Yoshihide Hayashizaki

According to our database, Yoshihide Hayashizaki authored at least 34 papers between 2002 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2021

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.

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

Nucleic Acids Res., 2021

2019

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases.

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

Nucleic Acids Res., 2019

2018

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

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

PLoS Comput. Biol., 2018

2017

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

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

Nucleic Acids Res., 2017

2016

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase.

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

Database J. Biol. Databases Curation, 2016

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Imad Abugessaisa, Hisashi Shimoji, Serkan Sahin, Atsushi Kondo, Jayson Harshbarger, Marina Lizio, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Takeya Kasukawa, Hideya Kawaji

Database J. Biol. Databases Curation, 2016

2015

Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response.

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

PLoS Comput. Biol., 2015

2014

A promoter-level mammalian expression atlas.

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

Nat., 2014

MOIRAI: A Compact Workflow System for CAGE Analysis.

Timo Lassmann, Akira Hasegawa, Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki

BMC Bioinform., 2014

2011

The RIKEN integrated database of mammals.

Hiroshi Masuya, Yuko Makita, Norio Kobayashi, Koro Nishikata, Yuko Yoshida, Yoshiki Mochizuki, Koji Doi, Terue Takatsuki, Kazunori Waki, Nobuhiko Tanaka, Manabu Ishii, Akihiro Matsushima, Satoshi Takahashi, Atsushi Hijikata, Kouji Kozaki, Teiichi Furuichi, Hideya Kawaji, Shigeharu Wakana, Yukio Nakamura, Atsushi Yoshiki, Takehide Murata, Kaoru Fukami-Kobayashi, S. Sujatha Mohan, Osamu Ohara, Yoshihide Hayashizaki, Riichiro Mizoguchi, Yuichi Obata, Tetsuro Toyoda

Nucleic Acids Res., 2011

Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation.

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

Nucleic Acids Res., 2011

SAMStat: monitoring biases in next generation sequencing data.

Timo Lassmann, Yoshihide Hayashizaki, Carsten O. Daub

Bioinform., 2011

Optimization of turn-back primers in isothermal amplification.

Yasumasa Kimura, Michiel J. L. de Hoon, Shintaro Aoki, Yuri Ishizu, Carsten O. Daub, Alexander Lezhava, Erik Arner, Yoshihide Hayashizaki, Yuki Kawai, Yasushi Kogo

Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

2010

NGSView: an extensible open source editor for next-generation sequencing data.

Erik Arner, Yoshihide Hayashizaki, Carsten O. Daub

Bioinform., 2010

2009

Data-driven normalization strategies for high-throughput quantitative RT-PCR.

Jessica Cara Mar, Yasumasa Kimura, Kate Schroder, Katharine M. Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David A. Hume, John Quackenbush

BMC Bioinform., 2009

SDRF2GRAPH - a visualization tool of a spreadsheet-based description of experimental processes.

Hideya Kawaji, Yoshihide Hayashizaki, Carsten O. Daub

BMC Bioinform., 2009

TagDust - a program to eliminate artifacts from next generation sequencing data.

Timo Lassmann, Yoshihide Hayashizaki, Carsten O. Daub

Bioinform., 2009

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.

Takehiro Hashimoto, Michiel J. L. de Hoon, Sean M. Grimmond, Carsten O. Daub, Yoshihide Hayashizaki, Geoffrey J. Faulkner

Bioinform., 2009

2007

Large-scale clustering of CAGE tag expression data.

Kazuro Shimokawa, Yuko Okamura-Oho, Takio Kurita, Martin C. Frith, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki

BMC Bioinform., 2007

2006

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

Hideya Kawaji, Takeya Kasukawa, Shiro Fukuda, Shintaro Katayama, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki

Nucleic Acids Res., 2006

LOCATE: a mouse protein subcellular localization database.

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

Nucleic Acids Res., 2006

PhosphoregDB: The tissue and sub-cellular distribution of mammalian protein kinases and phosphatases.

Alistair R. R. Forrest, Darrin F. Taylor, J. Lynn Fink, M. Milena Gongora, Cameron Flegg, Rohan D. Teasdale, Harukazu Suzuki, Mutsumi Kanamori, Chikatoshi Kai, Yoshihide Hayashizaki, Sean M. Grimmond

BMC Bioinform., 2006

Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes.

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

BMC Bioinform., 2006

2005

RNAdb - a comprehensive mammalian noncoding RNA database.

Ken C. Pang, Stuart Stephen, Pär G. Engström, Khairina Tajul-Arifin, Weisan Chen, Claes Wahlestedt, Boris Lenhard, Yoshihide Hayashizaki, John S. Mattick

Nucleic Acids Res., 2005

Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).

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

Bioinform., 2005

2004

EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes.

Itoshi Nikaido, Chika Saito, Akiko Wakamoto, Yasuhiro Tomaru, Takahiro Arakawa, Yoshihide Hayashizaki, Yasushi Okazaki

Nucleic Acids Res., 2004

Large-scale collection and characterization of promoters of human and mouse genes.

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

Silico Biol., 2004

Integrated analysis of the genome and the transcriptome by FANTOM.

Shintaro Katayama, Mutsumi Kanamori, Yoshihide Hayashizaki

Briefings Bioinform., 2004

2003

MaXML: mouse annotation XML.

Takeya Kasukawa, Hidemasa Bono, Yoshihide Hayashizaki, Yasushi Okazaki, Hideo Matsuda

Silico Biol., 2003

Construction of reliable protein-protein interaction networks with a new interaction generality measure.

Rintaro Saito, Harukazu Suzuki, Yoshihide Hayashizaki

Bioinform., 2003

2002

The DT40 web site: sampling and connecting the genes of a B cell line.

Jean-Marie Buerstedde, Hiroshi Arakawa, Akira Watahiki, Piero Carninci, Yoshihide Hayashizaki, Bernhard Korn, Jiri Plachy

Nucleic Acids Res., 2002

READ: RIKEN Expression Array Database.

Hidemasa Bono, Takeya Kasukawa, Yoshihide Hayashizaki, Yasushi Okazaki

Nucleic Acids Res., 2002

FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones.

Hidemasa Bono, Takeya Kasukawa, Masaaki Furuno, Yoshihide Hayashizaki, Yasushi Okazaki

Nucleic Acids Res., 2002

Wavelet Profiles: Their Application in Oryza sativa DNA Sequence Analysis.

Nobuyuki Kawagashira, Yasuhiro Ohtomo, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi

Proceedings of the 1st IEEE Computer Society Bioinformatics Conference, 2002