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Shiro Fukuda
Researcher at University of Tokyo
Publications - 51
Citations - 11720
Shiro Fukuda is an academic researcher from University of Tokyo. The author has contributed to research in topics: Gene & Medicine. The author has an hindex of 24, co-authored 40 publications receiving 10697 citations. Previous affiliations of Shiro Fukuda include University of California, San Diego.
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Journal ArticleDOI
A promoter-level mammalian expression atlas
Alistair R. R. Forrest,Hideya Kawaji,Michael Rehli,J Kenneth Baillie,Michiel J. L. de Hoon,Vanja Haberle,Vanja Haberle,Timo Lassmann,Ivan V. Kulakovskiy,Ivan V. Kulakovskiy,Marina Lizio,Masayoshi Itoh,Robin Andersson,Christopher J. Mungall,Terrence F. Meehan,Sebastian Schmeier,Sebastian Schmeier,Nicolas Bertin,Mette C. Jørgensen,Emmanuel Dimont,Erik Arner,Christian Schmidl,Christian Schmidl,Ulf Schaefer,Yulia A. Medvedeva,Yulia A. Medvedeva,Charles Plessy,Morana Vitezic,Jessica Severin,Colin A. Semple,Yuri Ishizu,Robert Young,Margherita Francescatto,Margherita Francescatto,Intikhab Alam Altschuler,Davide Albanese,Gabriel M. Altschule,Takahiro Arakawa,John A.C. Archer,Peter Arner,Magda Babina,Sarah Rennie,Piotr J. Balwierz,Anthony G Beckhouse,Swati Pradhan-Bhatt,Judith A. Blake,Antje Blumenthal,Beatrice Bodega,Alessandro Bonetti,James Briggs,James Briggs,Frank Brombacher,Frank Brombacher,A. Maxwell Burroughs,Andrea Califano,Carlo Vittorio Cannistraci,Carlo Vittorio Cannistraci,Daniel Carbajo,Yun Chen,Marco Chierici,Yari Ciani,Hans Clevers,Hans Clevers,Emiliano Dalla,Carrie A. Davis,Michael Detmar,Alexander D. Diehl,Taeko Dohi,Finn Drabløs,Albert S.B. Edge,Matthias Edinger,Karl Ekwall,Mitsuhiro Endoh,Hideki Enomoto,Michela Fagiolini,Lynsey Fairbairn,Hai Fang,Mary C. Farach-Carson,Geoffrey J. Faulkner,Alexander V. Favorov,Alexander V. Favorov,Alexander V. Favorov,Malcolm E. Fisher,Martin C. Frith,Rie Fujita,Shiro Fukuda,Cesare Furlanello,Masaaki Furuno,Jun Ichi Furusawa,Teunis B. H. Geijtenbeek,Andrew P. Gibson,Thomas R. Gingeras,Dan Goldowitz,Julian Gough,Sven Guhl,Reto Guler,Reto Guler,Stefano Gustincich,Thomas J. Ha,Masahide Hamaguchi,Mitsuko Hara,Matthias Harbers,Jayson Harshbarger,Akira Hasegawa,Yuki Hasegawa,Takehiro Hashimoto,Meenhard Herlyn,Kelly J Hitchens,Shannan J. Ho Sui,Oliver Hofmann,Ilka Hoof,Fumi Hori,Lukasz Huminiecki,Kei Iida,Tomokatsu Ikawa,Boris R. Jankovic,Hui Jia,Anagha Joshi,Giuseppe Jurman,Bogumil Kaczkowski,Chieko Kai,Kaoru Kaida,Ai Kaiho,Kazuhiro Kajiyama,Mutsumi Kanamori-Katayama,Artem S. Kasianov,Takeya Kasukawa,Shintaro Katayama,Sachi Kato,Shuji Kawaguchi,Hiroshi Kawamoto,Yuki I. Kawamura,Tsugumi Kawashima,Judith S. Kempfle,Tony J. Kenna,Juha Kere,Juha Kere,Levon M. Khachigian,Toshio Kitamura,S. Peter Klinken,Alan J. Knox,Miki Kojima,Soichi Kojima,Naoto Kondo,Haruhiko Koseki,Shigeo Koyasu,Sarah Krampitz,Atsutaka Kubosaki,Andrew T. Kwon,Jeroen F. J. Laros,Weon Ju Lee,Andreas Lennartsson,Kang Li,Berit Lilje,Leonard Lipovich,Alan Mackay-Sim,Ri Ichiroh Manabe,Jessica C. Mar,Benoit Marchand,Anthony Mathelier,Niklas Mejhert,Alison M. Meynert,Yosuke Mizuno,David A. de Lima Morais,Hiromasa Morikawa,Mitsuru Morimoto,Kazuyo Moro,Efthymios Motakis,Hozumi Motohashi,Christine L. Mummery,Mitsuyoshi Murata,Sayaka Nagao-Sato,Yutaka Nakachi,Fumio Nakahara,Toshiyuki Nakamura,Yukio Nakamura,Kenichi Nakazato,Erik van Nimwegen,Noriko Ninomiya,Hiromi Nishiyori,Shohei Noma,Tadasuke Nozaki,Soichi Ogishima,Soichi Ogishima,Naganari Ohkura,Hiroko Ohmiya,Hiroshi Ohno,Mitsuhiro Ohshima,Mariko Okada-Hatakeyama,Yasushi Okazaki,Valerio Orlando,Dmitry A. Ovchinnikov,Arnab Pain,Robert Passier,Margaret Patrikakis,Helena Persson,Silvano Piazza,James Prendergast,Owen J. L. Rackham,Jordan A. Ramilowski,Mamoon Rashid,Timothy Ravasi,Patrizia Rizzu,Marco Roncador,Sugata Roy,Morten Beck Rye,Eri Saijyo,Antti Sajantila,Akiko Saka,Shimon Sakaguchi,Mizuho Sakai,Hiroki Sato,Hironori Satoh,Suzana Savvi,Suzana Savvi,Alka Saxena,Claudio Schneider,Erik Anthony Schultes,Gundula G. Schulze-Tanzil,Anita Schwegmann,Anita Schwegmann,Thierry Sengstag,Guojun Sheng,Hisashi Shimoji,Yishai Shimoni,Jay W. Shin,Christophe Simon,Daisuke Sugiyama,Takaaki Sugiyama,Masanori Suzuki,Naoko Suzuki,Rolf Swoboda,Peter A C 't Hoen,Michihira Tagami,Naoko Takahashi Tagami,Jun Takai,Hiroshi Tanaka,Hideki Tatsukawa,Zuotian Tatum,Mark Thompson,Hiroo Toyoda,Tetsuro Toyoda,Eivind Valen,Marc van de Wetering,Linda M. van den Berg,Roberto Verardo,Dipti Vijayan,Ilya E. Vorontsov,Wyeth W. Wasserman,Shoko Watanabe,Christine A. Wells,Louise N. Winteringham,Ernst J. Wolvetang,Emily J. Wood,Yoko Yamaguchi,Masayuki Yamamoto,Misako Yoneda,Yohei Yonekura,Shigehiro Yoshida,Susan E. Zabierowski,Peter G. Zhang,Xiaobei Zhao,Silvia Zucchelli,Kim M. Summers,Harukazu Suzuki,Carsten O. Daub,Jun Kawai,Peter Heutink,Winston Hide,Tom C. Freeman,Boris Lenhard,Boris Lenhard,Lenhard Vladimir B. Bajic,Martin S. Taylor,Vsevolod J. Makeev,Vsevolod J. Makeev,Vsevolod J. Makeev,Albin Sandelin,David A. Hume,Piero Carninci,Yoshihide Hayashizaki +280 more
TL;DR: For example, the authors mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body.
Journal ArticleDOI
Insights into social insects from the genome of the honeybee Apis mellifera
George M. Weinstock,Gene E. Robinson,Richard A. Gibbs,Kim C. Worley,Jay D. Evans,Ryszard Maleszka,Hugh M. Robertson,Daniel B. Weaver,Martin Beye,Peer Bork,Christine G. Elsik,Klaus Hartfelder,Greg J. Hunt,Evgeny M. Zdobnov,Gro V. Amdam,Mrcia M.G. Bitondi,Anita M. Collins,Alexandre S. Cristino,H. Michael G. Lattorff,Carlos H. Lobo,Robin F. A. Moritz,Francis M. F. Nunes,Robert E. Page,Zilá Luz Paulino Simões,Diana E. Wheeler,Piero Carninci,Shiro Fukuda,Yoshihide Hayashizaki,Chikatoshi Kai,Jun Kawai,Naoko Sakazume,Daisuke Sasaki,Michihira Tagami,Stefan Albert,Geert Baggerman,Kyle T. Beggs,Guy Bloch,Giuseppe Cazzamali,Mira Cohen,Mark D. Drapeau,Dorothea Eisenhardt,Christine Emore,Michael A. Ewing,Susan E. Fahrbach,Sylvain Forêt,Cornelis J. P. Grimmelikhuijzen,Frank Hauser,Amanda B. Hummon,Jurgen Huybrechts,Andrew K. Jones,Tatsuhiko Kadowaki,Noam Kaplan,Robert Kucharski,Grard Leboulle,Michal Linial,J. Troy Littleton,Alison R. Mercer,T.A. Richmond,Sandra L. Rodriguez-Zas,Elad B. Rubin,David B. Sattelle,David I. Schlipalius,Liliane Schoofs,Yair Shemesh,Jonathan V. Sweedler,Rodrigo A. Velarde,Peter Verleyen,Evy Vierstraete,Michael Williamson,Seth A. Ament,Susan J. Brown,Miguel Corona,Peter K. Dearden,W. Augustine Dunn,Michelle M. Elekonich,Tomoko Fujiyuki,Irene Gattermeier,Tanja Gempe,Martin Hasselmann,Eriko Kage,Azusa Kamikouchi,Takeo Kubo,Takekazu Kunieda,Marcé D. Lorenzen,Natalia V. Milshina,Mizue Morioka,Kazuaki Ohashi,Ross Overbeek,Christian A. Ross,Morten Schioett,Teresa D. Shippy,Hideaki Takeuchi,Amy L. Toth,Judith H. Willis,Megan J. Wilson,Karl H.J. Gordon,Ivica Letunic,Kevin J. Hackett,Jane Peterson,Adam Felsenfeld,Mark S. Guyer,Michel Solignac,Richa Agarwala,Jean Marie Cornuet,M. Monnerot,Florence Mougel,Justin T. Reese,Dominique Vautrin,Joseph J. Gillespie,Joseph J. Gillespie,Jamie J. Cannone,Robin R. Gutell,J. Spencer Johnston,Michael B. Eisen,Michael B. Eisen,Venky N. Iyer,Vivek Iyer,Peter Kosarev,Aaron J. Mackey,Victor V. Solovyev,Alexandre Souvorov,Katherine A Aronstein,Katarína Bíliková,Yanping Chen,Andrew G. Clark,Laura I. Decanini,William M. Gelbart,Charles Hetru,Dan Hultmark,Jean-Luc Imler,Haobo Jiang,Michael R. Kanost,Kiyoshi Kimura,Brian P. Lazzaro,Dawn Lopez,Jozef Šimúth,Graham J. Thompson,Zhen Zou,Pieter J. de Jong,Erica Sodergren,Miklós Csürös,Aleksandar Milosavljevic,Kazutoyo Osoegawa,Stephen Richards,Chung Li Shu,Laurent Duret,Eran Elhaik,Dan Graur,Juan Manuel Anzola,Kathryn S. Campbell,Kevin L. Childs,Derek Collinge,Madeline A. Crosby,C. Michael Dickens,L. Sian Grametes,Christina M. Grozinger,Peter L. Jones,Mireia Jordà,Xu Ling,Beverly B. Matthews,Jonathan Miller,Craig Mizzen,Miguel A. Peinado,Jeffrey G. Reid,Jeffrey G. Reid,Susan M. Russo,Andrew J. Schroeder,Susan E. St. Pierre,Ying Wang,Pinglei Zhou,Huaiyang Jiang,Paul Kitts,Barbara J. Ruef,Anand Venkatraman,Lan Zhang,Gildardo Aquino-Perez,Charles W. Whitfield,Susanta K. Behura,Stewart H. Berlocher,Walter S. Sheppard,Deborah R. Smith,Andrew V. Suarez,Neil D. Tsutsui,Xuehong Wei,David A. Wheeler,Paul Havlak,Bingshan Li,Yue Liu,Angela Jovilet,Sandra L. Lee,Lynne V. Nazareth,Ling Ling Pu,Rachel Thorn,Viktor Stolc,Thomas C. Newman,Manoj P. Samanta,Waraporn Tongprasit,Charles Claudianos,Charles Claudianos,May R. Berenbaum,Sunita Biswas,Sunita Biswas,Dirk C. de Graaf,René Feyereisen,Reed M. Johnson,John G. Oakeshott,Hilary Ranson,Mary A. Schuler,Donna M. Muzny,Joseph Chacko,Clay Davis,Huyen Dinh,Rachel Gill,Judith Hernandez,Sandra Hines,Jennifer Hume,La Ronda Jackson,Christie Kovar,Lora Lewis,George Miner,Margaret Morgan,Ngoc Nguyen,Geoffrey Okwuonu,Heidi Paul,Jireh Santibanez,Glenford Savery,Amanda F. Svatek,Donna Villasana,Rita A. Wright +228 more
TL;DR: The genome sequence of the honeybee Apis mellifera is reported, suggesting a novel African origin for the species A. melliferA and insights into whether Africanized bees spread throughout the New World via hybridization or displacement.
Journal ArticleDOI
Genome-wide analysis of mammalian promoter architecture and evolution
Piero Carninci,Albin Sandelin,Boris Lenhard,Boris Lenhard,Shintaro Katayama,Kazuro Shimokawa,Jasmina Ponjavic,Colin A. Semple,Martin S. Taylor,Pär G. Engström,Martin C. Frith,Alistair R. R. Forrest,Wynand Alkema,Sin Lam Tan,Charles Plessy,Rimantas Kodzius,Timothy Ravasi,Timothy Ravasi,Takeya Kasukawa,Shiro Fukuda,Mutsumi Kanamori-Katayama,Yayoi Kitazume,Hideya Kawaji,Chikatoshi Kai,Mari M. Nakamura,Hideaki Konno,Kenji Nakano,Salim Mottagui-Tabar,Salim Mottagui-Tabar,Salim Mottagui-Tabar,Peter Arner,Alessandra Chesi,Stefano Gustincich,Francesca Persichetti,Harukazu Suzuki,Sean M. Grimmond,Christine A. Wells,Valerio Orlando,Claes Wahlestedt,Claes Wahlestedt,Edison T. Liu,Matthias Harbers,Jun Kawai,Vladimir B. Bajic,Vladimir B. Bajic,David A. Hume,Yoshihide Hayashizaki,Yoshihide Hayashizaki +47 more
TL;DR: These tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini.
Journal ArticleDOI
Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice
Shoshi Kikuchi,Kouji Satoh,Toshifumi Nagata,Nobuyuki Kawagashira,Koji Doi,Naoki Kishimoto,Junshi Yazaki,Masahiro Ishikawa,Hitomi Yamada,Hisako Ooka,Isamu Hotta,Keiichi Kojima,Takahiro Namiki,Eisuke Ohneda,Wataru Yahagi,Kohji Suzuki,Chao Jie Li,Kenji Ohtsuki,Toru Shishiki,Yasuhiro Otomo,Kazuo Murakami,Yoshiharu Iida,Sumio Sugano,Tatsuto Fujimura,Yutaka Suzuki,Yuki Tsunoda,Takashi Kurosaki,Takeko Kodama,Hiromi Masuda,Michie Kobayashi,Quihong Xie,Min Lu,Ryuya Narikawa,Akio Sugiyama,Kouichi Mizuno,Satoko Yokomizo,Junko Niikura,Rieko Ikeda,Junya Ishibiki,Midori Kawamata,Akemi Yoshimura,Junichirou Miura,Takahiro Kusumegi,Mitsuru Oka,Risa Ryu,Mariko Ueda,Kenichi Matsubara,Jun Kawai,Piero Carninci,Jun Adachi,Katsunori Aizawa,Takahiro Arakawa,Shiro Fukuda,Ayako Hara,Wataru Hashidume,Norihito Hayatsu,Koichi Imotani,Yoshiki Ishii,Masayoshi Itoh,Ikuko Kagawa,Shinji Kondo,Hedeaki Konno,Ai Miyazaki,Naoki Osato,Yoshimi Ota,Rintaro Saito,Daisuke Sasaki,Kenjiro Sato,Kazuhiro Shibata,Akira Shinagawa,Toshiyuki Shiraki,Masayasu Yoshino,Yoshihide Hayashizaki +72 more
TL;DR: Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome, and protein informatics analysis against the InterPro database revealed the existence of proteins presented in rice but not in Arabidopsis.
Journal ArticleDOI
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man
Timothy Ravasi,Harukazu Suzuki,Carlo Vittorio Cannistraci,Shintaro Katayama,Vladimir B. Bajic,Vladimir B. Bajic,Kai Tan,Altuna Akalin,Sebastian Schmeier,Sebastian Schmeier,Mutsumi Kanamori-Katayama,Nicolas Bertin,Piero Carninci,Carsten O. Daub,Alistair R. R. Forrest,Julian Gough,Julian Gough,Sean M. Grimmond,Sean M. Grimmond,Jung Hoon Han,Jung Hoon Han,Takehiro Hashimoto,Winston Hide,Winston Hide,Winston Hide,Oliver Hofmann,Oliver Hofmann,Atanas Kamburov,Atanas Kamburov,Mandeep Kaur,Hideya Kawaji,Atsutaka Kubosaki,Timo Lassmann,Erik van Nimwegen,Erik van Nimwegen,Cameron Ross MacPherson,Chihiro Ogawa,Aleksandar Radovanovic,Ariel S. Schwartz,Rohan D. Teasdale,Rohan D. Teasdale,Jesper Tegnér,Jesper Tegnér,Jesper Tegnér,Boris Lenhard,Sarah A. Teichmann,Sarah A. Teichmann,Takahiro Arakawa,Noriko Ninomiya,Kayoko Murakami,Michihira Tagami,Shiro Fukuda,Kengo Imamura,Chikatoshi Kai,Ryoko Ishihara,Yayoi Kitazume,Jun Kawai,David A. Hume,David A. Hume,Trey Ideker,Yoshihide Hayashizaki +60 more
TL;DR: Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human.