Works by Forrest, Alistair

Results: 82
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    Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.

    Published in:
    Nature Genetics, 2014, v. 46, n. 6, p. 558, doi. 10.1038/ng.2965
    By:
    • Fort, Alexandre;
    • Hashimoto, Kosuke;
    • Yamada, Daisuke;
    • Salimullah, Md;
    • Keya, Chaman A;
    • Saxena, Alka;
    • Bonetti, Alessandro;
    • Voineagu, Irina;
    • Bertin, Nicolas;
    • Kratz, Anton;
    • Noro, Yukihiko;
    • Wong, Chee-Hong;
    • de Hoon, Michiel;
    • Andersson, Robin;
    • Sandelin, Albin;
    • Suzuki, Harukazu;
    • Wei, Chia-Lin;
    • Koseki, Haruhiko;
    • Hasegawa, Yuki;
    • Forrest, Alistair R R
    Publication type:
    Article
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    Corrigendum: Tiny RNAs associated with transcription start sites in animals.

    Published in:
    2009
    By:
    • Taft, Ryan J;
    • Glazov, Evgeny A;
    • Cloonan, Nicole;
    • Simons, Cas;
    • Stephen, Stuart;
    • Faulkner, Geoffrey J;
    • Lassmann, Timo;
    • Forrest, Alistair R R;
    • Grimmond, Sean M;
    • Schroder, Kate;
    • Irvine, Katharine;
    • Arakawa, Takahiro;
    • Nakamura, Mari;
    • Kubosaki, Atsutaka;
    • Hayashida, Kengo;
    • Kawazu, Chika;
    • Murata, Mitsuyoshi;
    • Nishiyori, Hiromi;
    • Fukuda, Shiro;
    • Kawai, Jun
    Publication type:
    Correction Notice
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    The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

    Published in:
    Nature Genetics, 2009, v. 41, n. 5, p. 553, doi. 10.1038/ng.375
    By:
    • 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
    Publication type:
    Article
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    The regulated retrotransposon transcriptome of mammalian cells.

    Published in:
    Nature Genetics, 2009, v. 41, n. 5, p. 563, doi. 10.1038/ng.368
    By:
    • Faulkner, Geoffrey J.;
    • Kimura, Yasumasa;
    • Daub, Carsten O.;
    • Shivangi Wani;
    • 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
    Publication type:
    Article
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    Tiny RNAs associated with transcription start sites in animals.

    Published in:
    Nature Genetics, 2009, v. 41, n. 5, p. 572, doi. 10.1038/ng.312
    By:
    • Taft, Ryan J.;
    • Glazov, Evgeny A.;
    • Cloonan, Nicole;
    • Simons, Cas;
    • Stephen, Stuart;
    • Faulkner, Geoffrey J.;
    • Lassmann, Timo;
    • Forrest, Alistair R. R.;
    • Grimmond, Sean M.;
    • Schroder, Kate;
    • Irvine, Katharine;
    • Arakawa, Takahiro;
    • Nakamura, Mari;
    • Kubosaki, Atsutaka;
    • Hayashida, Kengo;
    • Kawazu, Chika;
    • Murata, Mitsuyoshi;
    • Nishiyori, Hiromi;
    • Fukuda, Shiro;
    • Kawai, Jun
    Publication type:
    Article
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    Corrigendum: Genome-wide analysis of mammalian promoter architecture and evolution.

    Published in:
    2007
    By:
    • Carninci, Piero;
    • Sandelin, Albin;
    • Lenhard, Boris;
    • Katayama, Shintaro;
    • Shimokawa, Kazuro;
    • Ponjavic, Jasmina;
    • Semple, Colin A. M.;
    • Taylor, Martin S.;
    • Engström G, 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
    Publication type:
    Correction Notice
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    Genome-wide analysis of mammalian promoter architecture and evolution.

    Published in:
    Nature Genetics, 2006, v. 38, n. 6, p. 626, doi. 10.1038/ng1789
    By:
    • 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.;
    • Sin Lam Tan;
    • Plessy, Charles;
    • Kodzius, Rimantas;
    • Ravasi, Timothy;
    • Kasukawa, Takeya;
    • Fukuda, Shiro;
    • Kanamori-Katayama, Mutsumi;
    • Kitazume, Yayoi
    Publication type:
    Article
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    LRRN4 and UPK3B Are Markers of Primary Mesothelial Cells.

    Published in:
    PLoS ONE, 2011, v. 6, n. 10, p. 1, doi. 10.1371/journal.pone.0025391
    By:
    • Kanamori-Katayama, Mutsumi;
    • Kaiho, Ai;
    • Ishizu, Yuri;
    • Okamura-Oho, Yuko;
    • Hino, Okio;
    • Abe, Masaaki;
    • Kishimoto, Takumi;
    • Sekihara, Hisahiko;
    • Nakamura, Yukio;
    • Suzuki, Harukazu;
    • Forrest, Alistair R. R.;
    • Hayashizaki, Yoshihide
    Publication type:
    Article
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    Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis.

    Published in:
    BMC Genomics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12864-019-6063-9
    By:
    • Ha, Thomas J.;
    • Zhang, Peter G. Y.;
    • Robert, Remi;
    • Yeung, Joanna;
    • Swanson, Douglas J.;
    • Mathelier, Anthony;
    • Wasserman, Wyeth W.;
    • Im, Sujin;
    • Itoh, Masayoshi;
    • Kawaji, Hideya;
    • Lassmann, Timo;
    • Daub, Carsten O.;
    • Arner, Erik;
    • Carninci, Piero;
    • Hayashizaki, Yoshihide;
    • Forrest, Alistair R. R.;
    • Goldowitz, Daniel
    Publication type:
    Article
    18

    Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.

    Published in:
    Molecular Systems Biology, 2015, v. 11, n. 12, p. n/a, doi. 10.15252/msb.20156492
    By:
    • Fraser, James;
    • Ferrai, Carmelo;
    • Chiariello, Andrea M;
    • Schueler, Markus;
    • Rito, Tiago;
    • Laudanno, Giovanni;
    • Barbieri, Mariano;
    • Moore, Benjamin L;
    • Kraemer, Dorothee CA;
    • Aitken, Stuart;
    • Xie, Sheila Q;
    • Morris, Kelly J;
    • Itoh, Masayoshi;
    • Kawaji, Hideya;
    • Jaeger, Ines;
    • Hayashizaki, Yoshihide;
    • Carninci, Piero;
    • Forrest, Alistair RR;
    • Semple, Colin A;
    • Dostie, Josée
    Publication type:
    Article
    19

    Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection.

    Published in:
    Cerebellum, 2018, v. 17, n. 3, p. 308, doi. 10.1007/s12311-017-0912-3
    By:
    • Zhang, Peter G. Y.;
    • Yeung, Joanna;
    • Gupta, Ishita;
    • Ramirez, Miguel;
    • Ha, Thomas;
    • Swanson, Douglas J.;
    • Nagao-Sato, Sayaka;
    • Itoh, Masayoshi;
    • Kawaji, Hideya;
    • Lassmann, Timo;
    • Daub, Carsten O.;
    • Arner, Erik;
    • de Hoon, Michiel;
    • the FANTOM consortium;
    • Carninci, Piero;
    • Forrest, Alistair R. R.;
    • Hayashizaki, Yoshihide;
    • Goldowitz, Dan
    Publication type:
    Article
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    Sensitization to immune checkpoint blockade through activation of a STAT1/NK axis in the tumor microenvironment.

    Published in:
    Science Translational Medicine, 2019, v. 11, n. 501, p. 1, doi. 10.1126/scitranslmed.aav7816
    By:
    • Zemek, Rachael M.;
    • De Jong, Emma;
    • Chin, Wee Loong;
    • Schuster, Iona S.;
    • Fear, Vanessa S.;
    • Casey, Thomas H.;
    • Forbes, Cath;
    • Dart, Sarah J.;
    • Leslie, Connull;
    • Zaitouny, Ayham;
    • Small, Michael;
    • Boon, Louis;
    • Forrest, Alistair R. R.;
    • Muiri, Daithi O.;
    • Degli-Esposti, Mariapia A.;
    • Millward, Michael J.;
    • Nowak, Anna K.;
    • Lassmann, Timo;
    • Bosco, Anthony;
    • Lake, Richard A.
    Publication type:
    Article
    23

    Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease.

    Published in:
    PLoS Genetics, 2017, v. 13, n. 3, p. 1, doi. 10.1371/journal.pgen.1006641
    By:
    • Baillie, J. Kenneth;
    • Arner, Erik;
    • Daub, Carsten;
    • De Hoon, Michiel;
    • Itoh, Masayoshi;
    • Kawaji, Hideya;
    • Lassmann, Timo;
    • Carninci, Piero;
    • Forrest, Alistair R. R.;
    • Hayashizaki, Yoshihide;
    • null, null;
    • Faulkner, Geoffrey J.;
    • Wells, Christine A.;
    • Rehli, Michael;
    • Pavli, Paul;
    • Summers, Kim M.;
    • Hume, David A.
    Publication type:
    Article
    24

    Systematic analysis of transcription start sites in avian development.

    Published in:
    PLoS Biology, 2017, v. 15, n. 9, p. 1, doi. 10.1371/journal.pbio.2002887
    By:
    • Lizio, Marina;
    • Deviatiiarov, Ruslan;
    • Nagai, Hiroki;
    • Galan, Laura;
    • Arner, Erik;
    • Itoh, Masayoshi;
    • Lassmann, Timo;
    • Kasukawa, Takeya;
    • Hasegawa, Akira;
    • Ros, Marian A.;
    • Hayashizaki, Yoshihide;
    • Carninci, Piero;
    • Forrest, Alistair R. R.;
    • Kawaji, Hideya;
    • Gusev, Oleg;
    • Sheng, Guojun
    Publication type:
    Article
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    Transcriptome analysis of periodontitis-associated fibroblasts by CAGE sequencing identified DLX5 and RUNX2 long variant as novel regulators involved in periodontitis.

    Published in:
    Scientific Reports, 2016, p. 33666, doi. 10.1038/srep33666
    By:
    • Horie, Masafumi;
    • Yamaguchi, Yoko;
    • Saito, Akira;
    • Nagase, Takahide;
    • Lizio, Marina;
    • Itoh, Masayoshi;
    • Kawaji, Hideya;
    • Lassmann, Timo;
    • Carninci, Piero;
    • Forrest, Alistair R. R.;
    • Hayashizaki, Yoshihide;
    • Suzutani, Tatsuo;
    • Kappert, Kai;
    • Micke, Patrick;
    • Ohshima, Mitsuhiro
    Publication type:
    Article
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    On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2016, v. 2016, p. 1, doi. 10.1093/database/baw144
    By:
    • Ienasescu, Hans;
    • Kang Li;
    • Andersson, Robin;
    • Vitezic, Morana;
    • Rennie, Sarah;
    • Yun Chen;
    • Vitting-Seerup, Kristoffer;
    • Lagoni, Emil;
    • Boyd, Mette;
    • Bornholdt, Jette;
    • de Hoon, Michiel J. L.;
    • Hideya Kawaji;
    • Lassmann, Timo;
    • Yoshihide Hayashizaki;
    • Forrest, Alistair R. R.;
    • Carninci, Piero;
    • Sandelin, Albin
    Publication type:
    Article
    35

    FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2016, v. 2016, p. 1, doi. 10.1093/database/baw105
    By:
    • Abugessaisa, Imad;
    • Hisashi Shimoji;
    • Serkan Sahin;
    • Atsushi Kondo;
    • Harshbarger, Jayson;
    • Lizio, Marina;
    • Yoshihide Hayashizaki;
    • Carninci, Piero;
    • Forrest, Alistair;
    • Takeya Kasukawa;
    • Hideya Kawaji
    Publication type:
    Article
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    CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

    Published in:
    BMC Genomics, 2014, v. 15, n. 1, p. 3494, doi. 10.1186/1471-2164-15-1177
    By:
    • Vitezic, Morana;
    • Bertin, Nicolas;
    • Andersson, Robin;
    • Lipovich, Leonard;
    • Kawaji, Hideya;
    • Lassmann, Timo;
    • Sandelin, Albin;
    • Heutink, Peter;
    • Goldowitz, Dan;
    • Ha, Thomas;
    • Peter Zhang;
    • Patrizi, Annarita;
    • Fagiolini, Michela;
    • Forrest, Alistair R. R.;
    • Carninci, Piero;
    • Saxena, Alka
    Publication type:
    Article
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    Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules.

    Published in:
    BMC Genomics, 2014, v. 15, n. 1, p. 729, doi. 10.1186/1471-2164-15-729
    By:
    • Grison, Alice;
    • Zucchelli, Silvia;
    • Urzì, Alice;
    • Zamparo, Ilaria;
    • Lazarevic, Dejan;
    • Pascarella, Giovanni;
    • Roncaglia, Paola;
    • Giorgetti, Alejandro;
    • Garcia-Esparcia, Paula;
    • Vlachouli, Christina;
    • Simone, Roberto;
    • Persichetti, Francesca;
    • Forrest, Alistair R. R.;
    • Yoshihide Hayashizaki;
    • Carloni, Paolo;
    • Ferrer, Isidro;
    • Lodovichi, Claudia;
    • Plessy, Charles;
    • Carninci, Piero;
    • Gustincich, Stefano
    Publication type:
    Article
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    Effects of cytosine methylation on transcription factor binding sites.

    Published in:
    BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-119
    By:
    • Medvedeva, Yulia A.;
    • Khamis, Abdullah M.;
    • Kulakovskiy, Ivan V.;
    • Wail Ba-Alawi;
    • Bhuyan, Md Shariful I.;
    • Kawaji, Hideya;
    • Lassmann, Timo;
    • Harbers, Matthias;
    • Forrest, Alistair R. R.;
    • Bajic, Vladimir B.
    Publication type:
    Article
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    Antisense Transcription in Loci Associated to Hereditary Neurodegenerative Diseases.

    Published in:
    Molecular Neurobiology, 2019, v. 56, n. 8, p. 5392, doi. 10.1007/s12035-018-1465-2
    By:
    • Zucchelli, Silvia;
    • Fedele, Stefania;
    • Vatta, Paolo;
    • Calligaris, Raffaella;
    • Heutink, Peter;
    • Rizzu, Patrizia;
    • Itoh, Masayoshi;
    • Persichetti, Francesca;
    • Santoro, Claudio;
    • Kawaji, Hideya;
    • Lassmann, Timo;
    • Hayashizaki, Yoshihide;
    • Carninci, Piero;
    • Forrest, Alistair R. R.;
    • Gustincich, Stefano
    Publication type:
    Article
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    Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease.

    Published in:
    Frontiers in Immunology, 2020, v. 11, p. N.PAG, doi. 10.3389/fimmu.2020.01269
    By:
    • Brown, Cheryl Y.;
    • Sadlon, Timothy;
    • Hope, Christopher M.;
    • Wong, Ying Y.;
    • Wong, Soon;
    • Liu, Ning;
    • Withers, Holly;
    • Brown, Katherine;
    • Bandara, Veronika;
    • Gundsambuu, Batjargal;
    • Pederson, Stephen;
    • Breen, James;
    • Robertson, Sarah Anne;
    • Forrest, Alistair;
    • Beyer, Marc;
    • Barry, Simon Charles
    Publication type:
    Article
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    The commitment of the human cell atlas to humanity.

    Published in:
    Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-54306-x
    By:
    • Amit, Ido;
    • Ardlie, Kristin;
    • Arzuaga, Fabiana;
    • Awandare, Gordon;
    • Bader, Gary;
    • Bernier, Alexander;
    • Carninci, Piero;
    • Donnelly, Stacey;
    • Eils, Roland;
    • Forrest, Alistair R. R.;
    • Greely, Henry T.;
    • Guigo, Roderic;
    • Hacohen, Nir;
    • Haniffa, Muzlifah;
    • Kirby, Emily Sarah;
    • Knoppers, Bartha Maria;
    • Kriegstein, Arnold;
    • Lein, Ed S.;
    • Linnarsson, Sten;
    • Majumder, Partha P.
    Publication type:
    Article
    45

    Stem cell transcriptome profiling via massive-scale mRNA sequencing.

    Published in:
    Nature Methods, 2008, v. 5, n. 7, p. 613, doi. 10.1038/nmeth.1223
    By:
    • 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.;
    • Lee, Clarence C.;
    • Ranade, Swati S.;
    • Peckham, Heather E.;
    • Manning, Jonathan M.;
    • McKernan, Kevin J.;
    • Grimmond, Sean M.
    Publication type:
    Article
    46

    Missing Plasma, Faulty Gel, or Something Else?

    Published in:
    Clinical Chemistry, 2020, v. 66, n. 4, p. 625, doi. 10.1093/clinchem/hvaa015
    By:
    • Tsui, Albert K. Y.;
    • Füzéry, Anna K.;
    • Szkotak, Artur;
    • Forrest, Alistair
    Publication type:
    Article
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