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Publication list

  1. Taira J*, Yoshida K, Takemoto M, Hanada K, Sakamoto H. Dephosphorylation of clustered phosphoserine residues in human Grb14 by protein phosphatase 1 and its effect on insulin receptor complex formation. J. Peptide Science in press
  2. Mega R, Abe F, Kim JS, Tsuboi Y, Tanaka K, Kobayashi H, Sakata Y, Hanada K, Tsujimoto H, Kikuchi J, Cutler SR, Okamoto M. Tuning water-use efficiency and drought tolerance in wheat using abscisic acid receptors. Nature Plants. 2019 5(2):153-159.[PUBMED] *Press Release (Japansese)
  3. Naito T, Yasunaga JI, Mitobe Y, Shirai K, Sejima H, Ushirogawa H, Tanaka Y, Nakamura T, Hanada K, Fujii M, Matsuoka M, Saito M. Distinct gene expression signatures induced by viral transactivators of different HTLV-1 subgroups that confer a different risk of HAM/TSP. Retrovirology. 2018 15(1):72.[PUBMED]
  4. Nakaminami K, Okamoto M, Higuchi-Takeuchi M, Yoshizumi T, Yamaguchi Y, Fukao Y, Shimizu M, Ohashi C, Tanaka M, Matsui M, Shinozaki K, Seki M, Hanada K. AtPep3 is a hormone-like peptide that plays a role in the salinity stress tolerance of plants. Proc Natl Acad Sci U S A. 115 (22), 5810-5815 [PUBMED]
    *Press Release (Japanese)
  5. Edet OU, Kim JS, Okamoto M, Hanada K, Takeda T, Kishii M, Gorafi YSA, Tsujimoto H. Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers. BMC Genet. 2018 19 (1), 18. [PUBMED]
  6. Hanada K., Tezuka A., Nozawa M., Suzuki Y., Sugano S., Nagano A. J., Ito M., Morinaga S-I. Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis. DNA Research 25 (3), 327-339 [PUBMED].
  7. Ushijima T, Hanada K, Gotoh E, Yamori W, Kodama Y, Tanaka H, Kusano M, Fukushima A, Tokizawa M, Yamamoto YY, Tada Y, Suzuki S, Matsushita T. Light controls protein localization through phytochrome-mediated alternative promoter selection. Cell 2017 30;171(6):1316-1325.e12. [PUBMED]
    *Press Release (Japanese) Nature Review Genetis (Research Highlight)
  8. Shirai K., Matsuda F., Nakabayashi R., Okamoto M., Tanaka M., Fujimoto A., Shimizu M., Shinozaki K., Seki M., Saito K., Hanada K. A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana Accessions. Mol. Bio. Evo. 2017 34, 12:3111-3122.[PUBMED]
    *Press Release (Japanese) (English)
  9. Kohzuma K, Chiba M, Nagano S, Anai T, Ueda M, Oguchi R, Shirai K, Hanada K, Hikosaka K, Fujii N. Mutant selection in the self-incompatible plant radish (Raphanus sativus L. var. sativus) using two-step TILLING. Breed Sci. 2017 67(3):268-276. [PUBMED]
  10. Rasheed S., Bashir K, Nakaminami K, Hanada K, Matsui A, Seki M. Drought stress differentially regulates the expression of small open reading frames (sORFs) in Arabidopsis roots and shoots. Plant Signal Behav. 2016 11:e1215792. [PUBMED]
  11. Bunsupa S, Hanada K, Maruyama A, Aoyagi K, Komatsu K, Ueno H, Yamashita M, Sasaki R, Oikawa A, Saito K, Yamazaki M. Molecular Evolution and Functional Characterization of a Bifunctional Decarboxylase Involved in Lycopodium Alkaloid Biosynthesis.Plant Physiol. 2016 171(4):2432-2444 [PUBMED]
    *Press Release (Japanese)
  12. Tsugea, T, Harimotoa Y, Hanada K, ,Akagic Y, Kodama M, Akimitsud K, Yamamoto M. Evolution of pathogenicity controlled by small, dispensable chromosomes in Alternaria alternata pathogens. Physiological and Molecular Plant Pathology 2016, 95: 27–31 [link]
  13. Oguchi R, Ozaki H, Hanada K, Hikosaka K. What plant trait explains the variations in relative growth rate and in its response to the elevated CO2 concentration among Arabidopsis thaliana ecotypes derived from a variety of habitats? Oecologia 2016 180: 865-76. [PUBMED]
  14. Sugawara S., Mashiguchi K, Tanaka K, Hishiyama S, Sakai T, Hanada K, Kinoshita -Tsujimura K, Yu H, Dai X, Takebayashi Y, Takeda -Kamiya N, Kakimoto T, Kawaide H, Natsume M, Estelle M, Zhao Y, Hayashi KI, Kamiya Y and Kasahara H. Distinct transport characteristics of indole-3-acetic acid and phenylacetic acid, two naturally occurring auxins in plants.  Plant Cell Physiology 2015, 56:1641-1654. [PUBMED]
    *Press Release (Japanese)
  15. Kubota S., Iwasaki T., Hanada K., Nagano A., Fujiyama A., Toyoda T., Sugano S., Suzuki Y., Hikosaka K., Ito M., Morinaka S-I. A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species. PLoS Genet. 2015 14, 11(7):e1005361 [PUBMED]
  16. Shikata H[e], Hanada K[e], Ushijima T, Nakashima M, Suzuki Y, Matsushita T* [e] equal contribution Phytochrome controls alternative splicing to mediate light responses in Arabidopsis. Proc Natl Acad Sci U S A. 2014 30;111:18781-18786. [PUBMED]
  17. Bashir K, Hanada K, Shimizu M, Seki M, Nakanishi H and Nishizawa NK*. Transcriptomic analysis of rice in response to iron deficiency and excess. Rice. 2014. 7:18 [Link]
  18. Okamoto M, Higuchi-Takeuchi M, Shimizu M, Shinozaki K, Hanada K*. Substantial expression of novel small open reading frames in Oryza sativa. Plant Signaling & Behavior 9:e27848, 2014. [PUBMED]
  19. Lyons R, Iwase A, Gänsewig T, Sherstnev A, Duc C, Barton GJ, Hanada K, Higuchi-Takeuchi M, Matsui M, Sugimoto K, Kazan K, Simpson GG, Shirasu K. The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation. Scientific Reports. 3, 2866, 2013.[PUBMED]
  20. Hanada K[e]*, Higuchi-Takeuchi M[e], Okamoto M, Yoshizumi T, Shimizu M, Nakaminami K, Nishi R, Ohashi C, Iida K, Tanaka M, Horii Y, Kawashima M, Matsui K, Toyoda T, Shinozaki K, Seki M, Matsui M.[e] equal contribution. Small open reading frames associated with morphogenesis are hidden in plant genomes. Proc Natl Acad Sci U S A. 110. 2395-2400. 2013. [PUBMED *Press Release (English, Japanese)
    *This paper is introduced in RIKEN RISEARCH (2013, May) (English, Japanese)
  21. Kawaguchi S, Iida K, Harada E, Hanada K, Matsui A, Okamoto M, Shinozaki K, Seki M, and ToyodaT.
    Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads.Bioinformatics (2012) 28:929-937 [PUBMED]
  22. Endo A[e], Tatematsu K[e], Hanada K[e], Duermeyer L, Okamoto M, Yonekura-Sakakibara K, Saito K, Toyoda T, Kawakami N, Kamiya Y, Seki M, Nambara E. equal contribution.
    Tissue-specific Transcriptome Analysis Reveals Cell Wall Metabolism, Flavonol Biosynthesis, and Defense Responses are Activated in the Endosperm of Germinating Arabidopsis thaliana Seeds. Plant Cell Physiol. Plant Cell Physiol (2012) 53: 16-27. [PUBMED]
  23. Yonekura-Sakakibara K, Fukushima A, Nakabayashi R, Hanada K, Matsuda F, Sugawara S, Inoue E, Kuromori T, Ito T, Shinozaki K, Wangwattana B, Yamazaki M, Saito K.
    Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana. Plant J. 2012 69(1):154-167. [PUBMED]
  24. Hanada K, Hase T, Toyoda T, Shinozaki K and Okamoto M.
    Origin and evolution of genes related to ABA metabolism and its signaling pathways. Journal of Plant Research 2011 124:455-65. [PUBMED]
  25. Iida K, Kawaguchi S, Kobayashi N, Yoshida Y, Ishii M, Harada E, Hanada K, Matsui A, Okamoto M, Ishida J, Tanaka M, Morosawa T, Seki M, Toyoda T.
    ARTADE2DB: Improved Statistical Inferences for Arabidopsis Gene Functions and Structure Predictions by Dynamic-Structure-Based Dynamic Expression (DSDE) Analyses.Plant Cell Physiol. 2011. 52: 254-264. [PUBMED]
  26. Yonekura-Sakakibara K and Hanada K.
    An evolutionary view of functional diversity in family 1 glycosyltransferases. The Plant Journal. 2011. 66: 182-193 [PUBMED].
  27. Hanada K[e], Sawada Y[e], Kuromori T, Klausnitzer R, Saito K, Toyoda T, Shinozaki K, Li WH and Hirai M. equal contribution.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana. Mol Biol Evo. 2011, 28(1): 377-382. [PUBMED]
    *Press Release (English, Japanese)
    *This paper is introduced in RIKEN RISEARCH (2010, Oct) (English, Japanese)
  28. Hirai MY, Sawada Y, Kanaya S, Kuromori T, Kobayashi M, Klausnitzer R, Hanada K, Akiyama K, Sakurai T, Saito K, Shinozaki K.
    Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scale bioresources. J Plant Res. 2010 123:291-298. [PUBMED]
  29. Hanada K, Kuromori T, Myouga F, Toyoda T, Shinozaki K.
    Increased expression and protein divergence in duplicate genes is associated with morphological diversification. PLoS Genet. 2009 5:e1000781 [PUBMED]
    *Interview by JST science news (movie)
    *Press Release (English, Japanese)
    *This paper is introduced in RIKEN RESEARCH (2010, Feb) (English, Japanese)
  30. Hanada K, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu SH.
    sORF finder: a program package to identify small open reading frames(sORFs) with high coding potential.Bioinformatics.2010 Feb 1;26(3):399-400 [PUBMED]
  31. Hanada K[e], Kuromori T[e], Myouga F, Toyoda T, Li WH and Shinozaki K. [e] :equal contribution.
    Evolutionary Persistence of Functional Compensation by Duplicate Genes in Arabidopsis.Genome Biology and Evolution. 2009. 2009:409-414. [PUBMED]
    *This paper is introduced in RIKEN RESEARCH (2010, Feb) (English, Japanese)
    *This paper is introduced in RIKEN RISEARCH (2010, Oct) (English, Japanese)
  32. Makita Y, Kobayashi N, Mochizuki Y, Yoshida Y, Asano S, Heida N, Deshpande M, Bhatia R, Matsushima A, Ishii M, Kawaguchi S, Iida K, Hanada K, Kuromori T, Seki M, Shinozaki K, Toyoda T.
    PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants. Plant Cell Physiol. 2009 50:1249-1259. [PUBMED]
  33. Lehti-Shiu MD, Zou C, Hanada K, Shiu SH.
    Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. Plant Physiol. 2009 150:12-26. [PUBMED]
  34. Kurihara Y, Matsui A, Hanada K, Kawashima M, Ishida J, Morosawa T, Tanaka M, Kaminuma E, Mochizuki Y, Matsushima A, Toyoda T, Shinozaki K, Seki M.
    Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis. Proc Natl Acad Sci U S A. 2009 17, 106:2453-2458. [PUBMED]
    *This paper is selected by Faculty1000
  35. Hanada K[e], Vallejo V[e], Nobuta, K, Slotkin K, Lisch D, Meyers BC, Shiu SH, Jiang N. [e] :equal contribution.
    Functional role of Pack-MULEs in rice inferred from purifying selection and expression profile. Plant CELL 2009 21:25-38. [PUBMED]
    *My profile is introduced in Plant CELL
    *This paper is introduced by Dr. Eckardt in Plant CELL (in Brief)
  36. Hanada K, Zou C, D-Li-Shi M, Shinozaki K, Shiu SH.
    Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli. Plant Physiology. 2008 148(2):993-1003. [PUBMED]
  37. Genome Information Integration Project And H-Invitational 2 (138 co-authors).
    The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res. 2008 36:D793-9. [PUBMED]
  38. Rensing SA,... Hanada K, et al. (70 co-authors).
    The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants. Science 2008 319:64-69. [PUBMED]
  39. Matsuya A, ... Hanada K, et al (35 co-authors).
    Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. Nucleic Acids Res. 2008 36:D787-92.[PUBMED
  40. Gingerich DJ, Hanada K, Shiu SH, Vierstra RD.
    Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice. Plant Cell. 2007 :2329-2348. [PUBMED]
  41. Tanaka Y, Hanada K, Hanabusa H, Kurbanov F, Gojobori T, Mizokami M.
    Increasing Genetic Diversity of Hepatitis C Virus in Hemophiliacs with Human Immunodeficiency Virus Coinfection. Journal of General Virology. 2007. 88:2513-2519. [PUBMED]
  42. Hanada K, Shiu SH, Li WH.
    The Nonsynonymous/Synonymous Substitution Rate Ratio versus the Radical/Conservative Replacement Rate Ratio in the Evolution of Mammalian Genes. Mol Biol Evol. 2007 24:2235-2241. [PUBMED]
  43. Kubota R, Hanada K, Furukawa Y, Arimura K, Osame M, Gojobori T, and Izumo S.
    Genetic stability of human T lymphotropic virus type I despite antiviral pressures by cytotoxic T lymphocytes. Journal of Immunology 2007 178:5966-5972. [PUBMED]
  44. Hanada K, Zhang, X, Borevitz, J. O., Li, W.-H., and Shiu, S.-H.
    A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana Genome are transcribed and/or under purifying selection. Genome Research 2007 17:632-640. [PUBMED]
    This paper is selected by Faculty1000
  45. Hanada K, Tanaka Y, Mizokami M, Gojobori T and HJ Alter.
    A reduction in selective immune pressure during the course of chronic hepatitis C correlates with diminished biochemical evidence of hepatic inflammation. Virology 2007 361:27-33. [PUBMED]
  46. Hanada K, Gojobori T, Li WH.
    Radical Amino Acid Change versus Positive Selection in the Evolution of Viral Envelope Proteins. Gene. 2006 385:83-88. [PUBMED]
  47. Kiss I, Sami L, Kecskemite S, Hanada K.
    Genetic variation of the prevailing porcine respiratory and reproductive syndrome viruses occurring on a pig farm upon vaccination. Arch Virol. 2006 151:2269-2276. [PUBMED]
  48. Hanada K, Suzuki Y, Nakane T, Hirose O and Gojobori T.
    The origin and evolution of porcine reproductive and respiratory syndrome viruses Mol Biol Evol. 2005 22, 1024-1031. [PUBMED]
  49. Tanaka Y, Hanada K, Orito E, Akahane Y, Chayama K, Yoshizawa H, Sata M, Ohta N, Miyakawa Y, Gojobori T, Mizokami M.
    Molecular evolutionary analyses implicate injection treatment for schistosomiasis in the initial hepatitis C epidemics in Japan. J Hepatol. 2005 42:47-53. [PUBMED]
  50. Mizokami M, Gojobori T, Hanada K.
    Molecular evolutionary analysis of hepatitis C virus--detection of positive selective sites Nippon Rinsho. 2004 62:76-80. Review. [PUBMED]
  51. Hanada K., Gojobori T.
    Reorganization of Genome. Molecular Medicine 2004 41:101-109. Review
  52. Imanishi T, ..., Hanada K, et al. (156 co-authors).
    Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biol. 2004 2(6):e162. [PUBMED]
  53. Hanada K, Suzuki Y, Gojobori T.
    A Large Variation in the Rates of Synonymous Substitution for RNA Viruses and Its Relationship to a Diversity of Viral Infection and Transmission Modes. Mol Biol Evol. 2004 21, 1074-1080. [PUBMED]
  54. Saito M, Hanada K, Kodama D, Asquith B, Izumo S, Usuku K, Gojobori T, Bangham CR, Osame M.
    Naturally occurring mutations of HTLV-1 proviral genome within HAM/TSP patients and asymptomatic carriers; Relationship between proviral load, host genotype and disease state. AIDS RESEARCH AND HUMAN RETROVIRUSES 2003 19, S60-S60
  55. Pignatelli S, Dal Monte P, Rossini G, Chou S, Gojobori T, Hanada K, Guo JJ, Rawlinson W, Britt W, Mach M, Landini MP.
    Human cytomegalovirus glycoprotein N (gpUL73-gN) genomic variants: identification of a novel subgroup, geographical distribution and evidence of positive selective pressure. J Gen Virol. 2003 84, 647-655. [PUBMED]
  56. Tanaka Y, Hanada K, Mizokami M, Yeo AE, Shih JW, Gojobori T, Alter HJ.
    A comparison of the molecular clock of hepatitis C virus in the United States and Japan predicts that hepatocellular carcinoma incidence in the United States will increase over the next two decades. Proc Natl Acad Sci U S A. 2002 26, 15584-15689. [PUBMED]
(著者)
・ 著者多数(花田耕介含む)
進化学時点、共立出版、 2012年04月
・花田 耕介, 川口 修治, 豊田 哲郎, 篠崎 一雄
mRNAの転写活性を示すncRNA遺伝子の網羅的な探索 日本化学会情報化学部会誌 Vol. 26 (2008) , No. 3 September [pdf]

・花田 耕介・五條堀 孝
バイオディバーシティシリーズ第4巻 菌類の多様性と系統(地衣類、細菌、ウイルスを含む)の「ウイルスの多様性と分類」の章、P.369-395 昇華房 2005.
(その他)
日刊工業(理研最前線)にて研究紹介の記事、2010年、12月 ・花田 耕介 “生命情報学キーノート“E章 配列類似性の基準による「データベースの配列検索」の日本訳、P. 63-88 Springer 2003.
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