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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   75 Cited 80 times in Scopus80 3
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 78   96 Cited 98 times in Scopus98 171
RIKEN GER Group,, Wells, C. A., Frith, M., Ravasi, T., Pang, K. C., Hallinan, J. S., Mattick, J. S., Hume, D. A., Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M. and Nishida, H. (2005) Antisense transcription in the mammalian transcriptome. Science, 309 5740: 1564-1566. doi:10.1126/science.1112009 297   767 Cited 781 times in Scopus781 7
Tompa, Martin, Li, Nan, Bailey, Timothy L., Church, George M., De Moor, Bart, Eskin, Eleazar, Favorov, Alexander V., Frith, Martin C., Fu, Yutao, Kent, W.James, Makeev, Vsevolod J., Mironov, Andrei A., Noble, William Stafford, Pavesi, Giulio, Pesole, Graziano, Regnier, Mireille, Simonis, Nicolas, Sinha, Saurabh, Thijs, Gert, van Helden, Jacques, Vandenbogaert, Mathias, Weng, Zhiping, Workman, Christopher, Ye, Chun and Zhu, Zhou (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology, 23 1: 137-144. doi:10.1038/nbt1053 136   682 Cited 765 times in Scopus765 9
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
Frith, Martin C., Saunders, Neil F. W., Kobe, Bostjan and Bailey, Timothy L. (2008) Discovering sequence motifs with arbitrary insertions and deletions. PLoS Computational Biology, 4 5: e1000071.1-e1000071.12. doi:10.1371/journal.pcbi.1000071 59   69 Cited 77 times in Scopus77 9
Frith, MC, Ponjavic, J, Fredman, D, Kai, C, Kawai, J, Carninci, P, Hayshizaki, Y and Sandelin, A (2006) Evolutionary turnover of mammalian transcription start sites. Genome Research, 16 6: 713-722. doi:10.1101/gr.5031006 43   52 Cited 54 times in Scopus54 0
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
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 and Vijayan, Dipti (2014) Explaining the correlations among properties of mammalian promoters. Nucleic Acids Research, 42 8: 4823-4832. doi:10.1093/nar/gku115 43 2 1 Cited 0 times in Scopus0 1
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   574 Cited 584 times in Scopus584 10
Whitington, Tom, Frith, Martin C., Johnson, James and Bailey, Timothy L. (2011) Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Research, 39 15: e98-1-e98-11. doi:10.1093/nar/gkr341 63   31 Cited 30 times in Scopus30 1
Baxter, L. L., Hsu, B. J., Umayam, L., Wolfsberg, T. G., Larson, D. M., Frith, M. C., Kawai, J., Hayashizaki, Y., Carninci, P. and Pavan, W. J. (2007) Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function. Pigment Cell Research, 20 3: 201-209. doi:10.1111/j.1600-0749.2007.00372.x 51   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 27 times in Scopus27 13
Pang, K. C., Frith, M. C. and Mattick, J. S. (2006) Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends In Genetics, 22 1: 1-5. doi:10.1016/j.tig.2005.10.003 64   228 Cited 247 times in Scopus247 12
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 50   2 Cited 2 times in Scopus2 3
Frith, M. C., Carninci, P., Kai, C., Kawai, J., Bailey, T. L., Hayashizaki, Y. and Mattick, J. S. (2007) Splicing bypasses 3' end formation signals to allow complex gene architectures. Gene, 403 1-2: 188-193. doi:10.1016/j.gene.2007.08.012 56   5 Cited 5 times in Scopus5 0
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
Frith, MC, Pheasant, M and Mattick, JS (2005) The amazing complexity of the human transcriptome. European Journal of Human Genetics, 13 8: 894-897. doi:10.1038/sj.ejhg.5201459 62   75 Cited 81 times in Scopus81 0
The FANTOM Consortium, Gough, J., Frith, M. C., Ravasi, T., Wells, C., Forrest, A. R. R., Davis, M. J., Aturaliya, R. N., Bailey, T. L., Crowe, M. L., Faulkner, G., Pang, K. C., Teasdale, R. D., Grimmond, S. M., Mattick, J. S., Hume, D. A. and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Core Team) (2005) The transcriptional landscape of the mammalian genome. Science, 309 5740: 1559-1563. doi:10.1126/science.1112014 164   1381 Cited 1357 times in Scopus1357 5
Maeda, Norihiro, Kasukawa,Takeya, Frith, Martin, Aturaliya, Rajith N., Forrest, Alistair R. R., Ravasi,Timothy, Teasdale, Rohan D., Wells, Christine A., Hume,David A. and Hayashizaki,Yoshihide (2006) Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs. PLoS Genetics, 2 4: 498-503. doi:10.1371/journal.pgen.0020062 80   83 Cited 60 times in Scopus60 0