Molecular and Chemical Life Science :
Molecular and Network Genomics


Professor MAKINO Takashi
Campus Aobayama campus
Laboratory Evolutionary Genomics
Tel +81-22-795-5585
E-mail tamakino@tohoku.ac.jp
Website https://www.lifesci.tohoku.ac.jp/evolgenomics

I am conducting evolutionary and ecological research focused on genes duplicated in genomes.

Apr. 1993 – Mar. 1997 Department of Bioresources, Faculty of Bioresources, Mie University
Apr. 1997 – Mar. 1993 Master’s program (obtained master’s), Graduate School of Bioagricultural Sciences, Nagoya University
Apr. 1994 – Dec. 2012 Kikkoman Corporation
Jan. 2002 – Mar. 2002 Researcher, Computational Biology Research Center, AIST
Apr. 2002 – Mar. 2005 Doctoral course (obtained doctorate), School of Life Science, Graduate University for Advanced Studies
Apr. 2005 – Jun. 2005 Researcher, National Institute of Genetics
Jul. 2005 – Mar. 2006 International bioinformatics laboratory at a public company
Jul. 2005 – Mar. 2005 Contract Researcher, National Institute of Genetics
Apr. 2006 – Sep. 2006 Researcher, Immunotherapy Division, Shizuoka Cancer Center Research Institute
Oct. 2006 – Jul. 2009 Researcher, Smurfit Institute of Genetics, Trinity college, Ireland
Aug. 2009 – Jan. 2011 Assistant Professor, Ecosystem Adaptability Global COE, Graduate School of Life Sciences, Tohoku University
Feb. 2011 – Mar. 2014 Assistant Professor, Graduate School of Life Sciences, Tohoku University
Feb. 2014 – Apr. 2014 Visiting researcher, Biomedical Centre, Uppsala University
Apr. 2014 – Sep. 2018 Associate Professor, Graduate School of Life Sciences, Tohoku University
Oct. 2018 – present Professor, Graduate School of Life Sciences, Tohoku University
Selected Publications
  • Makino T, Rubin CJ, Carneiro M, Axelsson E, Andersson L and Webster MT. Elevated proportions of deleterious genetic variation in domestic animals and plants. Genome Biology and Evolution. 10(1):276-290, 2018
  • Sekine M and Makino T. Inference of causative genes for Alzheimer’s disease due to dosage imbalance. Molecular Biology and Evolution. 34(9):2396-2407, 2017
  • Tamate CS, Kawata M and Makino T. Contribution of non-ohnologous duplicated genes to high habitat variability in mammals. Molecular Biology and Evolution 31(7):1779-1786, 2014
  • Yoshida K, Makino T, et al. Sex chromosome turnover contributes to genomic divergence between incipient stickleback species. PLOS Genetics. 10(3): e1004223, 2014
  • McLysaght A, Makino T, Grayton H, Tropeano M, Mitchell K, Vassos E, Collier DA. Ohnologs are overrepresented in pathogenic copy number mutations. PNAS. 7;111(1):361-366, 2014
  • Makino T, McLysaght A and Kawata M. Genome-wide deserts for copy number variation in vertebrates. Nature Communications. 4:2283, 2013
  • Cádiz, A, Nagata N, Katabuchi M, Díaz LM, LEchenique-Díaz LM, Akashi HD, Makino T and Kawata M. Relative importance of habitat use, range expansion, and speciation in local species diversity of Anolis lizards in Cuba. Ecosphere. 4:art78, 2013
  • Makanae K, Kintaka R, Makino T, Kitano H and Moriya H. Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method. Genome Research. 23(2):300-311, 2013
  • Makino T and McLysaght A. Positionally-biased gene loss after whole genome duplication: evidence from human, yeast and plant. Genome Research. 22(12):2427-2435, 2012
  • Makino T and Kawata M. Habitat variability correlates with duplicate content of Drosophila genomes, Molecular Biology and Evolution. 29(10):3169-3179, 2012
  • Satake M, Kawata M, McLysaght A and Makino T*. Evolution of vertebrate tissues driven by differential modes of gene duplication. DNA Research. 19(4):305-316, 2012
  • Pessia E, Makino T, Bailly-Bechet M, McLysaght A and Marais GAB. Mammalian X Chromosome Inactivation evolved as a dosage compensation mechanism for dosage-sensitive genes on the X chromosome. PNAS. 109(14), 5144-5145, 2012
  • Tezuka A, Matsushima N, Nemoto Y, Akashi HD, Kawata M and Makino T. Comprehensive Primer Design for Analysis of Population Genetics in Non-Sequenced Organisms. PLoS ONE. 7(2): e32314, 2012
  • Kitano J, Kawagishi Y, Mori S, Peichel CL, Makino T, Kawata M and Kusakabe M. Divergence in Sex Steroid Hormone Signaling between Sympatric Species of Japanese Threespine Stickleback. PLoS ONE. 6(12): e29253, 2011
  • Makino T and McLysaght A. Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proceedings of The National Academy of Sciences. 107(20), 9270-9274, 2010
  • Perez-Bercoff A, Makino T and McLysaght A. Duplicability of self-interacting human genes. BMC Evolutionary Biology. 10:160, 2010
  • Makino T, Knowles DG and McLysaght A. Functional divergence of duplicated genes, In Evolution After Gene Duplication (Katharina Dittmar and David Liberles eds.), 23-30, John Wiley & Sons. 2010
  • Makino T and McLysaght A. The evolution of functional gene clusters in eukaryote genomes. In Evolutionary Biology from Concept to Application II (Pierre Pontarotti eds., Springer), 185-194, 2009
  • Makino T, Hokamp K and McLysaght A. Complex relationship of gene duplication and essentiality. Trends in Genetics. 25(4), 152-155, 2009
  • Makino T and McLysaght A. Evolutionary Analyses of Protein Interaction Networks. In Biological Data Mining in Protein Interaction Networks (Xiao-Li Li and See-Kiong Ng eds., IGI Global, USA), 169-181, 2009
  • Akihito, Fumihito A, Ikeda Y, Aizawa M, Makino T, Umehara Y, Kai Y, Hasegawa M, Nakabo T and Gojobori T. Evolution of Pacific Ocean and the Sea of Japan populations of the gobiid species, Pterogobius elapoides and Pterogobius zonoleucus, based on molecular and morphological analyses. Gene. 427:7-18, 2008
  • Makino T, McLysaght A. Interacting Gene Clusters and the Evolution of the Vertebrate Immune System. Mol Biol Evol. 25:1855-1862, 2008
  • Yamasaki C, et al. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research (Database issue):D793-799, 2008
  • Makino T and Gojobori T. Evolution of protein-protein interaction network, In Genome Dynamics: Gene and protein Evolution (Jean-Nicolas Volff eds.), Vol.3:13-29, S. Karger AG, Basel, 2007
  • Makino T, Suzuki Y, and Gojobori T. Differential evolutionary rates of duplicated genes in protein interaction network. Gene. 385:57-63, 2006
  • Makino T and Gojobori T. The evolutionary rate of a protein is influenced by features of the interacting partners. Mol. Biol. Evol. 23:784-789, 2006
  • Imanishi T, et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biology. 2:856-875, 2004
  • Kimura T, Ito J, Kawano A, Makino T, Kondo H, Karita S, Sakka K, Ohmiya K. Purification, characterization, and molecular cloning of acidophilic xylanase from penicillium sp.40. Bioscience, biotechnology, and biochemistry. 64(6):1230-1237, 2000
  • Kimura T, Makino T, Aburatani T, Kondo H, Karita S, Sakka K, Ohmiya K. Analysis of the Promoter Activity of the Taka-Amylase Gene and the Phosphoglycerate Kinase Gene in a Shoyu-koji Mold Aspergillus oryzae KBN616. Food Science and Technology Research. 6(1):44-47, 2000
Activities in Academic Societies
Society for Molecular Biology and Evolution, The Society of Evolutionary Studies, Japan, The Ecological Society of Japan, The Genetic Society of Japan
Molecular evolution (undergraduate)

Recent Activities

In the evolutionary process, genes are frequently duplicated. Duplicated genes are released from functional constraints and evolve into genes with new functions. However, we have found that there exist genes that rarely evolve regardless of whether they are duplicated. These genes are related to disease. In order to reveal the biological significance of the existence of such duplicated genes, we are engaged in evolutionary analysis utilizing vertebrate genomes. In addition, in order to reveal how the properties of duplicate genes, which could be said to be redundant, influence organismal evolution, we are researching the relationships between ecological characteristics and duplicate genes in animals.

Message to Students

Please contact us if you are interested in evolutionary studies of genes and genomes or life information science analyzed by bioinformatics.