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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 52   75 Cited 81 times in Scopus81 3
Wells, CA, Chalk, AM, Forrest, A, Taylor, D, Waddell, N, Schroder, K, Himes, SR, Faulkner, G, Lo, S, Kasukawa, T, Kawaji, H, Kai, C, Kawai, J, Katayama, S, Carninci, P, Hayashizaki, Y, Hume, DA and Grimmond, SM (2006) Alternate transcription of the Toll-like receptor signaling cascade. Genome Biology, 7 2: R10.1-R10.17. doi:10.1186/gb-2006-7-2-r10 77   33 Cited 41 times in Scopus41 0
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 35   7 Cited 6 times in Scopus6 31
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 84   102 Cited 104 times in Scopus104 233
Furuno, Masaaki, Pang, Ken C., Ninomiya, Noriko, Fukuda, Shiro, Frith, Martin C., Bult, Carol, Kai, Chikatoshi, Kawai, Jun, Carninci, P., Hayashizaki, Yoshihide, Mattick, John S. and Suzuki, Harukazu (2006) Clusters of internally primed transcripts reveal novel long noncoding RNAs. Plos Genetics, 2 4: 537-553. doi:10.1371/journal.pgen.0020037 154 154 85 Cited 63 times in Scopus63 0
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 49   3 Cited 3 times in Scopus3 23
Brahmachary, M., Schonbach, C., Yang, L., Huang, E. L., Tan, S. L., Chowdhary, R., Krishnan, S. P. T., Lin, C. Y., Hume, D. A., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y. and Bajic, V. B. (2006) Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes. Bmc Bioinformatics, 7 Supp. 5: Article number S8. doi:10.1186/1471-2105-7-S5-S8 84   17 Cited 17 times in Scopus17 1
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 110 3 42 Cited 47 times in Scopus47 2
Ravasi, T., Suzuki, H., Pang, K. C., Katayama, S., Furuno, M., Okunishi, R., Fukuda, S., Ru, K., Frith, M., Gongora, M., Grimmond, S., Hume, D. A., Hayashizaki, Y. and Mattick, J. S. (2006) Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Research, 16 1: 11-19. doi:10.1101/gr.4200206 87   204 Cited 216 times in Scopus216 0
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
Zavolan, M., Kondo, S., Schonbach, C., Adachi, J., Hume, D. A., Hayashizaki, Y., Gaasterland, T., RIKEN GER Grp and GLS Members (2003) Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Research, 13 6B: 1290-1300. doi:10.1101/gr.1017303 65   144 Cited 146 times in Scopus146 2
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
Sester, D. P., Trieu, A., Brion, K., Schroder, K., Ravasi, T., Robinson, J. A., McDonald, R. C., Ripoll, V., Wells, C. A., Suzuki, H., Hayashizaki, Y., Stacey, K. J., Hume, D. A. and Sweet, M. J. (2005) LPS regulates a set of genes in primary murine macrophages by antagonising CSF-1 action. Immunobiology, 210 2-4: 97-107. doi:10.1016/j.imbio.2005.05.004 130   26 Cited 29 times in Scopus29 0
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
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 27 times in Scopus27 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 57   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 72   3 Cited 6 times in Scopus6 27
Frith, Martin C., Forrest, Alistair R., Nourbakhsh, Ehsan, Pang, Ken C., Kai, Chikatoshi, Kawai, Jun, Carnici, Piero, Hayashizaki, Yoshihide, Bailey, Timothy L. and Grimmond, Sean M. (2006) The abundance of short proteins in the mammalian proteome. Plos Genetics, 2 4: 515-528. doi:10.1371/journal.pgen.0020052 47   62 Cited 61 times in Scopus61 3
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 29   4 Cited 6 times in Scopus6 25
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   71 Cited 74 times in Scopus74 0
Kawaji, H, Severin, J, Lizio, M, Forrest, ARR, van Nimwegen, E, Rehli, M, Schroder, K, Irvine, K, Suzuki, H, Carninci, P, Hayashizaki, Y and Daub, CO (2011) Update of the FANTOM web resource: From mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Research, 39 Supp. 1: D856-D860. doi:10.1093/nar/gkq1112 52   19 Cited 22 times in Scopus22 0