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Frith, Martin C., Valen, Eivind, Krogh, Anders, Hayashizaki, Yoshihide, Carninci, Piero and Sandelin, Albin (2008) A code for transcription initiation in mammalian genomes. Genome Research, 18 1: 1-12. doi:10.1101/gr.6831208 51   72 Cited 80 times in Scopus80 3
Rönnerblad, Michelle, Andersson, Robin, Olofsson, Tor, Douagi, Iyadh, Karimi, Mohsen, Lehmann, Sören, Hoof, Ilka, de Hoon, Michiel, Itoh, Masayoshi, Nagao-Sato, Sayaka, Kawaji, Hideya, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Sandelin, Albin, Ekwall, Karl, Amer, Erik, Lennartsson, Andreas, for the FANTOM consortium, Wells, Christine and Wolvetang, Ernst (2014) Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. Blood, 123 17: e79-e89. doi:10.1182/blood-2013-02-482893 33   7 Cited 5 times in Scopus5 31
Gustincich, Stefano, Batalov, Serge, Beisel, Kirk W., Bona, Hidemasa, Carninci, Piero, Fletcher, Colin F., Grimmond, Sean, Hirokawa, Nobutaka, Jarvis, Erich D., Jegla, Tim, Kawasawa, Yuka, LeMieux, Julianna, Miki, Harukata, Raviola, Elio, Teasdale, Rohan D., Tominaga, Naoko, Yagi, Ken, Zimmer, Andreas, RIKEN GER Group, GSL Members, Hayashizaki, Yoshihide and Okazaki, Yasushi (2003) Analysis of the mouse transcriptome for genes involved in the function of the nervous system. Genome Research, 13 6B: 1395-1401. doi:10.1101/gr.1135303 79   19 Cited 19 times in Scopus19 0
Andersson, Robin, Gebhard, Claudia, Miguel-Escalada, Irene, Hoof, Ilka, Bornholdt, Jette, Boyd, Mette, Chen, Yun, Zhao, Xiaobei, Schmidl, Christian, Suzuki, Takahiro, Ntini, Evgenia, Arner, Erik, Valen, Eivind, Li, Kang, Schwarzfischer, Lucia, Glatz, Dagmar, Raithel, Johanna, Lilje, Berit, Rapin, Nicolas, Bagger, Frederik Otzen, Jørgensen, Mette, Andersen, Peter Refsing, Bertin, Nicolas, Rackham, Owen, Burroughs, A. Maxwell, Baillie, J. Kenneth, Ishizu, Yuri, Shimizu, Yuri, Furuhata, Erina, Maeda, Shiori, Negishi, Yutaka, Mungall, Christopher J., Meehan, Terrence F., Lassmann, Timo, Itoh, Masayoshi, Kawaji, Hideya, Kondo, Naoto, Kawai, Jun, Lennartsson, Andreas, Daub, Carsten O., Heutink, Peter, Hume, David A., Jensen, Torben Heick, Suzuki, Harukazu, Hayashizaki, Yoshihide, Müller, Ferenc, The FANTOM consortium, Forrest, Alistair R. R., Carninci, Piero, Rehli, Michael, Sandelin, Albin, Beckhouse, Anthony G., Blumenthal, Antje, Briggs, James, Faulkner, Geoffrey J., Frith, Martin C., Hitchens, Kelly J., Kenna, Tony J., Ovchinnikov, Dmitry A., Vijayan, Dipti, Wells, Christine A. and Wolvetang, Ernst (2014) An atlas of active enhancers across human cell types and tissues. Nature, 507 7493: 455-461. doi:10.1038/nature12787 76   78 Cited 73 times in Scopus73 233
Ravasi, Timothy, Suzuki, Harukazu, Cannistraci, Carlo Vittorio, Katayama, Shintaro, Bajic, Vladimir B., Tan, Kai, Akalin, Altuna, Schmeier, Sebastian, Kanamori-Katayama, Mutsumi, Carninci, Piero, Bertin, Nicholas, Daub, Cartsten O., Forrest, Alistair R. R., Gough, Julian, Grimmond, Sean, Han, Jung-Hoon, Hashimoto, Takehiro, Hide, Winston, Hofmann, Oliver, Kamburov, Atanas, Kaur, Mandeep, Kawaji, Hideya, Kubosaki, Atsutaka, Lassmann, Timo, van Nimwegen, Erik, MacPherson, Cameron Ross, Ogawa, Chihiro, Radovanovic, Aleksandar, Schwartz, Ariel, Teasdale, Rohan D., Tegner, Jesper, Lenhard, Boris, Teichmann, Sarah A., Arakawa, Takahiro, Ninomiya, Noriko, Murakami, Kayoko, Tagami, Michihira, Fukuda, Shiro, Imamura, Kengo, Kai, Chikatoshi, Ishihara, Ryoko, Kitazume, Yayoi, Kawai, Jun, Hume, David A., Ideker, Trey and Hayashizaki, Yoshihide (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140 5: 744-752. doi:10.1016/j.cell.2010.01.044 111   232 Cited 248 times in Scopus248 17
Forest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, De Hoon, Michael J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicholas, Jorgensen, 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, Altschuler, Intikhab, Albanese, Davide, Altschule, 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, Drablos, 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, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guh, 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., Sui, Shannan J. Ho, Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Klinken, S. Peter, Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, De Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummer, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, Van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 'T Hoen, Peter A. C., Tagami, Michihira, Takahash, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, Van De Wetering ,Marc, Van Den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham,Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero and Hayashizaki, Yoshihide (2014) A promoter-level mammalian expression atlas. Nature, 507 7493: 462-470. doi:10.1038/nature13182 84   61 Cited 60 times in Scopus60 225
Rye, Morten, Sandve, Geir Kjetil, Daub, Carsten O., Kawaji, Hideya, Carninci, Piero, Forrest, Alistair R. R., Drabløs, Finn, The FANTOM consortium, Beckhouse, Anthony, Fearnley, Liam, Hitchens, Kelly, Kenna, Tony, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars, Vijayan, Dipti, Wells, Christine and Wolvetang, Ernst (2014) Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines. BMC Genomics, 15 120: 1-21. doi:10.1186/1471-2164-15-120 38   0 Cited 0 times in Scopus0 1
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, The FANTOM Consortium, Beckhouse, Anthony, Fearnley, Liam, Hitchens, Kelly, Kenna, Tony, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars, Vijayan, Dipti, Wells, Christine and Wolvetang, Ernst (2014) Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing. Genome Research, 24 4: 708-718. doi:10.1101/gr.156232.113 43   2 Cited 3 times in Scopus3 23
Engstrom, Par G., Suzuki, Harukazu, Ninomiya, Noriko, Akalin, Altuna, Sessa, Luca, Lavorgna, Giovanni, Brozzi, Alessandro, Luzi, Lucilla, Tan, Sin Lam, Yang, Liang, Kunarso, Galih, Ng, Edwin Lian-Chong, Batalov, Serge, Wahlestedt, Claes, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Wells, Christine, Bajic, Vladimir B., Orlando, Valerio, Reid, James F., Lenhard, Boris and Lipovich, Leonard (2006) Complex loci in human and mouse genomes. PLoS Genetics, 2 4: 564-577. doi:10.1371/journal.pgen.0020047 64   160 Cited 112 times in Scopus112 4
Schroder, Kate, Irvine, Katharine M., Taylor, Martin S., Bokil, Nilesh J., Le Cao, Kim-Anh, Masterman, Kelly-Anne, Labzin, Larisa I., Semple, Colin A., Kapetanovic, Ronan, Fairbairn, Lynsey, Akalin, Altuna, Faulkner, Geoffrey J., Baillie, John Kenneth, Gongora, Milena, Daub, Carsten O., Kawaji, Hideya, McLachlan, Geoffrey J., Goldman, Nick, Grimmond, Sean M., Carninci, Piero, Suzuki, Harukazu, Hayashizaki, Yoshihide, Lenhard, Boris, Hume, David A. and Sweet, Matthew J. (2012) Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proceedings of the National Academy of Sciences of the USA, 109 16: E944-E953. doi:10.1073/pnas.1110156109 108 3 37 Cited 46 times in Scopus46 3
de Hoon, Michiel J. L., Taft, Ryan J., Hashimoto, Takehiro, Kanamori-Katayama, Mutsumi, Kawaji, Hideya, Kawano, Mitsuoki, Kishima, Mami, Lassmann, Timo, Faulkner, Geoffrey J., Mattick, John S., Daub, Carsten O., Carninci, Piero, Kawai, Jun, Suzuki, Harukazu and Hayashizaki, Yoshihide (2010) Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Research, 20 2: 257-264. doi:10.1101/gr.095273.109 69   52 Cited 58 times in Scopus58 0
Fort, Alexandre, Hashimoto, Kosuke, Yamada, Daisuke, Salimullah, Md, Keya, Chaman A., Saxena, Alka, Bonetti, Alessandro, Voineagu, Irina, Bertin, Nicolas, Kratz, Anton, Noro, Yukihiko, Wong, Chee-Hong, de Hoon, Michiel, Andersson, Robin, Sandelin, Albin, Suzuki, Harukazu, Wei, Chia-Lin, Koseki, Haruhiko, Hasegawa, Yuki, Forrest, Alistair R. R., Carninci, Piero, FANTOM Consortium, Beckhouse, Anthony, Blumenthal, Antje, Briggs, James, Hitchens, Kelly, Kenna, Tony, Ovchinnikov, Dmitry, Vijayan, Dipti, Wells, Christine and Wolvetang, Ernst (2014) Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nature Genetics, 46 6: 558-566. doi:10.1038/ng.2965 51 1 15 Cited 16 times in Scopus16 59
Morikawa, Hiromasa, Ohkura, Naganari, Vandenbon, Alexis, Itoh, Masayoshi, Nagao-Sato, Sayaka, Kawaji, Hideya, Lassman, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Standley, Daron M., Date, Hiroshi, Sakaguchi, Shimon, FANTOM Consortium, Beckhouse, Anthony G., Blumenthal, Antje, Briggs, James, Hitchens, Kelly J., Kenna, Tony J., Ovchinnikov, Dmitry A., Vijayan, Dipti, Wells, Christine A. and Wolvetang, Ernst (2014) Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proceedings of the National Academy of Sciences of the United States of America, 111 14: 5289-5294. doi:10.1073/pnas.1312717110 27   5 Cited 5 times in Scopus5 3
Davis, Melissa J., Hanson, Kelly A., Clark, Francis, Fink, J. Lynn, Zhang, Fasheng, Kasukawa, Takeya, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide and Teasdale, Rohan D. (2006) Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. Plos Genetics, 2 4: 554-563. doi:10.1371/journal.pgen.0020046 81 44 20 Cited 13 times in Scopus13 0
Shukla, Ruchi, Upton, Kyle R., Muñoz-Lopez, Martin, Gerhardt, Daniel J., Fisher, Malcolm E., Thu Nguyen, Brennan, Paul M., Baillie, J. Kenneth, Collino, Agnese, Ghisletti, Serena, Sinha, Shruti, Iannelli, Fabio, Radaelli, Enrico, Dos Santos, Alexandre, Rapoud, Delphine, Guettier, Catherine, Samuel, Didier, Natoli, Gioacchino, Carninci, Piero, Ciccarelli, Francesca D., Luis Garcia-Perez, Jose, Faivre, Jamila and Faulkner, Geoffrey J. (2013) Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell, 153 1: 101-111. doi:10.1016/j.cell.2013.02.032 35   51 Cited 53 times in Scopus53 4
Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Frith, Martin C., Forrest, Alistair R. R., Ravasi, Timothy, Grimmond, Sean M., Wells, Christine A., Hume, David A. and Hayashizaki, Yoshihide (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nature Genetics, 38 6: 626-635. doi:10.1038/ng1789 114   573 Cited 582 times in Scopus582 10
Valen, Eivind, Pascarella, Giovanni, Chalk, Alistair, Maeda, Norihiro, Kojima, Miki, Kawazu, Chika, Murata, Mistuyoshi, 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 and Carninci, Piero (2009) Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Research, 19 2: 255-265. doi:10.1101/gr.084541.108 41   58 Cited 70 times in Scopus70 4
Forrest, Alistair R. R., Taylor, Darrin F., Crowe, Mark L., Chalk, Alistair M., Waddell, Nic J., Kolle, Gabriel, Faulkner, Geoffrey J., Kodzius, Rimantas, Katayama, Shintaro, Wells, Christine, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide and Grimmond, Sean M. (2006) Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biology, 7 1: R5.1-R5.15. doi:10.1186/gb-2006-7-1-r5 79   28 Cited 30 times in Scopus30 3
Fink, J. Lynn, Aturaliya, Rajith N., Davis, Melissa J., Zhang, Fasheng, Hanson, Kelly, Teasdale, Melvena S., Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide and Teasdale, Rohan D. (2006) LOCATE: a mouse protein subcellular localization database. Nucleic Acids Research, 34 Supp. 1: D213-D217. doi:10.1093/nar/gkj069 85   41 Cited 65 times in Scopus65 0
Grison, Alice, Zucchelli, Silvia, Urzi, Alice, Zamparo, Ilaria, Lazarevic, Dejan, Pascarella, Giovanni, Roncaglia, Paola, Giorgetti, Alejandro, Garcia-Esparcia, Paula, Vlachouli, Christina, Simone, Roberto, Persichetti, Francesca, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Carloni, Paolo, Ferrer, Isidro, Lodovichi, Claudia, Plessy, Charles, Carninci, Piero and Gustincich, Stefano (2014) Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules. BMC Genomics, 15 1: . doi:10.1186/1471-2164-15-729 14   Cited 1 times in Scopus1 5
Bajic, Vladimir B., Tan, Sin Lam, Christoffels, Alan, Schonbach, Christian, Lilpovich, Leonard, Yang, Liang, Hofmann, Oliver, Kruger, Adele, Hide, Winston, Kai, Chikatoshi, Kawai, Jun, Hume, David A., Carninci, Piero and Hayashizaki, Yoshihide (2006) Mice and men: Their promoter properties. Plos Genetics, 2 4: 614-626. doi:10.1371/journal.pgen.0020054 109 54 58 Cited 26 times in Scopus26 0
Pascarella, Giovanni, Lazarevic, Dejan, Plessy, Charles, Bertin, Nicolas, Akalin, Altuna, Vlachouli, Christina, Simone, Roberto, Faulkner, Geoffry J., Zucchelli, Silvia, Kawai, Jun, Daub, Carsten O., Hayashizaki, Yoshihide, Lenhard, Boris, Carninci, Piero and Gustincich, Stefano (2014) NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Frontiers in Cellular Neuroscience, 8 FEB: . doi:10.3389/fncel.2014.00041 21   3 Cited 4 times in Scopus4 0
Frith, Martin C., Wilming, Laurens G., Forrest, Alistair, Kawaji, Hideya, Tan, Sin Lam, Wahlestedt, Claes, Bajic, Vladimir B., Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Bailey, Timothy L. and Huminiecki, Lukasz (2006) Pseudo-messenger RNA: Phantoms of the transcriptome. PLOS Genetics, 2 4: 504-514. doi:10.1371/journal.pgen.0020023 48   37 Cited 26 times in Scopus26 13
Ohmiya, Hiroko, Vitezic, Morana, Frith, Martin C., Itoh, Masayoshi, Carninci, Piero, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Lassmann, Timo, FANTOM Consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam and Kenna, Tony (2014) RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). BMC Genomics, 15 . doi:10.1186/1471-2164-15-269 46   2 Cited 2 times in Scopus2 3
Motakis, Efthymios, Guhl, Sven, Ishizu, Yuri, Itoh, Masayoshi, Kawaji, Hideya, de Hoon, Michiel, Lassman, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Zuberbier, Torsten, Forrest, Alistair R. R., Babina, Magda, for The FANTOM Consortium, Wells, Christine and Wolvetang, Ernst (2014) Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood, 123 17: 58-67. doi:10.1182/blood-2013-02-483792 70   3 Cited 5 times in Scopus5 27
Taft, Ryan J., Glazov, Evgeny A., Lassmann, Timo, Hayashizaki, Yoshihide, Carninci, Piero and Mattick, John S. (2009) Small RNAs derived from snoRNAs. RNA, 15 7: 1233-1240. doi:10.1261/rna.1528909 61   180 Cited 186 times in Scopus186 4
Baillie, J. Kenneth, Barnett, Mark W., Upton, Kyle R., Gerhardt, Daniel J., Richmond, Todd A., De Sapio, Fioravante, Brennan. Paul M., Rizzu, Patrizia, Smith, Sarah, Fell, Mark, Talbot, Richard T., Gustincich, Stefano, Freeman, Thomas C., Mattick, John S., Hume, David A., Heutink, Peter, Carninci, Piero, Jeddeloh, Jeffrey A. and Faulkner, Geoffrey J. (2011) Somatic retrotransposition alters the genetic landscape of the human brain. Nature, 479 7374: 534-537. doi:10.1038/nature10531 49   164 Cited 171 times in Scopus171 95
Verardo, Roberto, Piazza, Silvano, Klaric, Enio, Ciani, Yari, Bussadori, Giulio, Marzinotto, Stefania, Mariuzzi, Laura, Cesselli, Daniela, Beltrami, Antonio P., Mano, Miguel, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Beltrami, Carlo A., Fantom Consortium, Schneider, Claudio and Blumenthal, Antje (2014) Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer. Stem Cells, 32 11: 2998-3011. doi:10.1002/stem.1791 9   0 Cited 0 times in Scopus0 1
Aturaliya,Rajith N., Fink, J. Lynn, Davis, Melissa J., Hanson, Kelly A., Miranda,Kevin C., Forrest,Alistair R. R., Grimmond, Sean M., Suzuki,Harukazu, Kanamori,Mutsumi, Kai,Chikatoshi, Kawai,Jun, Carninci,Piero, Hayashizaki,Yoshihide and Teasdale,Rohan D. (2006) Subcellular localization of mammalian type II membrane proteins. Traffic, 7 5: 613-625. doi:10.1111/j.1600-0854.2006.00407.x 67   16 Cited 18 times in Scopus18 0
Schmidl, Christian, Hansmann, Leo, Lassmann, Timo, Balwierz, Piotr J., Kawaji, Hideya, Itoh, Masayoshi, Kawai, Jun, Nagao-Sato, Sayaka, Suzuki, Harukazu, Andreesen, Reinhard, Hayashizaki, Yoshihide, Forrest, Alistair R. R., Carninci, Piero, Hoffmann, Petra, Edinger, Matthias, Rehli, Michael, for the FANTOM consortium, Wells, Christine and Wolvetang, Ernst (2014) The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations. Blood, 123 17: e68-e78. doi:10.1182/blood-2013-02-486944 28   4 Cited 6 times in Scopus6 25
Clark, Michael B., Amaral, Paulo P., Schlesinger, Felix J., Dinger, Marcel E., Taft, Ryan J., Rinn, John L., Ponting, Chris P., Stadler, Peter F., Morris, Kevin V., Morillon, Antonin, Rozowsky, Joel S., Gerstein, Mark B., Wahlestedt, Claes, Hayashizaki, Yoshihide, Carninci, Piero, Gingeras, Thomas R. and Mattick, John S. (2011) The reality of pervasive transcription. PLoS Biology, 9 7: e1000625.1-e1000625.6. doi:10.1371/journal.pbio.1000625 67 31 129 Cited 147 times in Scopus147 55
Faulkner, Geoffrey J., Kimura, Yasumasa, Daub, Carsten O., Wani, Shivangi, Plessy, Charles, Irvine, Katharine M., Schroder, Kate, Cloonan, Nicole, Steptoe, Anita L., Lassmann, Timo, Waki, Kazunori, Hornig, Nadine, Arakawa, Takahiro, Takahashi, Hazuki, Kawai, Jun, Forrest, Alistair R. R., Suzuki, Harukazu, Hayashizaki, Yoshihide, Hume, David A., Orlando, Valerio, Grimmond, Sean M. and Carninci, Piero (2009) The regulated retrotransposon transcriptome of mammalian cells. Nature genetics, 41 5: 563-571. doi:10.1038/ng.368 111   250 Cited 255 times in Scopus255 2
Nilsson, Roland, Bajic, Vladimir B., Suzuki, Harukazu, di Bernardo, Diego, Bjorkegren, Johan, Katayama, Shintaro, Reid, James F., Sweet, Matthew J., Gariboldi, Manuela, Carninci, Piero, Hayashizaki, Yosihide, Hume, David A., Tegner, Jesper and Ravasi, Timothy (2006) Transcriptional network dynamics in macrophage activation. Genomics, 88 2: 133-142. doi:10.1016/j.ygeno.2006.03.022 73   69 Cited 73 times in Scopus73 0
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