Publications by authors named "Charles Plessy"

46Publications

Analysis of hiPSCs differentiation toward hepatocyte-like cells upon extended exposition to oncostatin.

Differentiation 2020 Jul - Aug;114:36-48. Epub 2020 May 19.

CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.diff.2020.05.006DOI Listing
May 2020

Widespread use of the "ascidian" mitochondrial genetic code in tunicates.

F1000Res 2019 10;8:2072. Epub 2019 Dec 10.

Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, 904-0495, Japan.

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http://dx.doi.org/10.12688/f1000research.21551.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7047913.2PMC
June 2020

Characterization of liver zonation-like transcriptomic patterns in HLCs derived from hiPSCs in a microfluidic biochip environment.

Biotechnol Prog 2020 Sep 22;36(5):e3013. Epub 2020 May 22.

CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1002/btpr.3013DOI Listing
September 2020

Machine-driven parameter screen of biochemical reactions.

Nucleic Acids Res 2020 04;48(7):e37

RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama, Japan.

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http://dx.doi.org/10.1093/nar/gkaa079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144897PMC
April 2020

Transcriptome profiling of hiPSC-derived LSECs with nanoCAGE.

Mol Omics 2020 04 28;16(2):138-146. Epub 2020 Jan 28.

CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.

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http://dx.doi.org/10.1039/c9mo00135bDOI Listing
April 2020

Analysis of the transcription factors and their regulatory roles during a step-by-step differentiation of induced pluripotent stem cells into hepatocyte-like cells.

Mol Omics 2019 12;15(6):383-398

CNRS UMI 2820, Laboratory for Integrated Micro Mechatronic Systems, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.

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http://dx.doi.org/10.1039/c9mo00122kDOI Listing
December 2019

Optimized protocol for the hepatic differentiation of induced pluripotent stem cells in a fluidic microenvironment.

Biotechnol Bioeng 2019 07 29;116(7):1762-1776. Epub 2019 Mar 29.

Laboratory for Integrated Micro Mechatronic Systems, CNRS UMI 2820, Institute of Industrial Science, The University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1002/bit.26970DOI Listing
July 2019

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

Erratum to: NanoCAGE: A Method for the Analysis of Coding and Noncoding 5'-Capped Transcriptomes.

Methods Mol Biol 2017 ;1543:E1

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/10.1007/978-1-4939-6716-2_17DOI Listing
January 2017

NanoCAGE: A Method for the Analysis of Coding and Noncoding 5'-Capped Transcriptomes.

Methods Mol Biol 2017 ;1543:57-109

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/10.1007/978-1-4939-6716-2_4DOI Listing
February 2018

Targeted reduction of highly abundant transcripts using pseudo-random primers.

Biotechniques 2016 Apr 1;60(4):169-74. Epub 2016 Apr 1.

Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa, Japan.

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http://dx.doi.org/10.2144/000114400DOI Listing
April 2016

Multiplicity of 5' cap structures present on short RNAs.

PLoS One 2014 31;9(7):e102895. Epub 2014 Jul 31.

RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Japan; RIKEN Omics Science Center, Yokohama, Kanagawa, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102895PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117478PMC
October 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

Two independent transcription initiation codes overlap on vertebrate core promoters.

Nature 2014 Mar 16;507(7492):381-385. Epub 2014 Feb 16.

Institute of Clinical Sciences and MRC Clinical Sciences Center, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, United Kingdom.

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http://dx.doi.org/10.1038/nature12974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4820030PMC
March 2014

Comparison of RNA- or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation.

BMC Genomics 2013 Sep 30;14:665. Epub 2013 Sep 30.

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

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http://dx.doi.org/10.1186/1471-2164-14-665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3853366PMC
September 2013

Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.

Nucleic Acids Res 2013 Feb 24;41(3):e44. Epub 2012 Nov 24.

Omics Science Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1093/nar/gks1128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562004PMC
February 2013

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.

Genome Res 2013 Jan 30;23(1):169-80. Epub 2012 Aug 30.

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.139618.112
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http://dx.doi.org/10.1101/gr.139618.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530677PMC
January 2013

Community-driven computational biology with Debian Linux.

BMC Bioinformatics 2010 Dec 21;11 Suppl 12:S5. Epub 2010 Dec 21.

University Clinics of Schleswig-Holstein, Department of Dermatology, formerly University of Lübeck, Institute for Neuro- andBioinformatics, Ratzeburger Allee 160, 23530 Lübeck, Germany.

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http://dx.doi.org/10.1186/1471-2105-11-S12-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040531PMC
December 2010

NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes.

Cold Spring Harb Protoc 2011 Jan 1;2011(1):pdb.prot5559. Epub 2011 Jan 1.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4181851PMC
http://dx.doi.org/10.1101/pdb.prot5559DOI Listing
January 2011

Tunable fractionation of nucleic acids.

Biotechniques 2009 Dec;47(6):1041-3

Functional Genomics Technology Team, Omics Science Center (OSC), RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.2144/000113249DOI Listing
December 2009

Unexpected expression of alpha- and beta-globin in mesencephalic dopaminergic neurons and glial cells.

Proc Natl Acad Sci U S A 2009 Sep 26;106(36):15454-9. Epub 2009 Aug 26.

Sector of Neurobiology, International School for Advanced Studies, The Giovanni Armenise-Harvard Foundation Laboratory, and Consorzio per il Centro di Biomedicina Molecolare, AREA Science Park, Basovizza, 34012 Trieste, Italy.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0813216106
Publisher Site
http://dx.doi.org/10.1073/pnas.0813216106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732704PMC
September 2009

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

High-throughput verification of transcriptional starting sites by Deep-RACE.

Biotechniques 2009 Feb;46(2):130-2

Functional Genomics Technology Team, Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.2144/000113066DOI Listing
February 2009

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

Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes.

Trends Genet 2005 Apr;21(4):207-10

IGBMC, 1 rue Laurent Fries, BP 10142 67404 Illkirch Cedex, France.

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http://dx.doi.org/10.1016/j.tig.2005.02.006DOI Listing
April 2005

Conserved and acquired features of neurogenin1 regulation.

Development 2004 Nov 20;131(22):5627-37. Epub 2004 Oct 20.

Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, 67404 Illkirch Cedex, CU de Strasbourg, France.

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http://dx.doi.org/10.1242/dev.01455DOI Listing
November 2004

Her5 acts as a prepattern factor that blocks neurogenin1 and coe2 expression upstream of Notch to inhibit neurogenesis at the midbrain-hindbrain boundary.

Development 2004 May 31;131(9):1993-2006. Epub 2004 Mar 31.

Zebrafish Neurogenetics Junior Research Group, Institute of Virology, Technical University-Munich, Trogerstrasse 4b, D-81675 Munich, Germany.

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http://dx.doi.org/10.1242/dev.01093DOI Listing
May 2004

Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo.

Genome Res 2004 Feb 12;14(2):228-38. Epub 2004 Jan 12.

Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 10142, F-67404 Illkirch Cedex, C.U. de Strasbourg, France.

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http://dx.doi.org/10.1101/gr.1819204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC327098PMC
February 2004

Multiple regulatory elements with spatially and temporally distinct activities control neurogenin1 expression in primary neurons of the zebrafish embryo.

Mech Dev 2003 Feb;120(2):211-8

Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, C.U. de Strasbourg, France.

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http://dx.doi.org/10.1016/s0925-4773(02)00413-6DOI Listing
February 2003

Precocious expression of the Glide/Gcm glial-promoting factor in Drosophila induces neurogenesis.

Genetics 2002 Mar;160(3):1095-106

Institut de Génétique et Biologie Moléculaire et Cellulaire IGBMC/CNRS/ULP/INSERM-BP 163 67404 Illkirch, c.u. de Strasbourg, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1462002PMC
March 2002