Piero Carninci

Piero Carninci

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Piero Carninci

Publications by authors named "Piero Carninci"

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Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation.

Dev Cell 2019 Oct 29;51(1):21-34.e5. Epub 2019 Aug 29.

Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2019.07.023DOI Listing
October 2019

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

Cell Syst 2019 Oct 11. Epub 2019 Oct 11.

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
October 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

MicroRNA-27a/b-3p and PPARG regulate SCAMP3 through a feed-forward loop during adipogenesis.

Sci Rep 2019 Sep 25;9(1):13891. Epub 2019 Sep 25.

RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan.

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http://dx.doi.org/10.1038/s41598-019-50210-3DOI Listing
September 2019

SINEUP Non-coding RNA Targeting GDNF Rescues Motor Deficits and Neurodegeneration in a Mouse Model of Parkinson's Disease.

Mol Ther 2019 Aug 16. Epub 2019 Aug 16.

Central RNA Laboratory and Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), 16263 Genova, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.ymthe.2019.08.005DOI Listing
August 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

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation.

J Vis Exp 2019 Feb 1(144). Epub 2019 Feb 1.

Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences; TransSINE Technologies Co. Ltd.;

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http://dx.doi.org/10.3791/58627DOI Listing
February 2019

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA.

Genome Res 2018 12 7;28(12):1943-1956. Epub 2018 Nov 7.

Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.235937.118
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http://dx.doi.org/10.1101/gr.235937.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280763PMC
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

The Human Cell Atlas: Technical approaches and challenges.

Brief Funct Genomics 2018 07;17(4):283-294

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

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https://academic.oup.com/bfg/article/17/4/283/4571849
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http://dx.doi.org/10.1093/bfgp/elx029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063304PMC
July 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

Target-enrichment sequencing for detailed characterization of small RNAs.

Nat Protoc 2018 04 22;13(4):768-786. Epub 2018 Mar 22.

Division of Genomic Technologies, RIKEN Yokohama Campus, RIKEN Center for Life Science Technologies, Tsurumi-Ku, Yokohama, Japan.

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http://dx.doi.org/10.1038/nprot.2018.001DOI Listing
April 2018

The FANTOM5 Computation Ecosystem: Genomic Information Hub for Promoters and Active Enhancers.

Methods Mol Biol 2017 ;1611:199-217

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/10.1007/978-1-4939-7015-5_15DOI Listing
February 2018

SCPortalen: human and mouse single-cell centric database.

Nucleic Acids Res 2018 01;46(D1):D781-D787

Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1093/nar/gkx949DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753281PMC
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

The effect of genetic variation on promoter usage and enhancer activity.

Nat Commun 2017 11 7;8(1):1358. Epub 2017 Nov 7.

Department of Genetic Medicine and Development, University of Geneva, 1 Michel Servet, Geneva, CH1211, Switzerland.

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http://dx.doi.org/10.1038/s41467-017-01467-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677018PMC
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

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

DEIVA: a web application for interactive visual analysis of differential gene expression profiles.

BMC Genomics 2017 01 7;18(1):47. Epub 2017 Jan 7.

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

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http://dx.doi.org/10.1186/s12864-016-3396-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5219783PMC
January 2017

Isoforms of the Erythropoietin receptor in dopaminergic neurons of the Substantia Nigra.

J Neurochem 2016 11 30;139(4):596-609. Epub 2016 Sep 30.

Area of Neuroscience, SISSA, Trieste, Italy.

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http://dx.doi.org/10.1111/jnc.13757DOI Listing
November 2016

Identification of antisense long noncoding RNAs that function as SINEUPs in human cells.

Sci Rep 2016 09 20;6:33605. Epub 2016 Sep 20.

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

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http://dx.doi.org/10.1038/srep33605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5028707PMC
September 2016

Expression Specificity of Disease-Associated lncRNAs: Toward Personalized Medicine.

Curr Top Microbiol Immunol 2016 ;394:237-58

Division of Genomic Technologies, RIKEN Yokohama Campus, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama City, Kanagawa, 230-0045, Japan.

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http://link.springer.com/10.1007/82_2015_464
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http://dx.doi.org/10.1007/82_2015_464DOI Listing
July 2016

HSA21 Single-Minded 2 (Sim2) Binding Sites Co-Localize with Super-Enhancers and Pioneer Transcription Factors in Pluripotent Mouse ES Cells.

PLoS One 2015 8;10(5):e0126475. Epub 2015 May 8.

Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; University Hospitals of Geneva, Geneva, Switzerland; iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126475PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425456PMC
April 2016

Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.

Nucleic Acids Res 2016 Apr 15;44(7):3070-81. Epub 2015 Dec 15.

Institute of Clinical Sciences MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK Department of Informatics, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway

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http://dx.doi.org/10.1093/nar/gkv1354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838339PMC
April 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

Characterization of piRNAs across postnatal development in mouse brain.

Sci Rep 2016 04 26;6:25039. Epub 2016 Apr 26.

Division of Applied Mathematics and Computer Sciences, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1038/srep25039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4844963PMC
April 2016

Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome.

Biochim Biophys Acta 2016 Jan 23;1859(1):3-15. Epub 2015 Oct 23.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Campus, 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.bbagrm.2015.10.010DOI Listing
January 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

Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors.

Epigenetics Chromatin 2015 14;8:55. Epub 2015 Dec 14.

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

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http://dx.doi.org/10.1186/s13072-015-0043-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4678690PMC
December 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

Paradigm shifts in genomics through the FANTOM projects.

Mamm Genome 2015 Oct 8;26(9-10):391-402. Epub 2015 Aug 8.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, 230-0045, Japan.

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http://dx.doi.org/10.1007/s00335-015-9593-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602071PMC
October 2015

Engineering mammalian cell factories with SINEUP noncoding RNAs to improve translation of secreted proteins.

Gene 2015 Sep 2;569(2):287-93. Epub 2015 Jun 2.

Department of Health Science and Interdisciplinary Research Center on Autoimmune Diseases, Università del Piemonte Orientale, Novara, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2015.05.070DOI Listing
September 2015

STAP cells are derived from ES cells.

Nature 2015 Sep;525(7570):E4-5

Cell Asymmetry, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.

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http://dx.doi.org/10.1038/nature15366DOI Listing
September 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/
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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

Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline.

Mol Cell 2015 Aug 23;59(4):553-63. Epub 2015 Jul 23.

Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.06.024DOI Listing
August 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

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.

Nucleic Acids Res 2015 Apr 4;43(8):e51. Epub 2015 Feb 4.

Department of Molecular Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK Department of Informatics, University of Bergen, Høyteknologisenteret, Thormøhlensgate 55, N-5008 Bergen, Norway

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http://dx.doi.org/10.1093/nar/gkv054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417143PMC
April 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

Biased allelic expression in human primary fibroblast single cells.

Am J Hum Genet 2015 Jan 31;96(1):70-80. Epub 2014 Dec 31.

Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1211 Geneva, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2014.12.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289680PMC
January 2015

Telomerase reverse transcriptase regulates microRNAs.

Int J Mol Sci 2015 Jan 6;16(1):1192-208. Epub 2015 Jan 6.

Cancer Stem Cell Project, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.

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http://dx.doi.org/10.3390/ijms16011192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307298PMC
January 2015

Genomics: mice in the ENCODE spotlight.

Authors:
Piero Carninci

Nature 2014 Nov;515(7527):346-7

RIKEN Center for Life Science Technologies, Division of Genomic Technologies, RIKEN Yokohama Campus, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1038/515346aDOI Listing
November 2014