Chikatoshi Kai

Chikatoshi Kai

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Chikatoshi Kai

Chikatoshi Kai

Publications by authors named "Chikatoshi Kai"

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High sensitivity TSS prediction: estimates of locations where TSS cannot occur.

PLoS One 2010 Nov 15;5(11):e13934. Epub 2010 Nov 15.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013934PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981523PMC
November 2010

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

Hidden layers of human small RNAs.

BMC Genomics 2008 Apr 10;9:157. Epub 2008 Apr 10.

Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

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http://dx.doi.org/10.1186/1471-2164-9-157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2359750PMC
April 2008

Towards defining the nuclear proteome.

Genome Biol 2008 Jan 23;9(1):R15. Epub 2008 Jan 23.

ARC Centre of Excellence in Bioinformatics, The University of Queensland, St Lucia, Queensland, 4072, Australia.

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http://dx.doi.org/10.1186/gb-2008-9-1-r15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395251PMC
January 2008

Splicing bypasses 3' end formation signals to allow complex gene architectures.

Gene 2007 Nov 30;403(1-2):188-93. Epub 2007 Aug 30.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Centre (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1016/j.gene.2007.08.012DOI Listing
November 2007

Discrimination of non-protein-coding transcripts from protein-coding mRNA.

RNA Biol 2006 Jan-Mar;3(1):40-8. Epub 2006 Apr 3.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.4161/rna.3.1.2789DOI Listing
September 2007

Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters.

Genome Biol 2006 17;7(8):R78. Epub 2006 Aug 17.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1186/gb-2006-7-8-R78DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779604PMC
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Dynamic usage of transcription start sites within core promoters.

Genome Biol 2006 ;7(12):R118

NTT Software Corporation, 209 Yamashita-cho Nakak-ku, Yokohama, Kanagawa, 231-8551, Japan.

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http://dx.doi.org/10.1186/gb-2006-7-12-r118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794431PMC
May 2007

Gemin2 plays an important role in stabilizing the survival of motor neuron complex.

J Biol Chem 2007 Apr 16;282(15):11122-34. Epub 2007 Feb 16.

Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1074/jbc.M609297200DOI Listing
April 2007

Diversity of Ca2+-activated K+ channel transcripts in inner ear hair cells.

Gene 2007 Jan 5;386(1-2):11-23. Epub 2006 Aug 5.

Department of Biomedical Sciences, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA.

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http://dx.doi.org/10.1016/j.gene.2006.07.023DOI Listing
January 2007

Evolutionary turnover of mammalian transcription start sites.

Genome Res 2006 Jun 10;16(6):713-22. Epub 2006 May 10.

Genome Exploration Research Group, RIKEN Genomic Sciences Centre (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.5031006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1473182PMC
June 2006

Subcellular localization of mammalian type II membrane proteins.

Traffic 2006 May;7(5):613-25

Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, St. Lucia, Queensland 4072, Australia.

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http://dx.doi.org/10.1111/j.1600-0854.2006.00407.xDOI Listing
May 2006

Pseudo-messenger RNA: phantoms of the transcriptome.

PLoS Genet 2006 Apr 28;2(4):e23. Epub 2006 Apr 28.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan.

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http://dx.doi.org/10.1371/journal.pgen.0020023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449882PMC
April 2006

Heterotachy in mammalian promoter evolution.

PLoS Genet 2006 Apr 28;2(4):e30. Epub 2006 Apr 28.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.0020030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449885PMC
April 2006

Clusters of internally primed transcripts reveal novel long noncoding RNAs.

PLoS Genet 2006 Apr 28;2(4):e37. Epub 2006 Apr 28.

Mouse Genome Informatics Consortium, The Jackson Laboratory, Bar Harbor, Maine, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.0020037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449886PMC
April 2006

A method for similarity search of genomic positional expression using CAGE.

PLoS Genet 2006 Apr 28;2(4):e44. Epub 2006 Apr 28.

Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.

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http://dx.doi.org/10.1371/journal.pgen.0020044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449887PMC
April 2006

A simple physical model predicts small exon length variations.

PLoS Genet 2006 Apr 28;2(4):e45. Epub 2006 Apr 28.

Division of Bioinformatics, Biozentrum, University of Basel, Basel, Switzerland.

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https://dx.doi.org/10.1371/journal.pgen.0020045
Publisher Site
http://dx.doi.org/10.1371/journal.pgen.0020045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449888PMC
April 2006

The abundance of short proteins in the mammalian proteome.

PLoS Genet 2006 Apr 28;2(4):e52. Epub 2006 Apr 28.

Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan.

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http://dx.plos.org/10.1371/journal.pgen.0020052
Publisher Site
http://dx.doi.org/10.1371/journal.pgen.0020052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449894PMC
April 2006

CAGE: cap analysis of gene expression.

Nat Methods 2006 Mar;3(3):211-22

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://www.nature.com/doifinder/10.1038/nmeth0306-211
Publisher Site
http://dx.doi.org/10.1038/nmeth0306-211DOI Listing
March 2006

LOCATE: a mouse protein subcellular localization database.

Nucleic Acids Res 2006 Jan;34(Database issue):D213-7

ARC Centre in Bioinformatics, University of Queensland, St Lucia, Queensland 4072, Australia.

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http://dx.doi.org/10.1093/nar/gkj069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347432PMC
January 2006

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

Nucleic Acids Res 2006 Jan;34(Database issue):D632-6

NTT Software Corporation, Teisan Kannai Building 209, Yamashita-cho Naka-ku, Yokohama, Kanagawa, 231-8551, Japan.

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http://dx.doi.org/10.1093/nar/gkj034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347397PMC
January 2006

[Mammalian two hybrid assay].

Authors:
Chikatoshi Kai

Tanpakushitsu Kakusan Koso 2004 Dec;49(17 Suppl):2758-62

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December 2004

The PDZ protein tax-interacting protein-1 inhibits beta-catenin transcriptional activity and growth of colorectal cancer cells.

J Biol Chem 2003 Oct 21;278(40):38758-64. Epub 2003 Jul 21.

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M306324200
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http://dx.doi.org/10.1074/jbc.M306324200DOI Listing
October 2003

The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer.

Genome Res 2003 Jun;13(6B):1534-41

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://www.genome.org/cgi/doi/10.1101/gr.956303
Publisher Site
http://dx.doi.org/10.1101/gr.956303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403706PMC
June 2003

NF-kappaB activator Act1 associates with IL-1/Toll pathway adaptor molecule TRAF6.

FEBS Lett 2002 Dec;532(1-2):241-6

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

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http://dx.doi.org/10.1016/s0014-5793(02)03688-8DOI Listing
December 2002