Soichi Ogishima

Soichi Ogishima

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Soichi Ogishima

Publications by authors named "Soichi Ogishima"

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Authentication of Patients and Participants in Health Information Exchange and Consent for Medical Research: A Key Step for Privacy Protection, Respect for Autonomy, and Trustworthiness.

Front Genet 2018 1;9:167. Epub 2018 Jun 1.

Department of Biomedical Ethics and Public Policy, Graduate School of Medicine, Osaka University, Suita, Japan.

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http://dx.doi.org/10.3389/fgene.2018.00167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992519PMC
June 2018

[Human Genome Data and Drug Development].

Authors:
Soichi Ogishima

Gan To Kagaku Ryoho 2018 Apr;45(4):597-600

Dept. of Bioclinical Informatics, Group of Integrated Database Systems, Tohoku Medical Megabank Organization, Tohoku University.

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April 2018

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 Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia.

PLoS One 2016 27;11(10):e0162828. Epub 2016 Oct 27.

Department of Clinical Informatics, Tohoku University Graduate School of Medicine 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162828PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082890PMC
June 2017

Integrated Database And Knowledge Base For Genomic Prospective Cohort Study In Tohoku Medical Megabank Toward Personalized Prevention And Medicine.

Stud Health Technol Inform 2015 ;216:1057

Dept. of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.

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December 2016

AlzPathway, an Updated Map of Curated Signaling Pathways: Towards Deciphering Alzheimer's Disease Pathogenesis.

Methods Mol Biol 2016 ;1303:423-32

Department of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, 980-8575, Japan,

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http://dx.doi.org/10.1007/978-1-4939-2627-5_25DOI Listing
April 2016

Network-Based Analysis for Uncovering Mechanisms Underlying Alzheimer's Disease.

Methods Mol Biol 2016 ;1303:479-91

Department of Molecular Genetics, Center for Bioresources, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan.

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http://dx.doi.org/10.1007/978-1-4939-2627-5_29DOI Listing
April 2016

Network biology approach to epithelial-mesenchymal transition in cancer metastasis: three stage theory.

J Mol Cell Biol 2015 Jun 23;7(3):253-66. Epub 2015 Jun 23.

Department of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.

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http://dx.doi.org/10.1093/jmcb/mjv035DOI Listing
June 2015

Implementation of linked data in the life sciences at BioHackathon 2011.

J Biomed Semantics 2015 7;6. Epub 2015 Jan 7.

Department of Bioclinical informatics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-cho 4-1, Aoba-ku, Sendai-shi Miyagi, 980-8575 Japan.

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http://dx.doi.org/10.1186/2041-1480-6-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4429360PMC
May 2015

Modularity in the evolution of yeast protein interaction network.

Bioinformation 2015 31;11(3):127-30. Epub 2015 Mar 31.

Department of Bioclinical Informatics, Tohoku Medical and Megabank Organization, Tohoku University, Seiryo-cho 4-1, Aoba-ku, Sendai-shi Miyagi 980-8575 Japan.

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http://dx.doi.org/10.6026/97320630011127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403033PMC
April 2015

A method to associate all possible combinations of genetic and environmental factors using GxE landscape plot.

Bioinformation 2015 31;11(3):161-4. Epub 2015 Mar 31.

Dept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University ; Dept. of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University.

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http://dx.doi.org/10.6026/97320630011161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404419PMC
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

Identification of unstable network modules reveals disease modules associated with the progression of Alzheimer's disease.

PLoS One 2013 15;8(11):e76162. Epub 2013 Nov 15.

Department of Bioinformatics, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan ; Department of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai-shi, Miyagi, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076162PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858171PMC
July 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

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

Analysis of L-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli.

BMC Syst Biol 2013 Sep 22;7:92. Epub 2013 Sep 22.

Institute for Innovation, Ajinomoto Co, Inc,, Suzuki-cho 1-1, Kawasaki-ku, Kawasaki City, Kanagawa 210-8681, Japan.

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http://dx.doi.org/10.1186/1752-0509-7-92DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851129PMC
September 2013

Hub-centered gene network reconstruction using automatic relevance determination.

PLoS One 2012 3;7(5):e35077. Epub 2012 May 3.

ViroQuant Research Group Modeling, University of Heidelberg, BioQuant BQ26, Heidelberg, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0035077PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3343044PMC
January 2013

Prognostic value of matrix Gla protein in breast cancer.

Mol Med Rep 2009 Jul-Aug;2(4):549-53

Genome Center, Japanese Foundation for Cancer Research, Cancer Institute Hospital, Tokyo 135-8550, Japan.

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http://dx.doi.org/10.3892/mmr_00000135DOI Listing
October 2012

Human mesenchymal stem cells in synovial fluid increase in the knee with degenerated cartilage and osteoarthritis.

J Orthop Res 2012 Jun 6;30(6):943-9. Epub 2011 Dec 6.

Section of Cartilage Regeneration, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.

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http://dx.doi.org/10.1002/jor.22029DOI Listing
June 2012

AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease.

BMC Syst Biol 2012 May 30;6:52. Epub 2012 May 30.

Department of Bioinformatics, Tokyo Medical and Dental University, Yushima 1-5-45, Tokyo, 113-8510, Japan.

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http://dx.doi.org/10.1186/1752-0509-6-52DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411424PMC
May 2012

Omics-based identification of pathophysiological processes.

Methods Mol Biol 2011 ;719:499-509

Department of Computational Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan.

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http://dx.doi.org/10.1007/978-1-61779-027-0_23DOI Listing
June 2011

Combined in silico and in vivo analyses reveal role of Hes1 in taste cell differentiation.

PLoS Genet 2009 Apr 3;5(4):e1000443. Epub 2009 Apr 3.

Section of Molecular Craniofacial Embryology, Tokyo Medical and Dental University, Tokyo, Japan.

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http://dx.doi.org/10.1371/journal.pgen.1000443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655725PMC
April 2009

BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network.

Bioinformatics 2009 Feb 6;25(4):543-4. Epub 2009 Jan 6.

Department of Computational Biology, School of Medical Sciences, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo 113-8510, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btp008DOI Listing
February 2009

Missing link in the evolution of Hox clusters.

Gene 2007 Jan 30;387(1-2):21-30. Epub 2006 Aug 30.

Department of Bioinformatics, Graduate School of Tokyo Medical and Dental University Yushima 1-5-45, Tokyo 113-8510, Japan.

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http://dx.doi.org/10.1016/j.gene.2006.08.011DOI Listing
January 2007

Standardized phylogenetic tree: a reference to discover functional evolution.

J Mol Evol 2003 ;57 Suppl 1:S174-81

Department of Bioinformatics, MRI, Tokyo Medical and Dental University, Yushima 1-5-45, Bunkyo-ku, Tokyo, 113-8510, Japan.

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http://dx.doi.org/10.1007/s00239-003-0025-0DOI Listing
August 2004

Longitudinal phylogenetic tree of within-host viral evolution from noncontemporaneous samples: a distance-based sequential-linking method.

Gene 2003 Oct;317(1-2):89-95

Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo 113-8510, Japan.

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http://dx.doi.org/10.1016/s0378-1119(03)00656-5DOI Listing
October 2003