Hideya Kawaji

Hideya Kawaji

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Hideya Kawaji

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Cap Analysis of Gene Expression (CAGE): A Quantitative and Genome-Wide Assay of Transcription Start Sites.

Methods Mol Biol 2020 ;2120:277-301

RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Yokohama, Kanagawa, Japan.

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http://dx.doi.org/10.1007/978-1-0716-0327-7_20DOI Listing
January 2020

Evaluation of off-target effects of gapmer antisense oligonucleotides using human cells.

Genes Cells 2019 Dec 12;24(12):827-835. Epub 2019 Nov 12.

Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kawasaki, Kanagawa, Japan.

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http://dx.doi.org/10.1111/gtc.12730DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6915909PMC
December 2019

Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells.

Cell Syst 2019 Nov 16;9(5):446-458.e6. Epub 2019 Oct 16.

King Abdullah University Science and Technology (KAUST), BESE Division, KAUST Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia; IRCSS Fondazione, Santa Lucia, Epigenetics and Genome Reprogramming, Rome, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.09.005DOI Listing
November 2019

Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis.

BMC Genomics 2019 Sep 18;20(1):718. Epub 2019 Sep 18.

Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.

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http://dx.doi.org/10.1186/s12864-019-6063-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751898PMC
September 2019

refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites.

J Mol Biol 2019 Jun 8;431(13):2407-2422. Epub 2019 May 8.

RIKEN Center for Integrative Medical Sciences, 1-7-22, Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa 230-0045, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.04.045DOI Listing
June 2019

CXCL4/PF4 is a predictive biomarker of cardiac differentiation potential of human induced pluripotent stem cells.

Sci Rep 2019 03 15;9(1):4638. Epub 2019 Mar 15.

Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan.

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http://dx.doi.org/10.1038/s41598-019-40915-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420577PMC
March 2019

ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data.

EMBO Rep 2018 12 9;19(12). Epub 2018 Nov 9.

Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan

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http://embor.embopress.org/lookup/doi/10.15252/embr.20184625
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http://dx.doi.org/10.15252/embr.201846255DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280645PMC
December 2018

Promoter Usage and Dynamics in Vascular Smooth Muscle Cells Exposed to Fibroblast Growth Factor-2 or Interleukin-1β.

Sci Rep 2018 09 3;8(1):13164. Epub 2018 Sep 3.

Vascular Biology and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, 2052, Australia.

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http://dx.doi.org/10.1038/s41598-018-30702-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6120868PMC
September 2018

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection.

Cerebellum 2018 Jun;17(3):308-325

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.

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http://dx.doi.org/10.1007/s12311-017-0912-3DOI Listing
June 2018

Selective Activation of Alternative Core Promoters by Wnt-Responsive Enhancers.

Genes (Basel) 2018 May 23;9(6). Epub 2018 May 23.

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.3390/genes9060270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6027352PMC
May 2018

CD157 Marks Tissue-Resident Endothelial Stem Cells with Homeostatic and Regenerative Properties.

Cell Stem Cell 2018 03 8;22(3):384-397.e6. Epub 2018 Feb 8.

Department of Signal Transduction, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.01.010DOI Listing
March 2018

Genome Annotation.

Methods Mol Biol 2017 ;1525:107-121

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1007/978-1-4939-6622-6_5DOI Listing
January 2018

Correction to: Relatively frequent switching of transcription start sites during cerebellar development.

BMC Genomics 2018 01 11;19(1):39. Epub 2018 Jan 11.

Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, V5Z 4H4, Canada.

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http://dx.doi.org/10.1186/s12864-017-4291-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763542PMC
January 2018

FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Database (Oxford) 2016 9;2016. Epub 2016 Jul 9.

Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Kanagawa 230-0045, Japan

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http://dx.doi.org/10.1093/database/baw105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4940433PMC
November 2017

Restricted Presence of POU6F2 in Human Corneal Endothelial Cells Uncovered by Extension of the Promoter-level Expression Atlas.

EBioMedicine 2017 Nov 4;25:175-186. Epub 2017 Nov 4.

Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2017.10.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704063PMC
November 2017

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes.

EBioMedicine 2017 Oct 12;24:257-266. Epub 2017 Sep 12.

Micro-Signaling Regulation Technology Unit, RIKEN Center for Life Science Technologies, Wako, Saitama 3510198, Japan; Department of Laboratory Medicine, The Jikei University School of Medicine, Tokyo 1058461, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2017.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5652006PMC
October 2017

Hotspots of De Novo Point Mutations in Induced Pluripotent Stem Cells.

Cell Rep 2017 Oct;21(2):308-315

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama, Kanagawa 230-0045, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.09.060DOI Listing
October 2017

FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies.

Sci Data 2017 08 29;4:170107. Epub 2017 Aug 29.

RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1038/sdata.2017.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574367PMC
August 2017

FANTOM5 CAGE profiles of human and mouse samples.

Authors:
Shuhei Noguchi Takahiro Arakawa Shiro Fukuda Masaaki Furuno Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Kaoru Kaida Ai Kaiho Mutsumi Kanamori-Katayama Tsugumi Kawashima Miki Kojima Atsutaka Kubosaki Ri-Ichiroh Manabe Mitsuyoshi Murata Sayaka Nagao-Sato Kenichi Nakazato Noriko Ninomiya Hiromi Nishiyori-Sueki Shohei Noma Eri Saijyo Akiko Saka Mizuho Sakai Christophe Simon Naoko Suzuki Michihira Tagami Shoko Watanabe Shigehiro Yoshida Peter Arner Richard A Axton Magda Babina J Kenneth Baillie Timothy C Barnett Anthony G Beckhouse Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher Ailsa J Carlisle Hans C Clevers Carrie A Davis Michael Detmar Taeko Dohi Albert S B Edge Matthias Edinger Anna Ehrlund Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Mary C Farach-Carson Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley M Forrester Rie Fujita Jun-Ichi Furusawa Teunis B Geijtenbeek Thomas Gingeras Daniel Goldowitz Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Yuki Hasegawa Meenhard Herlyn Peter Heutink Kelly J Hitchens David A Hume Tomokatsu Ikawa Yuri Ishizu Chieko Kai Hiroshi Kawamoto Yuki I Kawamura Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura Sarah Klein S Peter Klinken Alan J Knox Soichi Kojima Haruhiko Koseki Shigeo Koyasu Weonju Lee Andreas Lennartsson Alan Mackay-Sim Niklas Mejhert Yosuke Mizuno Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Kelly J Morris Hozumi Motohashi Christine L Mummery Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Tadasuke Nozaki Soichi Ogishima Naganari Ohkura Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Swati Pradhan-Bhatt Xian-Yang Qin Michael Rehli Patrizia Rizzu Sugata Roy Antti Sajantila Shimon Sakaguchi Hiroki Sato Hironori Satoh Suzana Savvi Alka Saxena Christian Schmidl Claudio Schneider Gundula G Schulze-Tanzil Anita Schwegmann Guojun Sheng Jay W Shin Daisuke Sugiyama Takaaki Sugiyama Kim M Summers Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Andru Tomoiu Hiroo Toyoda Marc van de Wetering Linda M van den Berg Roberto Verardo Dipti Vijayan Christine A Wells Louise N Winteringham Ernst Wolvetang Yoko Yamaguchi Masayuki Yamamoto Chiyo Yanagi-Mizuochi Misako Yoneda Yohei Yonekura Peter G Zhang Silvia Zucchelli Imad Abugessaisa Erik Arner Jayson Harshbarger Atsushi Kondo Timo Lassmann Marina Lizio Serkan Sahin Thierry Sengstag Jessica Severin Hisashi Shimoji Masanori Suzuki Harukazu Suzuki Jun Kawai Naoto Kondo Masayoshi Itoh Carsten O Daub Takeya Kasukawa Hideya Kawaji Piero Carninci Alistair R R Forrest Yoshihide Hayashizaki

Sci Data 2017 08 29;4:170112. Epub 2017 Aug 29.

RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1038/sdata.2017.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574368PMC
August 2017

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types.

Sci Data 2017 08 29;4:170113. Epub 2017 Aug 29.

RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.

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http://dx.doi.org/10.1038/sdata.2017.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574373PMC
August 2017

Next-generation sequencing-based small RNA profiling of cerebrospinal fluid exosomes.

Neurosci Lett 2017 01 22;636:48-57. Epub 2016 Oct 22.

Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan; Center for Brain Integration Research (CBIR), Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.neulet.2016.10.042DOI Listing
January 2017

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs.

Bioinformatics 2016 09 9;32(18):2858-60. Epub 2016 Jun 9.

Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.

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http://dx.doi.org/10.1093/bioinformatics/btw337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018375PMC
September 2016

Novel biomarkers that assist in accurate discrimination of squamous cell carcinoma from adenocarcinoma of the lung.

BMC Cancer 2016 Sep 29;16(1):760. Epub 2016 Sep 29.

Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, 1-7-22 Suehiro-cho, Tsurumi-ku, 230-0045, Yokohama, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5041559PMC
http://dx.doi.org/10.1186/s12885-016-2792-1DOI Listing
September 2016

Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

Nucleic Acids Res 2016 Apr 21;44(7):3233-52. Epub 2016 Mar 21.

Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen 361021, China St. Laurent Institute, 317 New Boston St., Suite 201, Woburn, MA 01801, USA

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http://dx.doi.org/10.1093/nar/gkw162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838384PMC
April 2016

Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases.

Trends Genet 2016 Feb 15;32(2):76-88. Epub 2016 Jan 15.

RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.

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http://dx.doi.org/10.1016/j.tig.2015.11.004DOI Listing
February 2016

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.

Cancer Res 2016 Jan 9;76(2):216-26. Epub 2015 Nov 9.

RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan. Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Nedlands, Western Australia, Australia.

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http://dx.doi.org/10.1158/0008-5472.CAN-15-0484DOI Listing
January 2016

Mapping Mammalian Cell-type-specific Transcriptional Regulatory Networks Using KD-CAGE and ChIP-seq Data in the TC-YIK Cell Line.

Front Genet 2015 18;6:331. Epub 2015 Nov 18.

RIKEN Center for Life Science Technologies Yokohama, Japan ; Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan ; QEII Medical Centre and Centre for Medical Research, Harry Perkins Institute of Medical Research, The University of Western Australia Nedlands, WA, Australia.

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http://dx.doi.org/10.3389/fgene.2015.00331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650373PMC
December 2015

Identification of chromatin marks at TERRA promoter and encoding region.

Biochem Biophys Res Commun 2015 Nov 13;467(4):1052-7. Epub 2015 Oct 13.

Division of Genomic Technologies, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2015.09.176DOI Listing
November 2015

The frequent evolutionary birth and death of functional promoters in mouse and human.

Genome Res 2015 Oct 30;25(10):1546-57. Epub 2015 Jul 30.

MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom;

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http://dx.doi.org/10.1101/gr.190546.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4579340PMC
October 2015

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.

Nucleic Acids Res 2015 Aug 27;43(14):6787-98. Epub 2015 Jun 27.

Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, 14183, Sweden Science for Life Laboratory, Karolinska Institute, Solna, 17121, Sweden RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, 230-0045, Japan RIKEN Omics Science Center1, Yokohama, Kanagawa, 230-0045, Japan

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gkv608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538815PMC
August 2015

Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

Nucleic Acids Res 2015 Aug 27;43(14):6969-82. Epub 2015 Jun 27.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan Riken Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan

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http://dx.doi.org/10.1093/nar/gkv646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538831PMC
August 2015

The BioMart community portal: an innovative alternative to large, centralized data repositories.

Authors:
Damian Smedley Syed Haider Steffen Durinck Luca Pandini Paolo Provero James Allen Olivier Arnaiz Mohammad Hamza Awedh Richard Baldock Giulia Barbiera Philippe Bardou Tim Beck Andrew Blake Merideth Bonierbale Anthony J Brookes Gabriele Bucci Iwan Buetti Sarah Burge Cédric Cabau Joseph W Carlson Claude Chelala Charalambos Chrysostomou Davide Cittaro Olivier Collin Raul Cordova Rosalind J Cutts Erik Dassi Alex Di Genova Anis Djari Anthony Esposito Heather Estrella Eduardo Eyras Julio Fernandez-Banet Simon Forbes Robert C Free Takatomo Fujisawa Emanuela Gadaleta Jose M Garcia-Manteiga David Goodstein Kristian Gray José Afonso Guerra-Assunção Bernard Haggarty Dong-Jin Han Byung Woo Han Todd Harris Jayson Harshbarger Robert K Hastings Richard D Hayes Claire Hoede Shen Hu Zhi-Liang Hu Lucie Hutchins Zhengyan Kan Hideya Kawaji Aminah Keliet Arnaud Kerhornou Sunghoon Kim Rhoda Kinsella Christophe Klopp Lei Kong Daniel Lawson Dejan Lazarevic Ji-Hyun Lee Thomas Letellier Chuan-Yun Li Pietro Lio Chu-Jun Liu Jie Luo Alejandro Maass Jerome Mariette Thomas Maurel Stefania Merella Azza Mostafa Mohamed Francois Moreews Ibounyamine Nabihoudine Nelson Ndegwa Céline Noirot Cristian Perez-Llamas Michael Primig Alessandro Quattrone Hadi Quesneville Davide Rambaldi James Reecy Michela Riba Steven Rosanoff Amna Ali Saddiq Elisa Salas Olivier Sallou Rebecca Shepherd Reinhard Simon Linda Sperling William Spooner Daniel M Staines Delphine Steinbach Kevin Stone Elia Stupka Jon W Teague Abu Z Dayem Ullah Jun Wang Doreen Ware Marie Wong-Erasmus Ken Youens-Clark Amonida Zadissa Shi-Jian Zhang Arek Kasprzyk

Nucleic Acids Res 2015 Jul 20;43(W1):W589-98. Epub 2015 Apr 20.

Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia

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http://dx.doi.org/10.1093/nar/gkv350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489294PMC
July 2015

A draft network of ligand-receptor-mediated multicellular signalling in human.

Nat Commun 2015 Jul 22;6:7866. Epub 2015 Jul 22.

1] RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045 Japan [2] Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, PO Box 7214, 6 Verdun Street, Nedlands, Perth, Western Australia 6008, Australia.

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http://dx.doi.org/10.1038/ncomms8866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4525178PMC
July 2015

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells.

J Leukoc Biol 2015 May 25;97(5):985-995. Epub 2015 Feb 25.

*The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan

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http://dx.doi.org/10.1189/jlb.6TA1014-477RRDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398258PMC
May 2015

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Authors:
Erik Arner Carsten O Daub Kristoffer Vitting-Seerup Robin Andersson Berit Lilje Finn Drabløs Andreas Lennartsson Michelle Rönnerblad Olga Hrydziuszko Morana Vitezic Tom C Freeman Ahmad M N Alhendi Peter Arner Richard Axton J Kenneth Baillie Anthony Beckhouse Beatrice Bodega James Briggs Frank Brombacher Margaret Davis Michael Detmar Anna Ehrlund Mitsuhiro Endoh Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley Forrester Daniel Goldowitz Reto Guler Thomas Ha Mitsuko Hara Meenhard Herlyn Tomokatsu Ikawa Chieko Kai Hiroshi Kawamoto Levon M Khachigian S Peter Klinken Soichi Kojima Haruhiko Koseki Sarah Klein Niklas Mejhert Ken Miyaguchi Yosuke Mizuno Mitsuru Morimoto Kelly J Morris Christine Mummery Yutaka Nakachi Soichi Ogishima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Xian-Yang Qin Sugata Roy Hiroki Sato Suzana Savvi Alka Saxena Anita Schwegmann Daisuke Sugiyama Rolf Swoboda Hiroshi Tanaka Andru Tomoiu Louise N Winteringham Ernst Wolvetang Chiyo Yanagi-Mizuochi Misako Yoneda Susan Zabierowski Peter Zhang Imad Abugessaisa Nicolas Bertin Alexander D Diehl Shiro Fukuda Masaaki Furuno Jayson Harshbarger Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Yuri Ishizu Masayoshi Itoh Tsugumi Kawashima Miki Kojima Naoto Kondo Marina Lizio Terrence F Meehan Christopher J Mungall Mitsuyoshi Murata Hiromi Nishiyori-Sueki Serkan Sahin Sayaka Nagao-Sato Jessica Severin Michiel J L de Hoon Jun Kawai Takeya Kasukawa Timo Lassmann Harukazu Suzuki Hideya Kawaji Kim M Summers Christine Wells David A Hume Alistair R R Forrest Albin Sandelin Piero Carninci Yoshihide Hayashizaki

Science 2015 Feb 12;347(6225):1010-4. Epub 2015 Feb 12.

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http://dx.doi.org/10.1126/science.1259418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433PMC
February 2015

A transient disruption of fibroblastic transcriptional regulatory network facilitates trans-differentiation.

Nucleic Acids Res 2014 Aug 10;42(14):8905-13. Epub 2014 Jul 10.

RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-Ku, Yokohama 230-0045, Japan RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-Ku, Yokohama 230-0045, Japan

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http://dx.doi.org/10.1093/nar/gku567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132712PMC
August 2014

The evolution of human cells in terms of protein innovation.

Mol Biol Evol 2014 Jun 1;31(6):1364-74. Epub 2014 Apr 1.

Department of Computer Science, University of Bristol, Bristol, United KingdomMedical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom

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http://dx.doi.org/10.1093/molbev/mst139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032124PMC
June 2014

Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions.

Mol Genet Metab 2014 May 16;112(1):73-83. Epub 2013 Dec 16.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK; The University of Queensland Northside Clinical School, Prince Charles Hospital, Chermside 4032, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.ymgme.2013.12.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019825PMC
May 2014

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.

Blood 2014 Apr 26;123(17):e46-57. Epub 2014 Mar 26.

Department of Bioscience and Nutrition, Center for Biosciences, NOVUM, Karolinska Institutet, Stockholm, Sweden;

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http://dx.doi.org/10.1182/blood-2013-02-483537DOI Listing
April 2014

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.

Proc Natl Acad Sci U S A 2014 Apr 27;111(14):5289-94. Epub 2014 Mar 27.

Departments of Experimental Immunology and Systems Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.

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http://dx.doi.org/10.1073/pnas.1312717110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986152PMC
April 2014

CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments.

Bioinformatics 2014 04 27;30(8):1183-1184. Epub 2014 Mar 27.

Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115, USA, RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045 Japan, Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan and RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btu125DOI Listing
April 2014

Effects of cytosine methylation on transcription factor binding sites.

BMC Genomics 2014 Mar 26;15:119. Epub 2014 Mar 26.

Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/1471-2164-15-119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986887PMC
March 2014

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

Interactive visualization and analysis of large-scale sequencing datasets using ZENBU.

Nat Biotechnol 2014 Mar;32(3):217-9

1] RIKEN Center for Life Science Technologies (Division of Genomic Technologies), Suehiro-cho, Tsurumi-ku, Yokohama, Japan. [2] RIKEN Omics Science Center (OSC), Yokohama, Japan.

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http://dx.doi.org/10.1038/nbt.2840DOI Listing
March 2014