Publications by authors named "Jay W Shin"

42Publications

An era of single-cell genomics consortia.

Exp Mol Med 2020 Sep 15;52(9):1409-1418. Epub 2020 Sep 15.

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

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http://dx.doi.org/10.1038/s12276-020-0409-xDOI Listing
September 2020

Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids.

Cell Tissue Res 2020 Jul 31. Epub 2020 Jul 31.

Luxembourg Centre for Systems Biomedicine (LCSB), Developmental and Cellular Biology, University of Luxembourg, Belvaux, Luxembourg.

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http://dx.doi.org/10.1007/s00441-020-03249-yDOI Listing
July 2020

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Authors:
Jordan A Ramilowski Chi Wai Yip Saumya Agrawal Jen-Chien Chang Yari Ciani Ivan V Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher JF Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J Makeev Luigi Marchionni Yulia A Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J C Parr Owen J L Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A M Semple Youtaro Shibayama Divya M Sivaraman Takahiro Suzuki Suzannah C Szumowski Michihira Tagami Martin S Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E Vorontsov Chinatsu Yamamoto Robert S Young J Kenneth Baillie Alistair R R Forrest Roderic Guigó Michael M Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki Ken Yagi Michiel J L de Hoon Jay W Shin Piero Carninci

Genome Res 2020 07 27;30(7):1060-1072. Epub 2020 Jul 27.

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

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http://dx.doi.org/10.1101/gr.254219.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397864PMC
July 2020

Widely Distributed Neurotensinergic Neurons in the Brainstem Regulate NREM Sleep in Mice.

Curr Biol 2020 03 6;30(6):1002-1010.e4. Epub 2020 Feb 6.

International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2020.01.047DOI Listing
March 2020

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

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

Distinct transcriptional responses of lymphatic endothelial cells to VEGFR-3 and VEGFR-2 stimulation.

Sci Data 2017 08 29;4:170106. Epub 2017 Aug 29.

Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH) Zurich, 8093 Zurich, Switzerland.

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http://dx.doi.org/10.1038/sdata.2017.106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5574372PMC
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 essentiality of non-coding RNAs in cell reprogramming.

Noncoding RNA Res 2017 Mar 13;2(1):74-82. Epub 2017 Apr 13.

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

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https://linkinghub.elsevier.com/retrieve/pii/S24680540173000
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http://dx.doi.org/10.1016/j.ncrna.2017.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096403PMC
March 2017

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

Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection.

J Immunol 2015 Jun 8;194(12):6035-44. Epub 2015 May 8.

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

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http://dx.doi.org/10.4049/jimmunol.1402521DOI Listing
June 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

Repositioning monocyte TFRN into fibroblasts.

Methods Mol Biol 2014 ;1164:211-8

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

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http://link.springer.com/content/pdf/10.1007%2F978-1-4939-08
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http://link.springer.com/10.1007/978-1-4939-0805-9_17
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http://dx.doi.org/10.1007/978-1-4939-0805-9_17DOI Listing
January 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

Identification of ZNF395 as a novel modulator of adipogenesis.

Exp Cell Res 2013 Feb 7;319(3):68-76. Epub 2012 Nov 7.

Omics Science Center (OSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan.

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http://dx.doi.org/10.1016/j.yexcr.2012.11.003DOI Listing
February 2013

CpG site-specific alteration of hydroxymethylcytosine to methylcytosine beyond DNA replication.

Biochem Biophys Res Commun 2012 Sep 17;426(1):141-7. Epub 2012 Aug 17.

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

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http://dx.doi.org/10.1016/j.bbrc.2012.08.053DOI Listing
September 2012

Analysis of a novel highly metastatic melanoma cell line identifies osteopontin as a new lymphangiogenic factor.

Int J Oncol 2012 Oct 6;41(4):1455-63. Epub 2012 Jul 6.

Department of Medicine, Hematology and Oncology, University Hospital Muenster, D-48129 Muenster, Germany.

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http://dx.doi.org/10.3892/ijo.2012.1548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583651PMC
October 2012

CC chemokine ligand 2 and leukemia inhibitory factor cooperatively promote pluripotency in mouse induced pluripotent cells.

Stem Cells 2011 Aug;29(8):1196-205

RIKEN Omics Science Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan.

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http://dx.doi.org/10.1002/stem.673DOI Listing
August 2011

Tumor lymphangiogenesis and metastasis to lymph nodes induced by cancer cell expression of podoplanin.

Am J Pathol 2010 Aug 8;177(2):1004-16. Epub 2010 Jul 8.

Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland.

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http://dx.doi.org/10.2353/ajpath.2010.090703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913355PMC
August 2010

An exquisite cross-control mechanism among endothelial cell fate regulators directs the plasticity and heterogeneity of lymphatic endothelial cells.

Blood 2010 Jul 29;116(1):140-50. Epub 2010 Mar 29.

Departments of Surgery and of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1450 Biggy Street, Los Angeles, CA 90033, USA.

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http://dx.doi.org/10.1182/blood-2009-11-252270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2904577PMC
July 2010

Lymphatic-specific expression of dipeptidyl peptidase IV and its dual role in lymphatic endothelial function.

Exp Cell Res 2008 Oct 3;314(16):3048-56. Epub 2008 Aug 3.

Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zurich, Switzerland.

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http://linkinghub.elsevier.com/retrieve/pii/S001448270800294
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http://dx.doi.org/10.1016/j.yexcr.2008.07.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398155PMC
October 2008

Transcriptional profiling of VEGF-A and VEGF-C target genes in lymphatic endothelium reveals endothelial-specific molecule-1 as a novel mediator of lymphangiogenesis.

Blood 2008 Sep 9;112(6):2318-26. Epub 2008 Jul 9.

Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland.

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http://dx.doi.org/10.1182/blood-2008-05-156331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2532805PMC
September 2008

Prox-1 promotes invasion of kaposiform hemangioendotheliomas.

J Invest Dermatol 2008 Dec 26;128(12):2798-806. Epub 2008 Jun 26.

Department of Dermatology, Cutaneous Biology Research Center, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/jid.2008.176DOI Listing
December 2008

Prox1 promotes lineage-specific expression of fibroblast growth factor (FGF) receptor-3 in lymphatic endothelium: a role for FGF signaling in lymphangiogenesis.

Mol Biol Cell 2006 Feb 16;17(2):576-84. Epub 2005 Nov 16.

Cutaneous Biology Research Center and Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA.

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http://dx.doi.org/10.1091/mbc.e05-04-0368DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356570PMC
February 2006

Development of the lymphatic vascular system: a mystery unravels.

Dev Dyn 2004 Nov;231(3):462-73

Cutaneous Biology Research Center and Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Building 149, 13th Street, Charlestown, MA 02129, USA.

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http://dx.doi.org/10.1002/dvdy.20179DOI Listing
November 2004

Lymphatic reprogramming of blood vascular endothelium by Kaposi sarcoma-associated herpesvirus.

Nat Genet 2004 Jul 27;36(7):683-5. Epub 2004 Jun 27.

Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Building 149, 13th Street, Charlestown, Massachusetts 02129, USA.

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http://dx.doi.org/10.1038/ng1383DOI Listing
July 2004