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Giles, N., Forrest, A. and Gabrielli, B. (2003) 14-3-3 acts as an intramolecular bridge to regulate cdc25B localization and activity. Journal of Biological Chemistry, 278 31: 28580-28587. doi:10.1074/jbc.M304027200 265   56 Cited 53 times in Scopus53 0
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   32 Cited 40 times in Scopus40 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 31   6 Cited 4 times in Scopus4 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 61   63 Cited 59 times in Scopus59 232
Rae, F. K., Martinez, G., Gillinder, K. R., Smith, A., Shooter, G., Forrest, A. R., Grimmond, S. M. and Little, M. H. (2004) Anlaysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol/fatty acid synthetic pathways as a possible major target of WT1. Oncogene, 23 17: 3067-3079. doi:10.1038/sj.onc.1207360 92   18 Cited 18 times in Scopus18 0
Pagan, Julia K., Arnold, Jeremy, Hanchard, Kim J., Kumar, Raman, Bruno, Tiziana, Jones, Mathew J.K., Richard, Derek J., Forrest, Alistair, Spurdle, Amanda, Verdin, Eric, Crossley, Merlin, Fanciulli, Maurizio, Chenevix-Trench, Georgia, Young, David B. and Khanna, Kum Kum (2007) A novel corepressor, BCoR-L1, represses transcription through an interaction with CtBP. Journal of Biological Chemistry, 282 20: 15248-15257. doi:10.1074/jbc.M700246200 107   18 Cited 18 times in Scopus18 0
Maguire, T. L., Grimmond, S. M., Forrest, A. R., Iturbe-Ormaeche, I., Meksem, K. and Gresshoff, P.M. (2002). CDNA microarray analysis of soybean: monitoring expression profiles of 4,100 genes. In: The International Conference on the Status of Plant, Animal and Microbe Genomes Research. International Plant & Animal Genome Conference, San Diego, (45-45). 12-16 January 2002. 84  
Sousa-Nunes, R., Rana, A. A., Kettleborough, R., Brickman, J. M., Clements, M., Forrest, A., Grimmond, S., Avner, P., Smith, J. C. and Dunwoodie, S. L. (2003) Characterizing embryonic gene expression patterns in the mouse using nonredundant sequence-based selection. Genome Research, 13 12: 2609-2620. doi:10.1101/gr1362303 45   21 Cited 21 times in Scopus21 0
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 35   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 38   2 Cited 2 times in Scopus2 23
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 and Wolvetang, Ernst (2014) Effects of cytosine methylation on transcription factor binding sites. BMC Genomics, 15 119: 1-12. doi:10.1186/1471-2164-15-119 29   3 Cited 5 times in Scopus5 3
Forrest, A. R., Taylor, D., RIKEN GER Group,, GSL Members, and Grimmond, S. M. (2003) Exploration of the cell-cycle genes found within the RIKEN FANTOM2 data set. Genome Research, 13 6B: 1366-1375. doi:10.1101/gr.1012403 46   5 Cited 6 times in Scopus6 0
Ravasi, T., Wells, C., Forrest, A., Walsh, N., Underhill, D. M., Wainwright, B. J., Aderem, A., Grimmond, S. and Hume, D. A. (2002) Generation of Diversity in the Innate Immune System: Macrophage Heterogeneity Arises From Gene-Autonomous Transcriptional Probability of Individual Inducible Genes. Journal of Immunology, 168 1: 44-50. 67   57 Cited 58 times in Scopus58
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 111   565 Cited 580 times in Scopus580 10
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
Prasad, Punit, Rönnerblad, Michelle, Arner, Erik, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Daub, Carsten O., Forrest, Alistair R. R., Lennartsson, Andreas, Ekwall, Karl, for the FANTOM Consortium, Wells, Christine and Wolvetang, Ernst (2014) High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis. Blood, 123 17: e46-e57. doi:10.1182/blood-2013-02-483537 18   2 Cited 2 times in Scopus2 31
Forrest, A. R. R., McCormack, A. K., DeSouza, C. P. C., Sinnamon, J. M., Tonks, I. D., Hayward, N. K., Ellem, K. A. O. and Gabrielli, B. G. (1999) Multiple splicing variants of cdc25B regulate G2/M progression. Biochemical and Biophysical Research Communications, 260 2: 510-515. doi:10.1006/bbrc.1999.0870 45   52 Cited 49 times in Scopus49 3
Ingram, W. J., Wicking, C. A., Grimmond, S. M., Forrest, A. R. and Wainwright, B. J. (2002) Novel genes regulated by Sonic Hedgehog in pluripotent mesenchymal cells. Oncogene, 21 53: 8196-8205. doi:10.1038/sj.onc.1205975 72   85 Cited 79 times in Scopus79 0
McGlinn, Edwina, Lammerts van Bueren, Kelly, Fiorenza, Salvatore, Mo, Rong, Poh, Alisa M., Forrest, Alistair, Soares, Marcelo Bento, Bonaldo, Maria de Fatima, Grimmond, Sean, Hui, Chi-chung, Wainwright, Brandon and Wicking, Carol (2005) Pax9 and Jagged1 act downstream of Gli3 in vertabrate limb development. Mechanisms of Development, 122 11: 1218-1233. doi:10.1016/j.mod.2005.06.012 93   42 Cited 47 times in Scopus47 0
Forrest, Alistair R. R., Taylor, Darrin F., Fink, J. Lynn, Gongora, M. Milena, Flegg, Cameron, Teasdale, Rohan D., Suzuki, Harukazu, Kanamori, Mutsumi, Kai, Chikatoshi, Hayashizaki, Yoshihide and Grimmond, Sean M. (2006) PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases. BMC Bioinformatics, 7 82: 1-11. doi:10.1186/1471-2105-7-82 69   11 Cited 9 times in Scopus9 0
Forrest, Alistair R. R., Ravasi, Timothy, Taylor, Darrin, Huber, Thomas L., Hume, David A., RIKEN GER Group, GSL Members and Grimmond, Sean (2003) Phosphoregulators: Protein kinases and protein phosphatases of mouse. Genome Research, 13 6B: 1443-1454. doi:10.1101/gr.954803 39   31 Cited 32 times in Scopus32 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 46   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 33   2 Cited 1 times in Scopus1 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 60   3 Cited 3 times in Scopus3 27
Cloonan, Nicole, Forrest, Alistair R. R., Kolle, Gabriel, Gardiner, Brooke B. A., Faulkner, Geoffrey J., Brown, Mellissa K., Taylor, Darrin F ., Steptoe, Anita L., Wani, Shivangi, Bethel, Graeme, Robertson, Alan J., Perkins, Andrew C., Bruce, Stephen J., Clarence, C. Lee, Ranade, Swati S., Peckham, Heather E, Manning, Jonathan M, McKernan, Kevin J and Grimmond, Sean M (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nature Methods, 5 7: 613-619. doi:10.1038/nmeth.1223 208   474 Cited 502 times in Scopus502 20
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 65   16 Cited 18 times in Scopus18 0
Ravasi, T., Huber, T. L., Zavolan, M., Forrest, A. R., Gaasterland, T., Grimmond, S. M., RIKEN GER Group,, GSL Members, and Hume, D. A. (2003) Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome Research, 13 6B: 1430-1442. doi:10.1101/gr.949803 78   53 Cited 54 times in Scopus54 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 25   4 Cited 6 times in Scopus6 25
Cloonan, Nicole, Brown, Mellissa K., Steptoe, Anita L., Wani, Shivangi, Chan, Wei Ling, Forrest, Alistair R. R., Kolle, Gabriel, Gabrielli, Brian and Grimmond, Sean M. (2008) The miR-17-5p microRNA is a key regulator of the G1/S phase cell cycle transition. Genome Biology, 9 8: R127.1-R127.14. doi:10.1186/gb-2008-9-8-r127 77   122 Cited 120 times in Scopus120 3
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   245 Cited 248 times in Scopus248 2
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 162   1341 Cited 1319 times in Scopus1319 5
Taft, RJ, Glazov, EA, Cloonan, N, Simons, C, Stephen, S, Faulkner, GJ, Lassmann, T, Forrest, ARR, Grimmond, SM, Schroder, K, Irvine, K, Arakawa, T, Nakamura, M, Kubosaki, A, Hayashida, K, Kawazu, C, Murata, M, Nishiyori, H, Fukuda, S, Kawai, J, Daub, CO, Hume, DA, Suzuki, H, Orlando, V, Carninci, P, Hayashizaki, Y and Mattick, JS (2009) Tiny RNAs associated with transcription start sites in animals. Nature Genetics, 41 5: 572-578. doi:10.1038/ng.312 105   187 Cited 207 times in Scopus207 2
Maguire, T. L., Grimmond, S., Forrest, A., Iturbe-Ormaetxe, I., Meksem, K. and Gresshoff, P. (2002) Tissue-specific gene expression in soybean (Glycine max) detected by cDNA microarray analysis. Journal of Plant Physiology, 159 12: 1361-1374. doi:10.1078/0176-1617-00858 111   24 Cited 25 times in Scopus25 0
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 75   82 Cited 59 times in Scopus59 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 48   17 Cited 22 times in Scopus22 0