論文（2012年以降）
  1. Tanaka KM, Takahashi K, Rice G, Rebeiz M, Kamimura Y, Takahashi A (2022) Trichomes on female reproductive tract: rapid diversification and underlying gene regulatory network in Drosophila suzukii and its related species. bioRxiv.
  2. McQueen EW, Afkhami M, Atallah J, Belote JM, Gompel N, Heifetz Y, Kamimura Y, Kornhaeuser SC, Masly JP, O’Grady P, Peláez J, Rebeiz M, Rice G, Sánchez-Herrero E, Nunes MDS, Rampasso AS, Schnakenberg SL, Siegal ML, Takahashi A, Tanaka KM, Turetzek N, Zelinger E, Courtier-Orgogozo V, Toda MJ, Wolfner MF, Yassin A (2022) A standardized nomenclature and atlas of the female terminalia of Drosophila melanogaster. Fly (in press).
  3. Akiyama N, Sato S, Tanaka KM, Sakai T, Takahashi A (2022) The role of the epidermis enhancer element in positive and negative transcriptional regulation of ebony in Drosophila melanogaster. G3 12: jkac010.
  4. Nozawa M, Minakuchi Y, Satomura K, Kondo S, Toyoda A, Tamura K (2021) Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila. Genome Res. 31:2069–2079.
  5. Fukutomi Y, Koshikawa S (2021) Mechanism of color pattern formation in insects. In: Hashimoto H, Goda M, Futahashi R, Kelsh R, Akiyama T (eds) Pigments, pigment cells and pigment patterns.
  6. Kim BY, Wang JR, Miller DE, Barmina O, Delaney E, Thompson A, Comeault AA, Peede D, D’Agostino ERR, Pelaez J, Aguilar JM, Haji D, Matsunaga T, Armstrong EE, Zych M, Ogawa Y, Stamenković-Radak M, Jelić M, Savić Veselinović M, Tanasković M, Erić P, Gao J, Katoh TK, Toda M, Watabe H, Watada M, Davis J, Moyle L, Manoli G, Bertolini E, Košťál V, Hawley RS, Takahashi A, Jones CD, Price DK, Whiteman N, Kopp A, Matute DR, Petrov DA (2021) Highly contiguous assemblies of 101 drosophilid genomes. eLife 10: e66405.
  7. Sato A, Tanaka M K, Yew J Y and Takahashi A (2021) Drosophila suzukii avoidance of microbes in oviposition choice. Roy. Soc. open sci. 8: 201601.
  8. Tao Q, Tamura K, S Kumar S (2021) Efficient Methods for Dating Evolutionary Divergences. The Molecular Evolutionary Clock, 197-219.
  9. Kumar S, Chroni A, Tamura K, Sanderford M, Oladeinde O, Aly V, Vu T, Miura S (2020) PathFinder: Bayesian inference of clone migration histories in cancer. Bioinformatics 36: i675-i683.
  10. Stecher G, Tamura K, Kumar S (2020) Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Mol. Biol. Evol. 37: 1237–1239.
  11. Hagen JFD, Mendes CC, Booth SR, Jimenez JF, Tanaka KM, Franke FA, Baudouin-Gonzalez L, Ridgway AM, Arif S, Nunes MDS, McGregor AP (2020) Unravelling the genetic basis for the rapid diversification of male genitalia between Drosophila species. Mol. Biol. Evol. 38:437–448.
  12. Miyazaki K, Watanabe H, Yoshikawa G, Chen K, Hidaka R, Aitani Y, Osawa K, Takeda R, Ochi Y, Tani-ichi S, Uehata T, Takeuchi O, Ikuta K, Ogawa S, Kondoh G, Lin YC, Ogata H, Miyazaki M (2020) The transcription factor E2A activates multiple enhancers that drive Rag expression in developing T and B cells. Science Immunology 5: eabb1455.
  13. Massey JH, Akiyam N, Bien T, Dreisewerd K, Wittkopp PJ, Yew JY, Takahashi A (2019) Pleiotropic effects of ebony and tan on pigmentation and cuticular hydrocarbon composition in Drosophila melanogaster. Front. Physiol. 538090.
  14. Moriguchi N, Uchiyama K, Miyagi R, Moritsuka E, Takahashi A, Tamura K, Tsumura Y, Teshima KM, Tachida H, Kusumi J (2019) Inferring the demographic history of Japanese cedar, Cryptomeria japonica, using amplicon sequencing. Heredity (in press)
  15. Tao Q, Tamura K, Battistuzzi FU, Kumar S (2019) A machine learning method for detecting autocorrelation of evolutionary rates in large phylogenies. Mol. Biol. Evol. 36:811–824.
  16. Battistuzzi FU, Tao Q, Jones L, Tamura K, Kumar S (2018) RelTime relaxes the strict molecular clock throughout the phylogeny. Genome Biol. Evol. 10:1631-1636 2.
  17. Patel R, Scheinfeldt LB, Sanderford MD, Lanham TR, Tamura K, Platt A, Glicksberg BS, Xu K, Dudley JT, Kumar S (2018) Adaptive landscape of protein variation in human exomes. Mol. Biol. Evol. 35:2015-2025.
  18. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35:1547-1549.
  19. Tamura K, Tao Q, Kumar S (2018) Theoretical foundation of the RelTime method for estimating divergence times from variable evolutionary rates. Mol. Biol. Evol. 35:1770-1782
  20. Muto L, Kamimura Y, Tanaka KM, Takahashi A (2018) An innovative ovipositor for niche exploitation impacts genital coevolution between sexes in a fruit-damaging Drosophila. Proc. Royal Soc. B. 285:20181635
  21. Tanaka KM, Kamimura Y, Takahashi A (2018) Mechanical incompatibility caused by modifications of multiple male genital structures using genomic introgression in Drosophila. Evolution 72 (11), 2406-2418.
  22. Yuyama I, Ishikawa M, Nozawa M, Yoshida MA, Ikeo K (2018) Transcriptomic changes with increasing algal symbiont reveal the detailed process underlying establishment of coral-algal symbiosis. Sci. Rep. 8:16802.
  23. Matsunami M, Nozawa M, Suzuki R, Toga K, Masuoka Y, Yamaguchi K, Maekawa K, Shigenobu S, Miura T (2018) Caste-specific microRNA expression in termites: insights into soldier differentiation. Insect Mol. Biol. 28:86-98.
  24. Nozawa M, Ikeo K, Gojobori T (2018) Gene-by-gene or localized dosage compensation on the neo-X chromosome in Drosophila miranda. Genome Biol. Evol. 10:1875-1881.
  25. Sultana Z, Asakura A, Kinjo S, Nozawa M, Nakano T, Ikeo K (2018) Molecular phylogeny of ten intertidal hermit crabs of the genus Pagurus inferred from multiple mitochondrial genes, with special emphasis on evolutionary relationship of Pagurus lanuginosus and Pagurus maculosus. Genetica 146:369-381.
  26. Yamaguchi R, Yamanaka T, Liebhold AM (2019) Consequences of hybridization during the invasion on establishment success. Theor. Ecol. 1-9.
  27. Yamaguchi R, Suefuji S, Odagiri K, Peggie D, Yata O (2018) A color pattern difference in the fifth instar larva of two subspecies of Faunis menado Hewitson (Lepidoptera, Nymphalidae). Lepido. Sci. 69:67-73.
  28. Booton RD, Yamaguchi R, Iwasa Y (2018) A population model for diapausing multivoltine insects under asymmetric cannibalism. Popul. Ecol. 61:35-44.
  29. Booton R D, Yamaguchi R, Marshall J A R, Childs D Z, Iwasa Y (2018) Interactions between immunotoxicants and parasite stress: implications for host health. J. Theor. Biol. 445:120-127.
  30. Shimmori Y, Kanesaki Y, Nozawa M, Yoshikawa H, Ehira S*. (2018) Transcriptional activation of glycogen catabolism and oxidative pentose phosphate pathway by NrrA facilitates cell survival under nitrogen starvation in the cyanobacterium Synechococcus sp. strain PCC 7002. Plant Cell Physiol. 59:1225-1233.
  31. Hanada K*, Tezuka A, Nozawa M, Suzuki Y, Sugano S, Nagano AJ, Ito M, Morinaga S-I. (2018) Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis. DNA Res. 25:327-339.
  32. Noyszewski AK，Liu YC，Tamura K，Smith AG. (2017) Polymorphism and structure of style–specific arabinogalactan proteins as determinants of pollen tube growth in Nicotiana. BMC Evol. Biol. 17:186.
  33. Loh SYM，Ogawa Y，Kawana S，Tamura K，Lee HK. (2017) Semi-automated quantitative Drosophila wings measurements. BMC Bioinformatics 18:319.
  34. Osada N, Miyagi R, Takahashi A* (2017) Cis- and trans-regulatory effects on gene expression in a natural population of Drosophila melanogaster. Genetics 206: 2139-2148.
  35. Takada Y, Miyagi R, Takahashi A, Endo T, Osada N* (2017) A generalized linear model for decomposing cis-regulatory, parent-of-origin, and maternal effects on allele-specific gene expression. G3 7: 2227-2234.
  36. Fraimout A, Debat V, Fellous S, Hufbauer RA, Foucaud J, Pudlo P, Marin J-M, Price DK, Cattel J, Chen X, Deprá M, Duyck PF, Guedot C, Kenis M, Kimura MT, Loeb G, Loiseau A, Martinez-Sañudo I, Pascual M, Richmond MP, Shearer P, Singh N, Tamura K, Xuéreb A, Zhang J, Estoup A. (2017) Deciphering the routes of invasion of Drosophila suzukii by means of ABC random forest. Mol. Biol. Evol. 34:980-996.
  37. Igawa T, Nozawa M, Suzuki DG, Reimer JD, Norov AR, Wang Y, Henmi Y, Yasui K*. (2017) Evolutionary history of the extant amphioxus lineage with shallow-branching diversification. Sci. Rep. 7:1157.
  38. Mello B, Tao Q, Tamura K, Kumar S. (2017) Fast and accurate estimates of divergence times from big data. Mol. Biol. Evol. 34:45-50.
  39. Fukushima K, Fang X, Alvarez-Ponce D, Cai H, Carretero-Paulet L, Chen C, Chang T-H, Farr KM, Fujita T, Hiwatashi Y, Hoshi Y, Imai T, Kasahara M, Librado P, Mao L, Mori H, Nishiyama T, Nozawa M, Palfalvi G, Pollard ST, Rozas J, Sanchez-Gracia A, Sankoff D, Shibata TF, Shigenobu S, Sumikawa N, Uzawa T, Xie M, Zheng C, Pollock DD, Albert VA, Li S, Hasebe M*. (2017) Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nature Ecol. Evol. 1:0059.
  40. Kudo A, Shigenobu S, Kadota K, Nozawa M, Shibata FT, Ishikawa Y, Matsuo T*. (2017) Comparative analysis of the brain transcriptome in a hyper-aggressive fruit fly, Drosophila prolongata. Insect Biochem. Mol. Biol. 82:11-20.
  41. Okamiya H*, Igawa T, Nozawa M, Sumida M, Kusano T. (2017) Development and Characterization of 23 Microsatellite Markers for the Montane Brown Frog (Rana ornativentris) Curr. Herpetol. 36:63-68.
  42. Kumar S, Stecher, G, Tamura K. (2016) MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol. 33:1870-1874.
  43. Sunaga S, Akiyama N, Miyagi R and Takahashi A*. (2016) Factors underlying natural variation in body pigmentation of Drosophila melanogaster. Genes Genet. Syst. 91: 127-137.
  44. Yoshida K, Miyagi R, Mori S, Takahashi A, Makino T, Toyoda A, Fujiyama A and Kitano J* (2016) Whole genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback. Ecol. Evol. 6: 2190-2204.
  45. Nozawa M*, Onizuka K, Fujimi M, Ikeo K, Gojobori T. (2016) Accelerated pseudogenization on the neo-X chromosome in Drosophila miranda. Nat. Commun. 7:13659.
  46. Komaki S, Lin S-M, Nozawa M, Oumi S, Sumida M, Igawa T*. (2016) Fine-scale demographic processes resulting from multiple overseas colonization events of the Japanese stream tree frog, Buergeria japonica. J Biogeogr. 12922.
  47. Ishikawa M, Shimizu H, Nozawa M, Ikeo K, Gojobori T*. (2016) Two-Step Evolution of Endosymbiosis between Hydra and Algae. Mol. Phyl. Evol. 103:19-25.
  48. Ishikawa M, Yuyama I, Shimizu H, Nozawa M, Ikeo K, Gojobori T*. (2016) Different endosymbiotic interactions inof two hydra species reflect the evolutionary history of endosymbiosis. Genome Biol. Evol. 8:2155-2163.
  49. Nozawa M*, Fujimi M, Iwamoto C, Onizuka K, Fukuda N, Ikeo K, Gojobori T. (2016) Evolutionary transitions of microRNA-target pairs. Genome Biol. Evol. 8:1621-1633.
  50. Koga H*, Fujitani H, Morino Y, Miyamoto N, Tsuchimoto J, Shibata TF, Nozawa M, Shigenobu S, Ogura A, Tachibana K, Kiyomoto M, Amemiya S, Wada H. (2016) Experimental approach reveals the role of alx1 in the evolution of the echinoderm larval skeleton. PLOS One 11:e0149067.
  51. Nozawa M*, Kinjo S. (2016) Origin and evolution of non-coding RNAs. Encyclopedia for Evol. Biol. 3:130-135.
  52. Kojima KK, Seto Y and Fujiwara H (2016) The Wide Distribution and Change of Target Specificity of R2 Non-LTR Retrotransposons in Animals. PLoS ONE 11:e0163496, 2016
  53. Satomura K, Tamura K. (2016) Ancient male recombination shaped genetic diversity of neo-Y chromosome in Drosophila albomicans. Mol. Biol. Evol. 33:367-374.
  54. Liu L, Tamura K, Sanderford M, Gray VE, Kumar S. A (2016) Molecular Evolutionary Reference for the Human Variome. Mol. Biol. Evol. 33:245-254.
  55. Ohta S, Seto Y, Tamura K, Ishikawa Y, Matsuo T. (2015) Comprehensive identification of odorant-binding protein genes in the seed fly, Delia platura (Diptera: Anthomyiidae). Applied Entomology and Zoology 50:457-463.
  56. Filipski A, Tamura K, Billing-Ross P, Murillo O, Kumar S. (2015) Phylogenetic placement of metagenomic reads using the minimum evolution principle. BMC Genomics 16:1-9.
  57. Miyagi R, Akiyama N, Osada N and Takahashi A*. (2015) Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster. Mol. Ecol. 24: 5829-5841.
  58. Tanaka KM, Takahashi A, Fuse N, and Takano-Shimizu-Kouno T. (2014) A novel cell death gene acts to repair patterning defects in Drosophila melanogaster. Genetics 197: 739-742.
  59. Filipski A, Murillo O, Freydenzon A, Tamura K, Kumar S. (2014) Prospects for building large timetrees using molecular data with incomplete gene coverage among species. Mol. Biol. Evol. 31:2542-2550.
  60. Takezaki N, Nei M, Tamura K. (2014) POPTREEW: Web version of POPTREE for constructing population trees from allele frequency data and computing some other quantities. Mol. Biol. Evol. 31:1622-1624.
  61. Stecher G, Liu L, Sanderford M, Peterson P, Tamura K, Kumar S. (2014) MEGA-MD: Molecular Evolutionary Genetics Analysis software with mutational diagnosis of amino acid variation. Bioinformatics 30:1305-1307.
  62. Ohta S, Seto Y, Tamura K, Ishikawa Y, Matsuo T. (2014) Identification of odorant-binding protein genes expressed in the antennae and the legs of the onion fly, Delia antiqua (Diptera: Anthomyiidae). Appl. Entomol. Zool. 49:89-95.
  63. Isobe K, Takahashi A, Tamura K. (2013) Cold tolerance and metabolic rate increased by cold acclimation in Drosophila albomicans from natural populations. Genes Genet. Syst. 88:289-300.
  64. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol. Evol. 30:2725-2729.
  65. Seto Y, Tamura K. (2013) Extensive Differences in Antifungal Immune Response in Two Drosophila Species Revealed by Comparative Transcriptome Analysis. Int. J. Genomics 2013:Article ID 542139.
  66. Takahashi A. (2013) Pigmentation and behavior: potential association through pleiotropic genes in Drosophila. Genes Genet. Syst. 88: 165-174.
  67. Tamura K, Battistuzzi FU, Billing-Ross P, Kumar S. (2012) Estimating Divergence Times in Large Molecular Phylogenies. Proc. Nat. Acad. Sci. USA 109:19333-19338.
  68. Kumar S, Stecher G, Peterson D, Tamura K. (2012) MEGA-CC: Computing Core of Molecular Evolutionary Genetics Analysis program for automated and iterative data analysis. Bioinformatics 28: 2685-2686. 2012.
  69. Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K. (2012) Statistics and Truth in Phylogenomics. Mol Biol. Evol. 29:457-472.
  70. Nishimura A, Ishida Y, Takahashi A, Okamoto H, Sakabe M, Itoh M, Takano-Shimizu T, Ozaki M. (2012) Starvation-induced elevation of taste responsiveness and expression of a sugar taste receptor gene in Drosophila melanogaster. J. Neurogenet. 26: 206-15.
  71. Takahashi A, Fujiwara-Tsujii N, Yamaoka R, Itoh M, Ozaki M, Takano-Shimizu T. (2012) Cuticular hydrocarbon content that affects male mate preference of Drosophila melanogaster from West Africa. Int. J. Evol. Biol. 2012:278903.