, Satija, Rahul, Schumacher, Ton N, Shalek, Alex, Shapiro, Ehud, Sharma, Padmanee, Shin, Jay W, Stegle, Oliver, Stratton, Michael, Stubbington, Michael J T, Theis, Fabian J, Uhlen, Matthias, van Oudenaarden, Alexander, Wagner, Allon, Watt, Fiona, Weissman, Jonathan, Wold, Barbara, Xavier, Ramnik, Yosef, Nir

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An integrated expression atlas of miRNAs and their promoters in human and mouse von de Rie, Derek, Abugessaisa, Imad, Alam, Tanvir, Arner, Erik, Arner, Peter, Ashoor, Haitham, Åström, Gaby, Babina, Magda, Bertin, Nicolas, Burroughs, A Maxwell, Carlisle, Ailsa J, Daub, Carsten O, Detmar, Michael, Deviatiiarov, Ruslan, Fort, Alexandre, Gebhard, Claudia, Goldowitz, Daniel, Guhl, Sven, Ha, Thomas J, Harshbarger, Jayson, Hasegawa, Akira, Hashimoto, Kosuke, Herlyn, Meenhard, Heutink, Peter, Hitchens, Kelly J, Hon, Chung Chau, Huang, Edward, Ishizu, Yuri, Kai, Chieko, Kasukawa, Takeya, Klinken, Peter, Lassmann, Timo, Lecellier, Charles-Henri, Lee, Weonju, Lizio, Marina, Makeev, Vsevolod, Mathelier, Anthony, Medvedeva, Yulia A, Mejhert, Niklas, Mungall, Christopher J, Noma, Shohei, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Persson, Helena, Rizzu, Patrizia, Roudnicky, Filip, Sætrom, Pål, Sato, Hiroki, Severin, Jessica, Shin, Jay W, Swoboda, Rolf K, Tarui, Hiroshi, Toyoda, Hiroo, Vitting-Seerup, Kristoffer, Winteringham, Louise, Yamaguchi, Yoko, Yasuzawa, Kayoko, Yoneda, Misako, Yumoto, Noriko, Zabierowski, Susan, Zhang, Peter G, Wells, Christine A, Summers, Kim M, Kawaji, Hideya, Sandelin, Albin, Rehli, Michael, Hayashizaki, Yoshihide, Carninci, Piero, Forrest, Alistair R R, de Hoon, Michiel J L

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

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A promoter-level mammalian expression atlas von Forrest, Alistair R R, Kawaji, Hideya, Rehli, Michael, Baillie, J Kenneth, de Hoon, Michiel J L, Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V, Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J, Meehan, Terrence F, Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A, Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A, Ishizu, Yuri, Young, Robert S, Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M, Arakawa, Takahiro, Archer, John A C, Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J, Beckhouse, Anthony G, Pradhan-Bhatt, Swati, Blake, Judith A, Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Burroughs, A Maxwell, Califano, Andrea, Cannistraci, Carlo V, Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C, Dalla, Emiliano, Davis, Carrie A, Detmar, Michael, Diehl, Alexander D, Dohi, Taeko, Drabløs, Finn, Edge, Albert S B, Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C, Faulkner, Geoffrey J, Favorov, Alexander V, Fisher, Malcolm E, Frith, Martin C, Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furino, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B, Gibson, Andrew P, Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J, Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J, Ho Sui, Shannan J, Hofmann, Oliver M, Hoof, Ilka, Hori, Furni, Huminiecki, Lukasz

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Functional annotation of lncRNA in high-throughput screening von Yip, Chi Wai, Sivaraman, Divya M, Prabhu, Anika V, Shin, Jay W

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Transcriptional profiling of VEGF-A and VEGF-C target genes in lymphatic endothelium reveals endothelial-specific molecule-1 as a novel mediator of lymphangiogenesis von Shin, Jay W., Huggenberger, Reto, Detmar, Michael

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Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids von Smits, Lisa M., Magni, Stefano, Kinugawa, Kaoru, Grzyb, Kamil, Luginbühl, Joachim, Sabate-Soler, Sonia, Bolognin, Silvia, Shin, Jay W., Mori, Eiichiro, Skupin, Alexander, Schwamborn, Jens C.

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Functional annotation of human long noncoding RNAs via molecular phenotyping von 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 JF, 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

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SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells von Moody, Jonathan, Kouno, Tsukasa, Chang, Jen-Chien, Ando, Yoshinari, Carninci, Piero, Shin, Jay W, Hon, Chung-Chau

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PAPD5-mediated 3′ adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease von Boele, Joost, Persson, Helena, Shin, Jay W., Ishizu, Yuri, Newie, Inga S., Søkilde, Rolf, Hawkins, Shannon M., Coarfa, Cristian, Ikeda, Kazuhiro, Takayama, Ken-ichi, Horie-Inoue, Kuniko, Ando, Yoshinari, Burroughs, A. Maxwell, Sasaki, Chihiro, Suzuki, Chizuru, Sakai, Mizuho, Aoki, Shintaro, Ogawa, Ayumi, Hasegawa, Akira, Lizio, Marina, Kaida, Kaoru, Teusink, Bas, Carninci, Piero, Suzuki, Harukazu, Inoue, Satoshi, Gunaratne, Preethi H., Rovira, Carlos, Hayashizaki, Yoshihide, de Hoon, Michiel J. L.

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An era of single-cell genomics consortia von Ando, Yoshinari, Kwon, Andrew Tae-Jun, Shin, Jay W.

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Single-nucleotide variant calling in single-cell sequencing data with Monopogen von Dou, Jinzhuang, Tan, Yukun, Kock, Kian Hong, Wang, Jun, Cheng, Xuesen, Tan, Le Min, Han, Kyung Yeon, Hon, Chung-Chau, Park, Woong-Yang, Shin, Jay W., Jin, Haijing, Wang, Yujia, Chen, Han, Ding, Li, Prabhakar, Shyam, Navin, Nicholas, Chen, Rui, Chen, Ken

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Annotation of nuclear lncRNAs based on chromatin interactions von Agrawal, Saumya, Buyan, Andrey, Severin, Jessica, Koido, Masaru, Alam, Tanvir, Abugessaisa, Imad, Chang, Howard Y, Dostie, Josée, Itoh, Masayoshi, Kere, Juha, Kondo, Naoto, Li, Yunjing, Makeev, Vsevolod J, Mendez, Mickaël, Okazaki, Yasushi, Ramilowski, Jordan A, Sigorskikh, Andrey I, Strug, Lisa J, Yagi, Ken, Yasuzawa, Kayoko, Yip, Chi Wai, Hon, Chung Chau, Hoffman, Michael M, Terao, Chikashi, Kulakovskiy, Ivan V, Kasukawa, Takeya, Shin, Jay W, Carninci, Piero, de Hoon, Michiel J L

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Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection von Roy, Sugata, Guler, Reto, Parihar, Suraj P, Schmeier, Sebastian, Kaczkowski, Bogumil, Nishimura, Hajime, Shin, Jay W, Negishi, Yutaka, Ozturk, Mumin, Hurdayal, Ramona, Kubosaki, Atsutaka, Kimura, Yasumasa, de Hoon, Michiel J L, Hayashizaki, Yoshihide, Brombacher, Frank, Suzuki, Harukazu

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FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs von 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, Kato, Masaki, Kobayashi, Norio, Shin, Jay, de Hoon, Michiel, Hayashizaki, Yoshihide, Carninci, Piero, Kawaji, Hideya, Kasukawa, Takeya

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