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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 99   113 Cited 113 times in Scopus113 233
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 203   86 Cited 79 times in Scopus79 224
Hurst, Laurence D., Sachenkova, Oxana, Daub, Carsten, Forrest, Alistair R. R., the FANTOM consortium, Huminiecki, Lukasz, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014) A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription factors are positive regulators. Genome Biology, 15 7: . doi:10.1186/s13059-014-0413-3 50 1 0
Tomaru, Yasuhiro, Hasegawa, Ryota, Suzuki, Takahiro, Sato, Taiji, Kubosaki, Atsutaka, Suzuki, Masanori, Kawaji, Hideya, Forrest, Alistair R. R., Hayashizaki, Yoshihide, FANTOM Consortium, Shin, Jay W., Suzuki, Harukazu, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Fearnley, Liam, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014) A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation. Nucleic Acids Research, 42 14: 8905-8913. doi:10.1093/nar/gku567 63 2 Cited 0 times in Scopus0 2
Dimont, Emmanuel, Hofmann, Oliver, Ho Sui, Shannan J., Forrest, Alistair R. R., Kawaji, Hideya, Hide, Winston, the FANTOM Consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam, Kenna, Tony, Blumenthal, Antje, Briggs, James and Ovchinnikov, Dmitry (2014) CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments. Bioinformatics, 30 8: 1183-1184. doi:10.1093/bioinformatics/btu125 78   0 Cited 0 times in Scopus0 8
Hasegawa, Yuki, Tang, Dave, Takahashi, Naoko, Hayashizaki, Yoshihide, Forrest, Alistair R. R., the FANTOM consortium, Suzuki, Harukazu, Blumenthal, Antje, Kenna, Tony, Briggs, James, Beckhouse, Anthony G., Hitchens, Kelly J., Ovchinnikov, Dmitry A., Vijayan, Dipti, Wells, Christine A. and Wolvetang, Ernst (2014) CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Scientific Reports, 4 Art No: 5228: . doi:10.1038/srep05228 31 5 3 Cited 1 times in Scopus1 65
Arner, Erik, Forrest, Alistair R. R., Ehrlund, Anna, Mejhert, Niklas, Itoh, Masayoshi, Kawaji, Hideya, Lassman, Timo, Laurencikiene, Jurga, Ryden, Mikael, Arner, Peter, the FANTOM Consortium, Beckhouse, Anthony G., Blumenthal, Antje, Briggs, James, Hitchens, Kelly, Kenna, Tony J., Ovchinnikov, Dmitry A., Vijayan, Dipti, Wells, Christine A. and Wolvetang, Ernst (2014) Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. PLoS One, 9 3: . doi:10.1371/journal.pone.0080274 47 1 1 Cited 1 times in Scopus1 2
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, Wolvetang, Ernst, Blumenthal, Antje, Ovchinnikov, Dmitry and Briggs, James (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 69 1 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, Wolvetang, Ernst, Blumenthal, Antje, Ovchinnikov, Dmitry and Briggs, James (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 72   4 Cited 4 times in Scopus4 23
Briggs, James A., Mason, Elizabeth A., Ovchinnikov, Dmitry A., Wells, Christine A. and Wolvetang, Ernst J. (2013) Concise review: new paradigms for down syndrome research using induced pluripotent stem cells: tackling complex human genetic disease. Stem Cells Translational Medicine, 2 3: 175-184. doi:10.5966/sctm.2012-0117 46 6 2 Cited 2 times in Scopus2 3
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 70 3 20 Cited 22 times in Scopus22 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, the 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 43   6 Cited 6 times in Scopus6 3
Medvedeva, Yulia A., Khamis, Abdullah M., Kulakovskiy, Ivan V., Ba-Alawi, Wail, Bhuyan, Md Shariful I., Kawaji, Hideya, Lassmann, Timo, Harbers, Matthias, Forrest, Alistair R. R., Bajic, Vladimir B., The FANTOM Consortium, Beckhouse, Anthony, Fearnley, Liam, Hitchens, Kelly, Kenna, Tony, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars, Vijayan, Dipti, Wells, Christine, Wolvetang, Ernst, Blumenthal, Antje, Briggs, James and Ovchinnikov, Dmitry (2014) Effects of cytosine methylation on transcription factor binding sites. BMC Genomics, 15 119: 1-12. doi:10.1186/1471-2164-15-119 60 1 6 Cited 6 times in Scopus6 3
Frith, Martin C., The FANTOM Consortium, Wolvetang, Ernst, Wells, Christine, Beckhouse, Anthony, Fearnley, Liam, Hitchens, Kelly, Kenna, Tony, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars, Vijayan, Dipti, Blumenthal, Antje, Briggs, James and Ovchinnikov, Dmitry (2014) Explaining the correlations among properties of mammalian promoters. Nucleic Acids Research, 42 8: 4823-4832. doi:10.1093/nar/gku115 74 6 1 Cited 0 times in Scopus0 1
Briggs, Maxwell James (2004). Facilitating a large scale collaborative venture (LSCV) project: An approach to economic growth based on a strategic marketing evaluation of the Multifunction Polis Project (1987 - 1990) PhD Thesis, School of Economics, The University of Queensland. 143 387
Briggs, James A., Sun, Jane, Shepherd, Jill, Ovchinnikov, Dmitry A., Chung, Tung-Liang, Nayler, Sam P., Kao, Li-Pin, Morrow, Carl A., Thakar, Nilay Y., Soo, Set-Yen, Peura, Teija, Grimmond, Sean and Wolvetang, Ernst J. (2013) Integration-free induced pluripotent stem cells model genetic and neural developmental features of Down Syndrome etiology. Stem Cells, 31 3: 467-478. doi:10.1002/stem.1297 91   15 Cited 17 times in Scopus17 2
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, the FANTOM Consortium, Carninci, Piero, Gustincich, Stefano, Beckhouse, Anthony, Briggs, James, Hitchens, Kelly, Kenna, Tony, Ovchinnikov, Dmitry, Vijayan, Dipti, Wells, Christine, Wolvetang, Ernst, Blumenthal, Antje, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014) Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules. BMC Genomics, 15 729: . doi:10.1186/1471-2164-15-729 56 3 Cited 1 times in Scopus1 5
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, Wolvetang, Ernst, Beckhouse, Anthony, Fearnley, Liam, Hitchens, Kelly, Kenna, Tony, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars, Vijayan, Dipti, Blumenthal, Antje, Ovchinnikov, Dmitry and Briggs, James (2014) Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood, 123 17: 58-67. doi:10.1182/blood-2013-02-483792 82   4 Cited 6 times in Scopus6 27
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., The Fantom Consortium, Schneider, Claudio, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Wolvetang, Ernst, Hitchens, Kelly, Kenna, Tony, Blumenthal, Antje, Briggs, James, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth and Nielsen, Lars (2014) Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer. Stem Cells (Durham), 32 11: 2998-3011. doi:10.1002/stem.1791 44 1 Cited 0 times in Scopus0 1
Sardar, Adam J., Oates, Mmatt E., Fang, Hai, Forrest, Alistair R. R., Kawaji, Hideya, The FANTOM Consortium, Gough, Julian, Rackham, Owen J. L., 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) The evolution of human cells in terms of protein innovation. Molecular Biology and Evolution, 31 6: 1364-1374. doi:10.1093/molbev/mst139 55   1 Cited 0 times in Scopus0 4
Barry, Guy, Briggs, J. A., Vanichkina, D. P., Poth, E. M., Beveridge, N. J., Vikram Ratnu, Nayler, S. P., Nones, K., Hu, J., Timothy Bredy, Nakagawa, S., Rigo, F., Taft, R. J., Cairns, M. J., Blackshaw, S., Wolvetang, E. J. and Mattick, J. S. (2013) The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Molecular Psychiatry, 19 4: 486-494. doi:10.1038/mp.2013.45 60   13 Cited 22 times in Scopus22 4
Arner, Erik, Beckhouse, Anthony, Briggs, James, Ovchinnikov, Dmitry, Wolvetang, Ernst, Wells, Christine and FANTOM Consortium (2015) Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science, 347 6225: 1010-1014. doi:10.1126/science.1259418 9   0 Cited 0 times in Scopus0 85