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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 269   57 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 79   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, Wolvetang, Ernst, Blumenthal, Antje, Kenna, Tony, Hitchens, Kelly, Ovchinnikov, Dmitry, Fearnley, Liam, Le Cao, Kim-Anh, Mason, Elizabeth, Nielsen, Lars and Vijayan, Dipti (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 45   7 Cited 7 times in Scopus7 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 109   113 Cited 113 times in Scopus113 233
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 101   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 118   19 Cited 19 times in Scopus19 0
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 35 5 3 Cited 1 times in Scopus1 65
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. 85  
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 47   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, 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 77 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 83   4 Cited 4 times in Scopus4 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, 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 69 1 6 Cited 6 times in Scopus6 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. 69   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 115   577 Cited 587 times in Scopus587 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 29   4 Cited 4 times in Scopus4 31
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 73 3 Cited 1 times in Scopus1 5
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 74   89 Cited 82 times in Scopus82 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 98   44 Cited 49 times in Scopus49 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 72   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 33 times in Scopus33 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, Kenna, Tony and Blumenthal, Antje (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:10.1186/1471-2164-15-269 102 1 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, 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 85   4 Cited 6 times in Scopus6 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 210   489 Cited 512 times in Scopus512 25
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 68   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 79   54 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 35   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 87   126 Cited 125 times in Scopus125 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   259 Cited 266 times in Scopus266 3
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   1396 Cited 1371 times in Scopus1371 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.312 106   196 Cited 216 times in Scopus216 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 113   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 84   85 Cited 63 times in Scopus63 0
Davis, Margaret R., Andersson, Robin, Severin, Jessica, de Hoon, Michiel, Bertin, Nicolas, Baillie, J. Kenneth, Kawaji, Hideya, Sandelin, Albin, Forrest, Alistair R.R., Summers, Kim M. and for the FANTOM Consortium (2014) Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions. Molecular Genetics and Metabolism, 112 1: 73-83. doi:10.1016/j.ymgme.2013.12.006 29   1 Cited 1 times in Scopus1 2
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 54   19 Cited 22 times in Scopus22 0