Genome-wide analysis of mammalian promoter architecture and evolution von Carninci, Piero, Sandelin, Albin, Lenhard, Boris, Katayama, Shintaro, Shimokawa, Kazuro, Ponjavic, Jasmina, Semple, Colin A M, Taylor, Martin S, Engström, Pär G, Frith, Martin C, Forrest, Alistair R R, Alkema, Wynand B, Tan, Sin Lam, Plessy, Charles, Kodzius, Rimantas, Ravasi, Timothy, Kasukawa, Takeya, Fukuda, Shiro, Kanamori-Katayama, Mutsumi, Kitazume, Yayoi, Kawaji, Hideya, Kai, Chikatoshi, Nakamura, Mari, Konno, Hideaki, Nakano, Kenji, Mottagui-Tabar, Salim, Arner, Peter, Chesi, Alessandra, Gustincich, Stefano, Persichetti, Francesca, Suzuki, Harukazu, Grimmond, Sean M, Wells, Christine A, Orlando, Valerio, Wahlestedt, Claes, Liu, Edison T, Harbers, Matthias, Kawai, Jun, Bajic, Vladimir B, Hume, David A, Hayashizaki, Yoshihide

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Widespread resetting of DNA methylation in glioblastoma-initiating cells suppresses malignant cellular behavior in a lineage-dependent manner von Stricker, Stefan H, Feber, Andrew, Engström, Pär G, Carén, Helena, Kurian, Kathreena M, Takashima, Yasuhiro, Watts, Colin, Way, Michael, Dirks, Peter, Bertone, Paul, Smith, Austin, Beck, Stephan, Pollard, Steven M

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Genomic regulatory blocks underlie extensive microsynteny conservation in insects von Engström, Pär G, Ho Sui, Shannan J, Drivenes, Oyvind, Becker, Thomas S, Lenhard, Boris

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Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs von Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engström, Pär G, Lenhard, Boris, Aturaliya, Rajith N, Batalov, Serge, Beisel, Kirk W, Bult, Carol J, Fletcher, Colin F, Forrest, Alistair R R, Furuno, Masaaki, Hill, David, Itoh, Masayoshi, Kanamori-Katayama, Mutsumi, Katayama, Shintaro, Katoh, Masaru, Kawashima, Tsugumi, Quackenbush, John, Ravasi, Timothy, Ring, Brian Z, Shibata, Kazuhiro, Sugiura, Koji, Takenaka, Yoichi, Teasdale, Rohan D, Wells, Christine A, Zhu, Yunxia, Kai, Chikatoshi, Kawai, Jun, Hume, David A, Carninci, Piero, Hayashizaki, Yoshihide

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In silico detection of sequence variations modifying transcriptional regulation von Andersen, Malin C, Engström, Pär G, Lithwick, Stuart, Arenillas, David, Eriksson, Per, Lenhard, Boris, Wasserman, Wyeth W, Odeberg, Jacob

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The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line von Suzuki, Harukazu, Forrest, Alistair R R, van Nimwegen, Erik, Daub, Carsten O, Balwierz, Piotr J, Irvine, Katharine M, Lassmann, Timo, Ravasi, Timothy, Hasegawa, Yuki, de Hoon, Michiel J L, Katayama, Shintaro, Schroder, Kate, Carninci, Piero, Tomaru, Yasuhiro, Kanamori-Katayama, Mutsumi, Kubosaki, Atsutaka, Akalin, Altuna, Ando, Yoshinari, Arner, Erik, Asada, Maki, Asahara, Hiroshi, Bailey, Timothy, Bajic, Vladimir B, Bauer, Denis, Beckhouse, Anthony G, Bertin, Nicolas, Björkegren, Johan, Brombacher, Frank, Bulger, Erika, Chalk, Alistair M, Chiba, Joe, Cloonan, Nicole, Dawe, Adam, Dostie, Josee, Engström, Pär G, Essack, Magbubah, Faulkner, Geoffrey J, Fink, J Lynn, Fredman, David, Fujimori, Ko, Furuno, Masaaki, Gojobori, Takashi, Gough, Julian, Grimmond, Sean M, Gustafsson, Mika, Hashimoto, Megumi, Hashimoto, Takehiro, Hatakeyama, Mariko, Heinzel, Susanne, Hide, Winston, Hofmann, Oliver, Hörnquist, Michael, Huminiecki, Lukasz, Ikeo, Kazuho, Imamoto, Naoko, Inoue, Satoshi, Inoue, Yusuke, Ishihara, Ryoko, Iwayanagi, Takao, Jacobsen, Anders, Kaur, Mandeep, Kawaji, Hideya, Kerr, Markus C, Kimura, Ryuichiro, Kimura, Syuhei, Kimura, Yasumasa, Kitano, Hiroaki, Koga, Hisashi, Kojima, Toshio, Kondo, Shinji, Konno, Takeshi, Krogh, Anders, Kruger, Adele, Kumar, Ajit, Lenhard, Boris, Lennartsson, Andreas, Lindow, Morten, Lizio, Marina, Macpherson, Cameron, Maeda, Norihiro, Maher, Christopher A, Maqungo, Monique, Mar, Jessica, Matigian, Nicholas A, Matsuda, Hideo, Mattick, John S, Meier, Stuart, Miyamoto, Sei, Miyamoto-Sato, Etsuko, Nakabayashi, Kazuhiko, Nakachi, Yutaka, Nakano, Mika, Nygaard, Sanne, Okayama, Toshitsugu, Okazaki, Yasushi, Okuda-Yabukami, Haruka, Orlando, Valerio, Otomo, Jun, Pachkov, Mikhail, Petrovsky, Nikolai

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Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes von Sandelin, Albin, Bailey, Peter, Bruce, Sara, Engström, Pär G, Klos, Joanna M, Wasserman, Wyeth W, Ericson, Johan, Lenhard, Boris

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Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes von Engström, Pär G, Fredman, David, Lenhard, Boris

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A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1 von Danovi, Davide, Folarin, Amos, Gogolok, Sabine, Ender, Christine, Elbatsh, Ahmed M O, Engström, Pär G, Stricker, Stefan H, Gagrica, Sladjana, Georgian, Ana, Yu, Ding, U, Kin Pong, Harvey, Kevin J, Ferretti, Patrizia, Paddison, Patrick J, Preston, Jane E, Abbott, N Joan, Bertone, Paul, Smith, Austin, Pollard, Steven M

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Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival von Engström, Pär G, Tommei, Diva, Stricker, Stefan H, Ender, Christine, Pollard, Steven M, Bertone, Paul

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RNAi screen indicates widespread biological function for human natural antisense transcripts von Faghihi, Mohammad Ali, Kocerha, Jannet, Modarresi, Farzaneh, Engström, Pär G, Chalk, Alistair M, Brothers, Shaun P, Koesema, Eric, St Laurent, Georges, Wahlestedt, Claes

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RNAdb 2.0--an expanded database of mammalian non-coding RNAs von Pang, Ken C, Stuart, Stephen, Dinger, Marcel E, Engström, Pär G, Lenhard, Boris, Mattick, John S

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RNAdb—a comprehensive mammalian noncoding RNA database von Pang, Ken C., Stephen, Stuart, Engström, Pär G., Tajul-Arifin, Khairina, Chen, Weisan, Wahlestedt, Claes, Lenhard, Boris, Hayashizaki, Yoshihide, Mattick, John S.

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Identification of functional SNPs in the 5-prime flanking sequences of human genes von Mottagui-Tabar, Salim, Faghihi, Mohammad A, Mizuno, Yosuke, Engström, Pär G, Lenhard, Boris, Wasserman, Wyeth W, Wahlestedt, Claes

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Systematic evaluation of spliced alignment programs for RNA-seq data von Engström, Pär G, Steijger, Tamara, Sipos, Botond, Grant, Gregory R, Kahles, André, Rätsch, Gunnar, Goldman, Nick, Hubbard, Tim J, Harrow, Jennifer, Guigó, Roderic, Bertone, Paul

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non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells von Castelo-Branco, Gonçalo, Amaral, Paulo P, Engström, Pär G, Robson, Samuel C, Marques, Sueli C, Bertone, Paul, Kouzarides, Tony

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Current chemotherapy protocols for childhood acute lymphoblastic leukemia induce loss of humoral immunity to viral vaccination antigens von Nilsson, Anna, De Milito, Angelo, Engström, Pär, Nordin, Margareta, Narita, Mitsuo, Grillner, Lena, Chiodi, Francesca, Björk, Olle

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Assessment of transcript reconstruction methods for RNA-seq von Steijger, Tamara, Abril, Josep F, Engström, Pär G, Kokocinski, Felix, Hubbard, Tim J, Guigó, Roderic, Harrow, Jennifer, Bertone, Paul

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Identification of conserved regulatory elements by comparative genome analysis von Lenhard, Boris, Sandelin, Albin, Mendoza, Luis, Engström, Pär, Jareborg, Niclas, Wasserman, Wyeth W

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Complex Loci in human and mouse genomes von Engström, Pär G, Suzuki, Harukazu, Ninomiya, Noriko, Akalin, Altuna, Sessa, Luca, Lavorgna, Giovanni, Brozzi, Alessandro, Luzi, Lucilla, Tan, Sin Lam, Yang, Liang, Kunarso, Galih, Ng, Edwin Lian-Chong, Batalov, Serge, Wahlestedt, Claes, Kai, Chikatoshi, Kawai, Jun, Carninci, Piero, Hayashizaki, Yoshihide, Wells, Christine, Bajic, Vladimir B, Orlando, Valerio, Reid, James F, Lenhard, Boris, Lipovich, Leonard

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