Searching journal content for Alistair R.R. Forrest in author.

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  1. Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
    • Michiel de Hoon,
    • Alessandro Bonetti,
    • Charles Plessy,
    • Yoshinari Ando,
    • Chung-Chau Hon,
    • Yuri Ishizu,
    • Masayoshi Itoh,
    • Sachi Kato,
    • Dongyan Lin,
    • Sho Maekawa,
    • Mitsuyoshi Murata,
    • Hiromi Nishiyori,
    • Jay W. Shin,
    • Jens Stolte,
    • Ana Maria Suzuki,
    • Michihira Tagami,
    • Hazuki Takahashi,
    • Supat Thongjuea,
    • Alistair R.R. Forrest,
    • Yoshihide Hayashizaki,
    • Juha Kere,
    • and Piero Carninci
    Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
    OPEN ACCESS ARTICLE
  2. Corrigendum: Corrigendum: Functional annotation of human long noncoding RNAs via molecular phenotyping
    • Jordan A. Ramilowski,
    • Chi Wai Yip,
    • Saumya Agrawal,
    • Jen-Chien Chang,
    • Yari Ciani,
    • Ivan V. Kulakovskiy,
    • Mickaël Mendez,
    • Jasmine Li Ching Ooi,
    • John F. Ouyang,
    • Nick Parkinson,
    • Andreas Petri,
    • Leonie Roos,
    • Jessica Severin,
    • Kayoko Yasuzawa,
    • Imad Abugessaisa,
    • Altuna Akalin,
    • Ivan V. Antonov,
    • Erik Arner,
    • Alessandro Bonetti,
    • Hidemasa Bono,
    • Beatrice Borsari,
    • Frank Brombacher,
    • Christopher J.F. Cameron,
    • Carlo Vittorio Cannistraci,
    • Ryan Cardenas,
    • Melissa Cardon,
    • Howard Chang,
    • Josée Dostie,
    • Luca Ducoli,
    • Alexander Favorov,
    • Alexandre Fort,
    • Diego Garrido,
    • Noa Gil,
    • Juliette Gimenez,
    • Reto Guler,
    • Lusy Handoko,
    • Jayson Harshbarger,
    • Akira Hasegawa,
    • Yuki Hasegawa,
    • Kosuke Hashimoto,
    • Norihito Hayatsu,
    • Peter Heutink,
    • Tetsuro Hirose,
    • Eddie L. Imada,
    • Masayoshi Itoh,
    • Bogumil Kaczkowski,
    • Aditi Kanhere,
    • Emily Kawabata,
    • Hideya Kawaji,
    • Tsugumi Kawashima,
    • S. Thomas Kelly,
    • Miki Kojima,
    • Naoto Kondo,
    • Haruhiko Koseki,
    • Tsukasa Kouno,
    • Anton Kratz,
    • Mariola Kurowska-Stolarska,
    • Andrew Tae Jun Kwon,
    • Jeffrey Leek,
    • Andreas Lennartsson,
    • Marina Lizio,
    • Fernando López-Redondo,
    • Joachim Luginbühl,
    • Shiori Maeda,
    • Vsevolod J. Makeev,
    • Luigi Marchionni,
    • Yulia A. Medvedeva,
    • Aki Minoda,
    • Ferenc Müller,
    • Manuel Muñoz-Aguirre,
    • Mitsuyoshi Murata,
    • Hiromi Nishiyori,
    • Kazuhiro R. Nitta,
    • Shuhei Noguchi,
    • Yukihiko Noro,
    • Ramil Nurtdinov,
    • Yasushi Okazaki,
    • Valerio Orlando,
    • Denis Paquette,
    • Callum J.C. Parr,
    • Owen J.L. Rackham,
    • Patrizia Rizzu,
    • Diego Fernando Sánchez Martinez,
    • Albin Sandelin,
    • Pillay Sanjana,
    • Colin A.M. Semple,
    • Youtaro Shibayama,
    • Divya M. Sivaraman,
    • Takahiro Suzuki,
    • Suzannah C. Szumowski,
    • Michihira Tagami,
    • Martin S. Taylor,
    • Chikashi Terao,
    • Malte Thodberg,
    • Supat Thongjuea,
    • Vidisha Tripathi,
    • Igor Ulitsky,
    • Roberto Verardo,
    • Ilya E. Vorontsov,
    • Chinatsu Yamamoto,
    • Robert S. Young,
    • J. Kenneth Baillie,
    • Alistair R.R. Forrest,
    • Roderic Guigó,
    • Michael M. Hoffman,
    • Chung Chau Hon,
    • Takeya Kasukawa,
    • Sakari Kauppinen,
    • Juha Kere,
    • Boris Lenhard,
    • Claudio Schneider,
    • Harukazu Suzuki,
    • Ken Yagi,
    • Michiel J.L. de Hoon,
    • Jay W. Shin,
    • and Piero Carninci
    Genome Res. September 2020 30: 1377-1; doi:10.1101/gr.270330.120
    OPEN ACCESS ARTICLE
  3. Research: Comparative transcriptomics of primary cells in vertebrates
    • Tanvir Alam,
    • Saumya Agrawal,
    • Jessica Severin,
    • Robert S. Young,
    • Robin Andersson,
    • Erik Arner,
    • Akira Hasegawa,
    • Marina Lizio,
    • Jordan A. Ramilowski,
    • Imad Abugessaisa,
    • Yuri Ishizu,
    • Shohei Noma,
    • Hiroshi Tarui,
    • Martin S. Taylor,
    • Timo Lassmann,
    • Masayoshi Itoh,
    • Takeya Kasukawa,
    • Hideya Kawaji,
    • Luigi Marchionni,
    • Guojun Sheng,
    • Alistair R.R. Forrest,
    • Levon M. Khachigian,
    • Yoshihide Hayashizaki,
    • Piero Carninci,
    • and Michiel J.L. de Hoon
    Genome Res. July 2020 30: 951-961; Published in Advance July 27, 2020, doi:10.1101/gr.255679.119
    OPEN ACCESS ARTICLE
  4. Resource: Functional annotation of human long noncoding RNAs via molecular phenotyping
    • Jordan A. Ramilowski,
    • Chi Wai Yip,
    • Saumya Agrawal,
    • Jen-Chien Chang,
    • Yari Ciani,
    • Ivan V. Kulakovskiy,
    • Mickaël Mendez,
    • Jasmine Li Ching Ooi,
    • John F. Ouyang,
    • Nick Parkinson,
    • Andreas Petri,
    • Leonie Roos,
    • Jessica Severin,
    • Kayoko Yasuzawa,
    • Imad Abugessaisa,
    • Altuna Akalin,
    • Ivan V. Antonov,
    • Erik Arner,
    • Alessandro Bonetti,
    • Hidemasa Bono,
    • Beatrice Borsari,
    • Frank Brombacher,
    • Christopher J.F. Cameron,
    • Carlo Vittorio Cannistraci,
    • Ryan Cardenas,
    • Melissa Cardon,
    • Howard Chang,
    • Josée Dostie,
    • Luca Ducoli,
    • Alexander Favorov,
    • Alexandre Fort,
    • Diego Garrido,
    • Noa Gil,
    • Juliette Gimenez,
    • Reto Guler,
    • Lusy Handoko,
    • Jayson Harshbarger,
    • Akira Hasegawa,
    • Yuki Hasegawa,
    • Kosuke Hashimoto,
    • Norihito Hayatsu,
    • Peter Heutink,
    • Tetsuro Hirose,
    • Eddie L. Imada,
    • Masayoshi Itoh,
    • Bogumil Kaczkowski,
    • Aditi Kanhere,
    • Emily Kawabata,
    • Hideya Kawaji,
    • Tsugumi Kawashima,
    • S. Thomas Kelly,
    • Miki Kojima,
    • Naoto Kondo,
    • Haruhiko Koseki,
    • Tsukasa Kouno,
    • Anton Kratz,
    • Mariola Kurowska-Stolarska,
    • Andrew Tae Jun Kwon,
    • Jeffrey Leek,
    • Andreas Lennartsson,
    • Marina Lizio,
    • Fernando López-Redondo,
    • Joachim Luginbühl,
    • Shiori Maeda,
    • Vsevolod J. Makeev,
    • Luigi Marchionni,
    • Yulia A. Medvedeva,
    • Aki Minoda,
    • Ferenc Müller,
    • Manuel Muñoz-Aguirre,
    • Mitsuyoshi Murata,
    • Hiromi Nishiyori,
    • Kazuhiro R. Nitta,
    • Shuhei Noguchi,
    • Yukihiko Noro,
    • Ramil Nurtdinov,
    • Yasushi Okazaki,
    • Valerio Orlando,
    • Denis Paquette,
    • Callum J.C. Parr,
    • Owen J.L. Rackham,
    • Patrizia Rizzu,
    • Diego Fernando Sánchez Martinez,
    • Albin Sandelin,
    • Pillay Sanjana,
    • Colin A.M. Semple,
    • Youtaro Shibayama,
    • Divya M. Sivaraman,
    • Takahiro Suzuki,
    • Suzannah C. Szumowski,
    • Michihira Tagami,
    • Martin S. Taylor,
    • Chikashi Terao,
    • Malte Thodberg,
    • Supat Thongjuea,
    • Vidisha Tripathi,
    • Igor Ulitsky,
    • Roberto Verardo,
    • Ilya E. Vorontsov,
    • Chinatsu Yamamoto,
    • Robert S. Young,
    • J. Kenneth Baillie,
    • Alistair R.R. Forrest,
    • Roderic Guigó,
    • Michael M. Hoffman,
    • Chung Chau Hon,
    • Takeya Kasukawa,
    • Sakari Kauppinen,
    • Juha Kere,
    • Boris Lenhard,
    • Claudio Schneider,
    • Harukazu Suzuki,
    • Ken Yagi,
    • Michiel J.L. de Hoon,
    • Jay W. Shin,
    • and Piero Carninci
    Genome Res. July 2020 30: 1060-1072; Published in Advance July 27, 2020, doi:10.1101/gr.254219.119
    OPEN ACCESS ARTICLE
  5. Research: CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors
    • Kosuke Hashimoto,
    • Ana Maria Suzuki,
    • Alexandre Dos Santos,
    • Christophe Desterke,
    • Agnese Collino,
    • Serena Ghisletti,
    • Emilie Braun,
    • Alessandro Bonetti,
    • Alexandre Fort,
    • Xian-Yang Qin,
    • Enrico Radaelli,
    • Bogumil Kaczkowski,
    • Alistair R.R. Forrest,
    • Soichi Kojima,
    • Didier Samuel,
    • Gioacchino Natoli,
    • Marie Annick Buendia,
    • Jamila Faivre,
    • and Piero Carninci
    Genome Res. December 2015 25: 1812-1824; Published in Advance October 28, 2015, doi:10.1101/gr.191031.115
    OPEN ACCESS ARTICLE
  6. Research: The frequent evolutionary birth and death of functional promoters in mouse and human
    • Robert S. Young,
    • Yoshihide Hayashizaki,
    • Robin Andersson,
    • Albin Sandelin,
    • Hideya Kawaji,
    • Masayoshi Itoh,
    • Timo Lassmann,
    • Piero Carninci,
    • The FANTOM Consortium,
    • Wendy A. Bickmore,
    • Alistair R. Forrest,
    • and Martin S. Taylor
    Genome Res. October 2015 25: 1546-1557; Published in Advance July 30, 2015, doi:10.1101/gr.190546.115
    OPEN ACCESS ARTICLE
  7. Method: Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing
    • Hideya Kawaji,
    • Marina Lizio,
    • Masayoshi Itoh,
    • Mutsumi Kanamori-Katayama,
    • Ai Kaiho,
    • Hiromi Nishiyori-Sueki,
    • Jay W. Shin,
    • Miki Kojima-Ishiyama,
    • Mitsuoki Kawano,
    • Mitsuyoshi Murata,
    • Noriko Ninomiya-Fukuda,
    • Sachi Ishikawa-Kato,
    • Sayaka Nagao-Sato,
    • Shohei Noma,
    • Yoshihide Hayashizaki,
    • Alistair R.R. Forrest,
    • Piero Carninci,
    • and The FANTOM Consortium
    Genome Res. April 2014 24: 708-717; Published in Advance March 27, 2014, doi:10.1101/gr.156232.113
    OPEN ACCESS ARTICLE
  8. Method: Unamplified cap analysis of gene expression on a single-molecule sequencer
    • Mutsumi Kanamori-Katayama,
    • Masayoshi Itoh,
    • Hideya Kawaji,
    • Timo Lassmann,
    • Shintaro Katayama,
    • Miki Kojima,
    • Nicolas Bertin,
    • Ai Kaiho,
    • Noriko Ninomiya,
    • Carsten O. Daub,
    • Piero Carninci,
    • Alistair R.R. Forrest,
    • and Yoshihide Hayashizaki
    Genome Res. July 2011 21: 1150-1159; Published in Advance May 19, 2011, doi:10.1101/gr.115469.110
  9. LETTER: Characterizing Embryonic Gene Expression Patterns in the Mouse Using Nonredundant Sequence-Based Selection
    • Rita Sousa-Nunes,
    • Amer Ahmed Rana,
    • Ross Kettleborough,
    • Joshua M. Brickman,
    • Melanie Clements,
    • Alistair Forrest,
    • Sean Grimmond,
    • Philip Avner,
    • James C. Smith,
    • Sally L. Dunwoodie,
    • and Rosa S.P. Beddington
    Genome Res. December 2003 13: 2609-2620; Published in Advance January 1, 2003, doi:10.1101/gr.1362303
  10. LETTER: Exploration of the Cell-Cycle Genes Found Within the RIKEN FANTOM2 Data Set
    • Alistair R.R. Forrest,
    • Darrin Taylor,
    • RIKEN GER Group,
    • GSL Members,
    • and Sean Grimmond
    Genome Res. June 2003 13: 1366-1375; doi:10.1101/gr.1012403
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