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Researcher Database
Name: SHIMADA Makoto
Keyword: Genome evolution, Splicing, Bioinformatics
HomePage: http://tinyurl.com/shimada-mk
E-Mail address: mshimada[at]fujita-hu.ac.jp

Research Information (#1)
Research section-1: Evoutionary Genomics, Bioinformatics, Population Genetics

Organization / Department (#1)
Organization-1: Fujita Health University
Department(1) 1: Institute for Comprehensive Medical Science
Department(2) 1: Division of Gene Expression Mechanism
Position-1: Senior Assistant Professor
Address-1: 1-98 Dengakugakubo Kutsukake-cho,Toyoake, Aichi 470-1192, JAPAN
other-1: EXPERIENCE
7/2008 - Senior Assistant Professor at Institute for Comprehensive Medical Science, Fujita Health University (Current Position)
4/2008 - 6/2008 Post-Doctoral Research Fellow at Biomedicinal Information Research Center
1/2006 - 3/2008 Post-Doctoral Research Fellow at Japan Biological Information Research Center
7/2005 - 1/2006 Perlegen Science, Japan K.K.
4/2003 - 6/2005 Postdoctoral Associate of Department of Genetics, Rutgers University (PI: Jody Hey, Professor)
9/2002 - 3/2004 Post-Doctoral Research Fellow at Faculty of Agriculture, Gifu University (PI: Miho Murayama, Associate Professor & Shi!#%ap!#%ichi Ito, Professor)
9/2000 - 8/2002 Post-Doctoral Research Fellow at Laboratory of Evolutionary Genetics, National Institute of Genetics (PI: Naruya Saitou, Professor)
4/1998 - 8/2000 Post-Doctoral Research Fellow at Section of Population Genetics, Primate Research Institute, Kyoto University (PI: Takayoshi Shotake, Professor)

EDUCATION
Kyoto University, Graduate School, Kyoto, Japan, Doctor of Science, conferred 1998.
Kyoto University, Graduate School, Kyoto, Japan,
Master of Science, conferred 1993.
International Christian University, Tokyo, Japan, Bachelor of Art, Natural Science, conferred 1990.

HONORS
The 5th Takashima Prize, The Japan Association for Nilo-Ethiopia Studies, awarded 1999

Academic Meeting / Research Meeting (#1)
Academic Meeting-1: Society of Molecular Biology and Evolution (SMBE)
Academic Meeting / Research Meeting (#2)
Academic Meeting-2: Society of Evolutional Studies, Japan
Academic Meeting / Research Meeting (#3)
Academic Meeting-3: Genetics Society of Japan
Academic Meeting / Research Meeting (#4)
Academic Meeting-4: Molecular Biology Society of Japan
Academic Meeting / Research Meeting (#5)
Academic Meeting-5: Primate Society of Japan

Research History [1997] (#4)
Papers-4: (1)Shimada MK, Shotake T: Genetic variation of blood proteins within and between local populations of grivet monkey (Cercopithecus aethiops aethiops) in central Ethiopia. Primates 38:399-414, 1997.
Speaker-4: (1)Shimada MK: Population Genetics of wild Old World Monkeys: the case of the Grivet Monkey (Cercopithecus aethiops aethiops). The Tri-National meeting on molecular evolution, Munich, Proceedings of the Tri-National Workshop on Molecular Evolution, 1997. Uyenoyama MK, von Haeseler A eds. Proceedings of the Tri-National Workshop on Molecular Evolution. Duke University Publications Group, Durham, NC, pp139-146, 1998.
Research History [1998] (#5)
Books-5: (1)Shimada MK: Population Genetics of Wild Old World Monkeys: The Case of the Grivet Monkey (Cercopithecus aethiops aethiops). In: Uyenoyama MK, von Haeseler A eds. Proceedings of the Tri-National Workshop on Molecular Evolution. Duke University Publications Group, Durham, NC, pp139-146, 1998
Speaker-5: (1)Shimada MK, Shotake T: Genetic diversity of mtDNA in Savanna monkeys (Cercopithecus aethiops). Fukuoka International Symposium of Population Genetics, Fukuoka, Japan., Aug. 19-23, 1998. Program & Abstracts, p.19.
Research History [1999] (#6)
Papers-6: (1)Matsuzawa T, Takemoto H, Hayakawa S, Shimada M: Diecke Forest in Guinea. Pan Africa News 6: 10-11, 1999.
Speaker-6: (1)Shimada MK: A study plan of gene flow between Chimpanzee group at Bossou and others. COE International Symposium: Evolution of the Apes and the Origin of the Human Beings. Nov. 18-20, 1999. Inuyama, Aichi. Program & Abstract p.59.
Award-6: The 5th Takashima Prize, The Japan Association for Nilo-Ethiopia Studies, awarded 1999
Research History [2000] (#7)
Papers-7: (1)Shimada MK, Nozawa K, Miwa N, Shotake T: Blood protein variations in chimpanzees, orangutans, gibbons, and humans. J Anim Genet 28: 3-12, 2000.

(2)Shimada MK: Geographic distribution of mitochondrial DNA variations among grivet (Cercopithecus aethiops aethiops) populations in central Ethiopia. Int J Primatol 21: 113-129, 2000.

(3)Shimada MK: The effect of the male migration on contrasting distribution pattern between nuclear and mitochondrial variation in grivet monkeys (Cercopithecus aethiops aethiops). Nilo-Ethiopian Studies 5-6: 39-45, 2000.

(4)Shimada MK: A Survey of Nimba Mountain, West Africa from three routes: confirmed new habitat and ant-catching wands use of chimpanzees. Pan African News 7: 7-10, 2000.
Speaker-7: (1)Shimada MK, Hayakawa S, Sugiyama Y: Progress report of the ecology and population genetics of wild chimpanzee groups at Bossou and Nimba, West Africa. The 3rd International SAGA Symposium. Inuyama, Nov. 9-10, 2000. Program A-4-1.
Research History [2001] (#8)
Speaker-8: (1)Shimada MK, Kim C-G, Saitou N: Evolutionary analysis of translocational region in hominoid chromosome using genome sequencing comparison., Symposium on Evolutionary genomics: new paradigm of biology in the 21st century, Nov. 4-6, 2001. Atami, Program & Abstracts p. 63.
(2)Kim C-G, Shimada MK, Takahashi A, Fujiyama A, Hayasaka I, Kohara Y, Saitou N: Comparison of Hox A cluster sequences among human, chimpanzee, gorilla, orangutan, and baboon., Symposium on Evolutionary genomics: new paradigm of biology in the 21st century, Nov. 4-6, 2001. Atami, Program & Abstracts p. 69.
(3)Shimada MK, Hayakawa S, Saitou N, Sugiyama Y: Mitochondrial DNA polymorphism in Pan: gene flow in wild population and comparison between captive chimpanzees and bonobos., Hayashibara Forum 2001/The 4th International SAGA symposium. Okayama, Nov.15-17, 2001 Abstracts p.83.
Research History [2002] (#9)
Papers-9: (1)Shimada MK, Terao T, Shotake T: Mitochondrial sequence diversity within a subspecies of savanna monkeys (Cercopithecus aethiops) is similar to that between subspecies. J Hered 93: 9-18, 2002.

(2)Takemura T, Yamashita M, Shimada MK, Ohkura S, Shotake T, Ikeda M, Miura T, Hayami M: High prevalence of simian T-lymphotropic virus type L in wild Ethiopian baboons. J Virol 76: 1642-1648, 2002.
Speaker-9: (1)Shimada MK, Hayakawa S, Saitou N, Sugiyama Y: Maternal gene flow of Chimpanzee population at Bossou and Nimba, West Africa, 19th Congress of the International Primatlogical Society, Aug.4-9, 2002. Beijing, China. Abstracts p.271.
Research History [2003] (#10)
Papers-10: Shinoda K, Udono T, Yoshihara K, Shimada M, Takenaka O: [Molecular identification of subspecies of captive chimpanzees reared in Japan using mitochondrial DNA. PRIMATE RESEARCH. 19: 145-155, 2003. (Japanese / English summary)]
Research History [2004] (#11)
Papers-11: (1)Shimada MK, Hayakawa S, Humle T, Fujita S, Hirata S, Sugiyama Y, Saitou N: Mitochondrial DNA genealogy of chimpanzees in Nimba Mountains and Bossou, West Africa. Am J Primatol 64: 261-275, 2004.

(2)Shimada MK, Inoue-Murayama, M., Ueda, Y., Maejima, M., Murayama, Y., Takenaka, O., Hayasaka, I., Ito, S: Polymorphism in the second intron of dopamine receptor D4 (DRD4) gene in humans and apes. Biochem Biophys Res Commun 316: 1186-1190, 2004.

(3)Ito H, Nara H, Inoue-Murayama M, Shimada MK, Koshimura A, Ueda Y, Kitagawa H, Takeuchi Y, Mori Y, Murayama Y, Morita M, Iwasaki T, Ota K, Tanabe Y, Ito S: Allele frequency distribution of the canine dopamine receptor D4 gene exon III and I in 23 breeds. J Vet Med Sci 66: 815-820, 2004.
Research History [2005] (#12)
Papers-12: (1)Shimada MK, Kim C-G, Kitano T, Ferrell R, Kohara Y, Saitou N: Nucleotide sequence comparison of a chromosome rearrangement on the human chromosome 12 and corresponding ape chromosomes. Cytogenet Genome Res 108: 83-90, 2005.
Speaker-12: (1)Shimada MK, Hey J: History of modern human population structure inferred from the worldwide survey on Xp11.22 sequences. The 74th Annual Meeting of American Association of Physical Anthropologists. Milwaukee, WI, Apr. 5-9, 2005, American Journal of Physical Anthropology Annual Meeting Issue 2005: Supplement 40: 190
*Introduced in Science 308: 490-491.
Other-12: *[Culotta, E: Archaic Gene in Modern People? (News) Science 308: 490-491, 22 April 2005.]
Research History [2006] (#13)
Speaker-13: (1)Shimada MK, Yamaguchi-Kabata Y, Imanishi T, Chakraborty R., Inoko H, Gojobori T: Genome-wide analysis of human microsatellite polymorphisms by integrating human gene and polymorphism databases. The 8th International Meeting of Human Genome Variation and complex Genome Analysis (HGV2006), Sept., 14-16, 2006, Hong Kong, China. Program & Abstracts p.137.
(2)Shimada MK, Hey J: A worldwide survey of 10.1 kb sequences at Xp11.22 indicates gene flow from archaic to modern human. Gordon Research Conference - Molecular Evolution, Feb. 5-10, 2006. Ventura, CA, USA.
Research History [2007] (#14)
Papers-14: (1)Shimada MK, Panchapakesan K, Tishkoff SA, Nato AQJr, Hey J: Divergent Haplotypes and Human History as Revealed in a Worldwide Survey of X-Linked DNA Sequence Variation. Mol. Biol. Evol. 24:687-698, 2007 / Epub 2006.
Speaker-14: (1)Shimada MK, Yamaguchi-Kabata Y, Yamasaki C, Imanishi T, Gojobori T: VaryGene, a new satellite database of annotated human polymorphism in the integrated human transcriptome database H-InvDB. 2007 American Society of Human Genetics (ASHG) Annual Meeting, Oct., 23-27, 2007, San Diego, CA, USA., Abstracts (Poster 2729T) p.510.
Research History [2008] (#15)
Papers-15: (1)Yamaguchi-Kabata Y, Shimada MK, Hayakawa Y, Minoshima S, Chakraborty R, Gojobori T, Imanishi T: Distribution and effects of nonsense polymorphisms in human genes. Plos One, 3: e3393, 2008.

(2)Genome Information Integration Project and H-Invitational 2: The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 36:D793-D799, 2008 / Epub 2007.
Research History [2009] (#16)
Papers-16: (1)Shimada MK, Matsumoto R, Hayakawa Y, Sanbonmatsu R, Gough C, Yamaguchi-Kabata Y, Yamasaki C, Imanishi T, Gojobori T: VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. Nucleic Acids Res 37: D810 - D815, 2009 (doi: 10.1093/nar/gkn79)/ Epub 2008.
(2)Shimada MK, Hayakawa S, Fujita S, Sugiyama Y, Saitou N: Skewed Matrilineal Genetic Composition in a Small Wild Chimpanzee Community. Folia Primatol 80: 19-32, 2009 (doi: 10.1159/000181187) / Epub 2008.
Research History [2010] (#17)
Papers-17: 1.Shimada MK, Hayakawa Y, Takeda J-i, Imanishi T, Gojobori T: A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing. BMC Evol Biol, 10:122, 2010.
Speaker-17: (1)Shimada MK: Wild chimpanzees in fragmented habitat: diversity in genetics and behavior. International 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), Nagoya, Japan, Jul. 31-Aug.3, 2010, Program & Abstracts p37.[Invited]
(2)Shimada MK, Uchiyama I, Mayeda A: Different mechanisms to splice micro-introns in Eukaryotes. Annual Meeting of the Society for Molecular Biology and Evolution (SMBE2010), Jul. 4-8, 2010, Lyon, France. P-S22-40.[Poster]
(3)Yamasaki C, Takeda J-i, Habara T, Ogawa M, Shimada M, Mamiya K, Noda A, Sakate R, Murakami K, Imanishi T, Gojobori T: H-InvDB: a comprehensive annotation resource for human transcriptome. 14th Human Genome Meeting 2010, May, 18 -21, 2010, Le Corum, France.
(4)Shimada MK, Haraguchi N, Mayeda A: Human transcript database search showed existence of extremely short introns. The Conference of the International Society for Biocuration (Biocuration 2010), Oct. 11-14, 2010, Odaiba, Tokyo, Japan. Abstract Book (P15-7) p. 104.
Other-17: Scientific committee member of International Primate Society 2010
Research History [2011] (#18)
Papers-18: Determination of linkage disequilibrium region suggests association of the ancient haplotype, hX with neural functionDetermination of linkage disequilibrium region suggests association of the ancient haplotype, hX with neural function. Shimada MK. Nature Precedings (http://hdl.handle.net/10101/npre.2011.6737.1)
Books-18: Shimada MK: Genetic variation in the chimpanzees of Bossou and Nimba. In: Matsuzawa T, Sugiyama Y eds. The Chimpanzees of Bossou and Nimba: A Cultural Primatology. Springer, Tokyo, Chap. 39, pp.339-345.

Shimada MK: DNA sequencing data. In: Matsuzawa T, Sugiyama Y eds. The Chimpanzees of Bossou and Nimba: A Cultural Primatology. Springer, Tokyo, Append E.
Speaker-18: (1) Shimada MK, Sasaki-Haraguchi N, Mayeda A: Characterization of Evolutionary Conserved Unusually Short Human Introns. Annual Meeting of the Society for Molecular Biology and Evolution (SMBE2011), Jul. 26-30, 2011, Kyoto, Japan. P1-128.
(2) Shimada MK, Sasaki-Haraguchi N, Mayeda A: Identification and Characterization of Unusually Small Introns, Termed Micro-introns, in the Human Genomes. The 16th Annual Meeting of the RNA Society and The RNA Society of Japan 13th Annual Meeting, Jun 14-18, 2011, Kyoto, Japan. Program & Abstracts (Oral Abstracts) #41.
Research History [2012] (#19)
Papers-19: (1)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: Prediction of protein-destabilizing polymorphisms by manual curation with protein structure. Plos One, 7(11) e50445.
(2)Shimada MK: Survival for All: Let’s Share Benefits and Hardships. Int J Evol 1:1, doi: 10.4172/ievj.1000e103, 2012 [Editorial].
(3)Sasaki-Haraguchi N, Shimada MK, Mayeda A: Mechanistic insights into human pre-mRNA splicing of human ultra-short introns: potential unusual mechanism identifies G-rich introns. Biochem Biophys Res Commun 423: 289-294, 2012.
Books-19: 1. Shimada MK: Unusual ancient haplotypes in modern human probe for archaic hominin admixture. In: Akazawa T et al. eds. RNMH Project 2010-2014. RNMH Project Series No. 001 pp62-63, RNMH Project Group, Tokyo, 2012
Research History [2013] (#20)
Speaker-20: Origin and function of ancient haplotypes found in modern humans Replacement of Neanderthals by Modern Humans (RNMH): Testing Evolutionary Models of Learning. In M. Yoneda (ed) Proceedings of the 5th Conference on RNMH. No.6: 120-121.
Research History [2014] (#21)
Other-21: Shimada MK: An attempt to predict the functional haplotype differences between archaic and modern humans. In: Saito Ho-on Kai Museum. Research Bulletin No.78, Saito Ho-on Kai Foundation, Sendai, pp77-85, 2014.
Research History [2015] (#22)
Papers-22: Shimada MK, Sasaki-Haraguchi N, Mayeda A: Identification and Validation of Evolutionarily Conserved Unusually Short Pre-mRNA Introns in the Human Genome. Int J Mol Sci 16: 10376-10388, 2015.
http://www.mdpi.com/1422-0067/16/5/10376
Speaker-22: Shimada MK, Sasaki-Haraguchi N, Mayeda A: Ultra-short G-rich introns with completely inefficient 5’ and 3’ splice sites are splied in vivo, but how? 2015 Cold Spring Harbor Laboratory Meeting “Eukaryotic mRNA processing”, Aug. 18-22, 2015, Cold Spring Harbor, NY.

Thu Aug 6 18:16:58 JST 2015

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