Shimada, Makoto

J-GLOBAL         Last updated: Oct 12, 2019 at 23:18
Shimada, Makoto
Fujita Health University
Institute for Comprehensive Medical Science
Job title
Senior Assistant Professor
Ph.D.(Kyoto University)
Other affiliation
Cyukyo Gakuin University
Research funding number

Research Areas



Apr 1986
Mar 1990
Natural Science, Liberal Arts, International Christian University
Apr 1991
Mar 1993
Primatology, Mater course, Kyoto University, Graduate School
Apr 1993
Mar 1998
Primatology, Doctor course, Kyoto University, Graduate School

Academic & Professional Experience

Apr 1990
Mar 1991
Researcher, Sec. of Variation, Primate Research Institute, Kyoto University
Apr 1998
Aug 2000
Post-Doctoral Research Fellow, Div. of Population Genetics, Primate Research Institute, Kyoto University
Sep 2000
Aug 2002
Post-Doctoral Research Fellow, Lab. of Evolutionary Genetics, National Institute of Genetics
Sep 2002
Mar 2003
Assistant Researcher, Lab. of Genetic Resources, Faculty of Agriculture, Gifu University
Mar 2003
Jun 2005
Postdoctoral Associate, Dept. of Genetics, Rutgers University
Jul 2005
Jan 2006
Researcher, Perlegen Science, Japan K.K.
Jan 2006
Mar 2008
Researcher, Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST)
Apr 2008
Jun 2008
Researcher, Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST)
Jul 2008
Senior Assistant Professor, Div. of Gene Expression, Institute for Comprehensive Medical Science, Fujita Health University

Published Papers

Shimada, Makoto K.; Nishida, Tsunetoshi
Molecular Phylogenetics and Evolution   109 409-414   Feb 2017   [Refereed]
We corrected a software bug of PHYLIP, the evolutionary study package with the longest history.
The bug had been left for more than 25 years.
This correction solves the redundancy in bootstrapping that cause incorrect inference of cons...
Makoto K. Shimada, Ryoko Sanbonmatsu, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Yoshiyuki Suzuki, Ranajit Chakraborty, Takashi Gojobori, Tadashi Imanishi
Molecular Genetics and Genomics   291(5) 1869   Aug 2016   [Refereed]
Shimada MK, Sasaki-Haraguchi N, Mayeda, A
International Journal of Molecular Sciences   16(5) 10376-10388   2015   [Refereed]
According to the length distribution of human introns, there is a large population of short introns with a threshold of 65 nucleotides (nt) and a peak at 85 nt. Using human genome and transcriptome databases, we investigated the introns shorter th...
Gough CA, Homma K, Yamaguchi-Kabata Y, Shimada MK, Chakraborty R, Fujii Y, Iwama H, Minoshima S, Sakamoto S, Sato Y, Suzuki Y, Tada-Umezaki M, Nishikawa K, Imanishi T, Gojobori T:
Plos One   7(11) e50445   Nov 2012   [Refereed]
The relationship between sequence polymorphisms and human disease has been studied mostly in terms of effects of single nucleotide polymorphisms (SNPs) leading to single amino acid substitutions that change protein structure and function. However,...
Shimada, Makoto K.
International Journal of Evolution   1(1) 1   Jul 2012   [Refereed][Invited]
Libraries have played a central role in the inheritance of human knowledge. Thus, publicity and systematic management are keys in accomplishing the library’s mission. In natural science, natural history museums have been functioning as a public do...


An attempt to predict the functional haplotype differences between archaic and modern humans
Shimada, Makoto
Research Bulletin, Saito Ho-on Kai Museum   78 77-85   Mar 2014   [Invited]
Shimada, Makoto K.
Progress Report of Reseach Team B01 (Aoki,K. ed.)   (3) 43-53   2013   [Invited]
Shimada, Makoto
Progress Report of Reseach Team B01 (Aoki,K. ed.)   (2) 51-58   Mar 2012   [Invited]
Unusual ancient haplotypes in modern human probe for archaic hominin admixture
Shimada, Makoto
In: Akazawa T et al. eds. RNMH Project 2010-2014.   001 62-63   2012
Shimada, Makoto K.; Kanasashi, Tsutomu
Nature Precedings      Dec 2011
Modern human populations are known to contain “ancient haplotypes” that originated from archaic humans by hybridization. Some of them had been reported before the development of human genomic diversity databases, such as HapMap. Consequently, some...

Books etc

Shimada, Makoto (Ediotrs: Matsuzawa, Tetsuro; Humle, Tatyana; Sugiyama, Yukimaru) (Part:Joint Work, Chap. 34, pp339-345, Genetic variation in the chimpanzees of Bossou and Nimba.; Append. E, DNA sequencing data, pp416-419)
Springer   Jun 2011   ISBN:4431539204

Conference Activities & Talks

Origin and function of ancient haplotypes found in modern humans
Shimada, Makoto
12 Jan 2013   Replacement of Neanderthals by Modern Humans (RNMH): Testing Evolutionary Models of Learning
An attempt to estimate the functional difference in haplotypes between archaic and modern humans
Shimada, Makoto
International Conference on Replacement of Neanderthals by Modern Humans: Testing Evolutionary Models of Learning (RNMH2012)   18 Nov 2012   
Characterization of Evolutionary Conserved Unusually Short Human Introns
Shimada MK, Sasaki-Haraguchi N, Mayeda A
Annual Meeting of the Society for Molecular Biology and Evolution (SMBE2011)   Jul 2011   
Identification and Characterization of Unusually Small Introns, Termed Micro-introns, in the Human Genomes
Shimada MK, Sasaki-Haraguchi N, Mayeda A
The 16th Annual Meeting of the RNA Society and The RNA Society of Japan 13th Annual Meeting   Jun 2011   
Kyoto, Japan. Program & Abstracts (Oral Abstracts) #41
Shimada MK
Symposium on Biodiversity Sciences, “Genome, Evolution and Environment” (ISBDS2010: Commemorating the 60th Anniversary of Nagoya City University & in Partnership with the 10th Conference of the Parties to the Convention of Biological Diversity, CBD-COP10)   1 Aug 2010   Graduate School of Natural Sciences, Nagoya City University
Decrease of natural forests have been accelerated by development of human activity, which leads to loss of biodiversity. Populations of great apes are vulnerable to forest loss because of their low fecundity and their high dependency on forests f...
Shimada MK, Hey J
The 74th Annual Meeting of American Association of Physical Anthropologists.   Apr 2005   
Culotta, E: Archaic Gene in Modern People? (News) Science 308: 490-491, 22 April 2005.

Committee Memberships

Feb 2016
Editorial Board member of "Advances in Bioinformatics"
Jun 2012
Editorial Board Member of "International Journal of Evolution"
Jun 2013
Editorial board member of “Sequencing”
International Primate Society  Scientific committee member of International Primate Society 2010

Research Grants & Projects

Ministry of Education,Culture,Sports,Science & Technology: Grant-in-Aid for Scientific Research (C)
Project Year: Apr 2018 - Mar 2021    Investigator(s): Makoto Shimada
Project Year: Apr 2012 - Mar 2016    Investigator(s): Shimada, Makoto
Ministry of Education, Culture, Sports, Science and Technology: Grants-in-Aid for Scientific Research on Innovative Areas "Replacement of Neanderthals by Modern Humans: Testing Evolutionary Models of Learning" #1201
Project Year: Apr 2011 - Mar 2013    Investigator(s): Makoto Shimada
The Saito Gratitude Foundation: Research fund (FY. 2012)
Project Year: Feb 2013       Investigator(s): Shimada, Makoto
The Ministry of Education,Culture,Sports,Science and Technology (MEXT): Grant-in-Aid for Scientific Research(C)
Project Year: Apr 2009 - Mar 2012    Investigator(s): Makoto Shimada

Social Contribution

[Planner, Organizing Member, Demonstrator]  Inst. Comprehensive Medical Sci., Fujita Health University  20 Apr 2019
[Planner, Organizing Member, Demonstrator]  22 Apr 2017
[Interviewee]  AAAS  Science (News)  (Science 308: 490-491, 22 April 2005)  22 Apr 2005
Report and Interview about my presentation at The 74th Annual Meeting of American Association of Physical Anthropologists.