Shintaro Katayama

Shintaro Katayama

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Shintaro Katayama

Publications by authors named "Shintaro Katayama"

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Acute wheeze-specific gene module shows correlation with vitamin D and asthma medication.

Eur Respir J 2019 Oct 16. Epub 2019 Oct 16.

Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden

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http://dx.doi.org/10.1183/13993003.01330-2019DOI Listing
October 2019

Delineating the Healthy Human Skin UV Response and Early Induction of Interferon Pathway in Cutaneous Lupus Erythematosus.

J Invest Dermatol 2019 Sep 8;139(9):2058-2061.e4. Epub 2019 Apr 8.

Department of Dermatology and Allergology, University of Helsinki, Helsinki University Central Hospital, Helsinki, Finland.

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http://dx.doi.org/10.1016/j.jid.2019.02.035DOI Listing
September 2019

Complement in Human Pre-implantation Embryos: Attack and Defense.

Front Immunol 2019 18;10:2234. Epub 2019 Sep 18.

Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.

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http://dx.doi.org/10.3389/fimmu.2019.02234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6759579PMC
September 2019

Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods.

BMC Bioinformatics 2019 Aug 13;20(1):418. Epub 2019 Aug 13.

Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden.

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http://dx.doi.org/10.1186/s12859-019-3017-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6693229PMC
August 2019

Cationic gold nanoparticles elicit mitochondrial dysfunction: a multi-omics study.

Sci Rep 2019 Mar 13;9(1):4366. Epub 2019 Mar 13.

Nanosafety & Nanomedicine Laboratory, Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, 171 77, Stockholm, Sweden.

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http://dx.doi.org/10.1038/s41598-019-40579-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416392PMC
March 2019

MANF protects human pancreatic beta cells against stress-induced cell death.

Diabetologia 2018 10 21;61(10):2202-2214. Epub 2018 Jul 21.

Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, PO Box 63, (Haartmaninkatu 8), 00014, Helsinki, Finland.

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http://dx.doi.org/10.1007/s00125-018-4687-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6133171PMC
October 2018

Human pluripotent reprogramming with CRISPR activators.

Nat Commun 2018 07 6;9(1):2643. Epub 2018 Jul 6.

Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland.

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http://dx.doi.org/10.1038/s41467-018-05067-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035213PMC
July 2018

Damaging heterozygous mutations in NFKB1 lead to diverse immunologic phenotypes.

J Allergy Clin Immunol 2017 Sep 21;140(3):782-796. Epub 2017 Jan 21.

Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Rare Diseases Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.

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http://dx.doi.org/10.1016/j.jaci.2016.10.054DOI Listing
September 2017

Optimizing bone morphogenic protein 4-mediated human embryonic stem cell differentiation into trophoblast-like cells using fibroblast growth factor 2 and transforming growth factor-β/activin/nodal signalling inhibition.

Reprod Biomed Online 2017 Sep 12;35(3):253-263. Epub 2017 Jun 12.

Competence Centre on Health Technologies, Tartu, Estonia; Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia; Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.

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http://dx.doi.org/10.1016/j.rbmo.2017.06.003DOI Listing
September 2017

Combined immunodeficiency and hypoglycemia associated with mutations in hypoxia upregulated 1.

J Allergy Clin Immunol 2017 04 29;139(4):1391-1393.e11. Epub 2016 Nov 29.

Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland; Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden.

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http://dx.doi.org/10.1016/j.jaci.2016.09.050DOI Listing
April 2017

The human PRD-like homeobox gene LEUTX has a central role in embryo genome activation.

Development 2016 10 30;143(19):3459-3469. Epub 2016 Aug 30.

Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden Science for Life Laboratory, Tomtebodavägen 23 A, Solna 171 21, Sweden Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Biomedicum 1, Haartmaninkatu 8, Helsinki 00290, Finland

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http://dx.doi.org/10.1242/dev.134510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5087614PMC
October 2016

Differences in gene expression between mouse and human for dynamically regulated genes in early embryo.

PLoS One 2014 4;9(8):e102949. Epub 2014 Aug 4.

Department of Biosciences and Nutrition; Center for Biosciences, Karolinska Institutet, Huddinge, Sweden; Molecular Neurology Program, Research Programs Unit, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102949PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121084PMC
April 2015

A promoter-level mammalian expression atlas.

Authors:
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 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 C 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 Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas 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 Furni 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 C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison 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 Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya 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 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 Takaai 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 Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado 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

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

Human Wound-Healing Research: Issues and Perspectives for Studies Using Wide-Scale Analytic Platforms.

Adv Wound Care (New Rochelle) 2014 Mar;3(3):264-271

Institute of Biomedicine, Pharmacology, Biomedicum, University of Helsinki , Helsinki, Finland .

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http://dx.doi.org/10.1089/wound.2013.0502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3955962PMC
March 2014

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization.

Bioinformatics 2013 Nov 31;29(22):2943-5. Epub 2013 Aug 31.

Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden, Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden and Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden.

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http://dx.doi.org/10.1093/bioinformatics/btt511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3810855PMC
November 2013

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

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

The complexity of the mammalian transcriptome.

J Physiol 2006 Sep 20;575(Pt 2):321-32. Epub 2006 Jul 20.

Sector of Neurobiology, International School for Advanced Studies (ISAS)-SISSA, AREA Science Park, SS 14, Km 163,5, Basovizza, 34012 Trieste, Italy.

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http://dx.doi.org/10.1113/jphysiol.2006.115568DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1819450PMC
September 2006

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome.

Genome Res 2006 Jan 12;16(1):11-9. Epub 2005 Dec 12.

ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia.

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http://dx.doi.org/10.1101/gr.4200206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356124PMC
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

Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis.

Genomics 2004 Dec;84(6):913-21

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1016/j.ygeno.2004.08.011DOI Listing
December 2004

[Inferring the genetic network using informatics].

Tanpakushitsu Kakusan Koso 2004 Dec;49(17 Suppl):2928-33

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December 2004

Integrated analysis of the genome and the transcriptome by FANTOM.

Brief Bioinform 2004 Sep;5(3):249-58

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

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http://dx.doi.org/10.1093/bib/5.3.249DOI Listing
September 2004

Identification of region-specific transcription factor genes in the adult mouse brain by medium-scale real-time RT-PCR.

FEBS Lett 2004 Aug;573(1-3):214-8

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

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http://dx.doi.org/10.1016/j.febslet.2004.07.068DOI Listing
August 2004

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.

Proc Natl Acad Sci U S A 2003 Dec 8;100(26):15776-81. Epub 2003 Dec 8.

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

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http://dx.doi.org/10.1073/pnas.2136655100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC307644PMC
December 2003