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ORCIDPiero Carninci
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- affiliation: RIKEN, Wako, Japan
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Journal Articles
- 2022
[j22]Jonathan Moody
, Tsukasa Kouno, Jen-Chien Chang, Yoshinari Ando, Piero Carninci, Jay W. Shin, Chung-Chau Hon:
SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells. Bioinform. 38(22): 5126-5128 (2022)- 2021
- [j21]Imad Abugessaisa, Jordan A. Ramilowski, Marina Lizio, Jesicca Severin, Akira Hasegawa, Jayson Harshbarger, Atsushi Kondo, Shuhei Noguchi, Chi Wai Yip, Jasmine Li Ching Ooi, Michihira Tagami, Fumi Hori, Saumya Agrawal, Chung-Chau Hon, Mélissa Cardon, Shuya Ikeda, Hiromasa Ono, Hidemasa Bono, Masaki Kato, Kosuke Hashimoto, Alessandro Bonetti, Norio Kobayashi, Jay W. Shin, Michiel J. L. de Hoon, Yoshihide Hayashizaki, Piero Carninci, Hideya Kawaji, Takeya Kasukawa:
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs. Nucleic Acids Res. 49(Database-Issue): D892-D898 (2021) - 2019
- [j20]Marina Lizio, Imad Abugessaisa, Shuhei Noguchi, Atsushi Kondo, Akira Hasegawa, Chung-Chau Hon, Michiel J. L. de Hoon, Jessica Severin, Shinya Oki, Yoshihide Hayashizaki, Piero Carninci, Takeya Kasukawa, Hideya Kawaji:
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases. Nucleic Acids Res. 47(Database-Issue): D752-D758 (2019) - 2018
- [j19]Imad Abugessaisa, Shuhei Noguchi, Michael Böttcher, Akira Hasegawa, Tsukasa Kouno, Sachi Kato, Yuhki Tada, Hiroki Ura, Kuniya Abe, Jay W. Shin, Charles Plessy, Piero Carninci, Takeya Kasukawa:
SCPortalen: human and mouse single-cell centric database. Nucleic Acids Res. 46(Database-Issue): D781-D787 (2018) - [j18]J. Kenneth Baillie, Andrew Bretherick, Christopher S. Haley, Sara Clohisey, Alan Gray, Lucile P. A. Neyton, Jeffrey Barrett, Eli A. Stahl, Albert Tenesa, Robin Andersson, J. Ben Brown, Geoffrey J. Faulkner, Marina Lizio, Ulf Schaefer, Carsten O. Daub, Masayoshi Itoh, Naoto Kondo, Timo Lassmann, Jun Kawai, IIBDGC Consortium, Damian Mole, Vladimir B. Bajic, Peter Heutink, Michael Rehli, Hideya Kawaji, Albin Sandelin, Harukazu Suzuki, Jack Satsangi, Christine A. Wells, Nir Hacohen, Tom C. Freeman, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, David A. Hume:
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS Comput. Biol. 14(3) (2018) - 2017
- [j17]Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jessica Severin, Chris Mungall, David J. Arenillas, Anthony Mathelier, Yulia A. Medvedeva, Andreas Lennartsson, Finn Drabløs, Jordan A. Ramilowski, Owen J. L. Rackham, Julian Gough, Robin Andersson, Albin Sandelin, Hans Ienasescu, Hiromasa Ono, Hidemasa Bono, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Takeya Kasukawa, Hideya Kawaji:
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res. 45(Database-Issue): D737-D743 (2017) - 2016
- [j16]Imad Abugessaisa, Hisashi Shimoji, Serkan Sahin, Atsushi Kondo, Jayson Harshbarger, Marina Lizio, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Takeya Kasukawa, Hideya Kawaji:
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. Database J. Biol. Databases Curation 2016 (2016) - [j15]Hans Ienasescu, Kang Li, Robin Andersson, Morana Vitezic, Sarah Rennie, Yun Chen, Kristoffer Vitting-Seerup, Emil Lagoni, Mette Boyd, Jette Bornholdt, Michiel J. L. de Hoon, Hideya Kawaji, Timo Lassmann, The Fantom Consortium, Yoshihide Hayashizaki, Alistair R. R. Forrest, Piero Carninci, Albin Sandelin:
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. Database J. Biol. Databases Curation 2016 (2016) - 2015
- [j14]Stuart Aitken, Shigeyuki Magi, Ahmad M. N. Alhendi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, Levon M. Khachigian, Mariko Okada-Hatakeyama, Colin A. M. Semple:
Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response. PLoS Comput. Biol. 11(4) (2015) - 2014
- [j13]Timo Lassmann, Akira Hasegawa, Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki:
MOIRAI: A Compact Workflow System for CAGE Analysis. BMC Bioinform. 15: 144 (2014) - [j12]Vanja Haberle, Nan Li, Yavor Hadzhiev, Charles Plessy, Christopher Previti, Chirag Nepal, Jochen Gehrig, Xianjun Dong, Altuna Akalin, Ana Maria Suzuki, Wilfred F. J. van IJcken, Olivier Armant, Marco Ferg, Uwe Strähle, Piero Carninci, Ferenc Müller, Boris Lenhard:
Two independent transcription initiation codes overlap on vertebrate core promoters. Nat. 507(7492): 381-385 (2014) - [j11]The Fantom Consortium, RIKEN PMII, RIKEN CLST (DGT), Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. M. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, 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, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, 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, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas R. Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, 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 M. 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, 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, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-Sim, Ri-ichiroh Manabe, Jessica Cara 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 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, 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 G. D. Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Sato, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C. 't Hoen, Michihira Tagami, Naoko Takahashi, 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 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, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, Yoshihide Hayashizaki:
A promoter-level mammalian expression atlas. Nat. 507(7493): 462-470 (2014) - 2011
- [j10]Margherita Francescatto, Luba Pardo, Patrizia Rizzu, Morana Vitezic, Javier Simón-Sánchez, Hazuki Takahashi, Carsten O. Daub, Piero Carninci, Peter Heutink:
Profiling transcription initiation in human aged brain using deep-CAGE. BMC Bioinform. 12(S-11): A8 (2011) - [j9]Hideya Kawaji, Jessica Severin, Marina Lizio, Alistair R. R. Forrest, Erik van Nimwegen, Michael Rehli, Kate Schroder, Katharine M. Irvine, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten O. Daub:
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Res. 39(Database-Issue): 856-860 (2011) - 2007
- [j8]Kazuro Shimokawa, Yuko Okamura-Oho, Takio Kurita, Martin C. Frith, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki:
Large-scale clustering of CAGE tag expression data. BMC Bioinform. 8 (2007) - 2006
- [j7]Manisha Brahmachary, Christian Schönbach, Liang Yang, Enli Huang, Sin Lam Tan, Rajesh Chowdhary, S. P. T. Krishnan, Chin-Yo Lin, David A. Hume, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Vladimir B. Bajic:
Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes. BMC Bioinform. 7(S-5) (2006) - [j6]J. Lynn Fink, Rajith N. Aturaliya, Melissa J. Davis, Fasheng Zhang, Kelly Hanson, Melvena S. Teasdale, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Rohan D. Teasdale:
LOCATE: a mouse protein subcellular localization database. Nucleic Acids Res. 34(Database-Issue): 213-217 (2006) - [j5]Hideya Kawaji, Takeya Kasukawa, Shiro Fukuda, Shintaro Katayama, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki:
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res. 34(Database-Issue): 632-636 (2006) - 2005
- [j4]Noriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, Hiroshi Yanagawa, Kenichi Higo, Koji Satoh, Yasuhiro Ohtomo, Tomomi Sunako, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Masaru Tomita:
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinform. 21(9): 1758-1763 (2005) - 2004
- [j3]Yutaka Suzuki, Riu Yamashita, Matsuyuki Shirota, Yuta Sakakibara, Joe Chiba, Junko Mizushima-Sugano, Alexander E. Kel, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Toshihisa Takagi, Kenta Nakai, Sumio Sugano:
Large-scale collection and characterization of promoters of human and mouse genes. Silico Biol. 4(4): 429-444 (2004) - 2002
- [j2]Jean-Marie Buerstedde, Hiroshi Arakawa, Akira Watahiki, Piero Carninci, Yoshihide Hayashizaki, Bernhard Korn, Jiri Plachy:
The DT40 web site: sampling and connecting the genes of a B cell line. Nucleic Acids Res. 30(1): 230-231 (2002) - 1990
- [j1]Piero Carninci, Stefano Gustincich, S. Bottega, C. Patrosso, G. Del Sal, Guidalberto Manfioletti, Claudio Schneider:
A simple discontinuous buffer system for increased resolution and speed in gel electrophoretic analysis of DNA sequence. Nucleic Acids Res. 18(1): 204 (1990)
Conference and Workshop Papers
- 2002
- [c1]Nobuyuki Kawagashira, Yasuhiro Ohtomo, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi:
Wavelet Profiles: Their Application in Oryza sativa DNA Sequence Analysis. CSB 2002: 345-346
Coauthor Index
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