Publication list

  1. Shirai K, Sato MP, Nishi R, Seki M, Suzuki Y, Hanada K*. (2021) Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants. Genome Research. 2021. 31(6), 1060-1068. link. *Press Release (Japanese)
  2. Ezoe A, Shirai K, Hanada K*. Degree of functional divergence in duplicates is associated with distinct roles in plant evolution. Molecular Biology and Evolution. 2021. 38 (4), 1447?1459. (link). *Press Release (Japanese)
  3. Higuchi-Takeuchi M, Kondo T, Shimizu M, Kim YW, Shinozaki K, Hanada*. Effect of small coding genes on the circadian rhythms under elevated CO 2 conditions in plants. Plant Molecular Biology. 2020. 104(1), 55-65. (link)
  4. Wang P, Yao S, Kosami KI, Guo T, Li J, Zhang Y, Fukao Y, Kaneko]Kawano Y, Zhang H, She YM, Wang P, Xing W, Hanada K, Liu R, Kawano Y*. Identification of endogenous small peptides involved in rice immunity through transcriptomics]and proteomics]based screening. Plant Biotechnology Journal. 2020. 18(2), 415-428. (link)
  5. Shirai K, Hanada K*. Contribution of Functional Divergence through Copy Number Variations to the Inter-Species and Intra-Species Diversity in Specialized Metabolites. Frontiers in Plant Science. 2019. 10, 1567. (link)
  6. Naito T, Shirai K, Mori K, Muratsu H, Ushirogawa H, Ohniwa RL, Hanada K, Saito M*. Tyr82 amino acid mutation in PB1 polymerase induces an influenza virus mutator phenotype. Journal of Virology. 2019. 93 (22), e00834-19. (link)
  7. Takahashi F*, Hanada K*, Kondo T, Shinozaki K. Hormone-like peptides and small coding genes in plant stress signaling and development. Current Opinion in Plant Biology. 2019. 51, 88-95. (link).
  8. 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. Journal of Peptide Science. 2019. 10, e3207. (link).
  9. 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.(link)
    @*Press Release (Japansese)
  10. 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.(link)
  11. 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. 2018. 115 (22), 5810-5815. (linkj *Press Release (Japanese)
  12. 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 Genetics. 2018. 19 (1), 18. (linkj
  13. 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. 2018. 25 (3), 327-339 (link)
  14. Ushijima T[e], Hanada K[e], Gotoh E, Yamori W, Kodama Y, Tanaka H, Kusano M, Fukushima A, Tokizawa M, Yamamoto YY, Tada Y, Suzuki S, Matsushita T*. [e] equal contribution. Light controls protein localization through phytochrome-mediated alternative promoter selection. Cell. 2017. 171 (6), 1316-1325. (link) *Press Release (Japanese) *Nature Review Genetis (Research Highlight)
  15. 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. Molecular Biology and Evolution. 2017. 34 (12), 3111-3122.(link) *Press Release (Japanese) (English)
  16. 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. Breeding Science. 2017. 67 (3), 268-276. (link)
  17. 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 Signaling & Behavior 2016. 11, e1215792. (link)
  18. 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 Physiology. 2016. 171 (4), 2432-2444 (link) *Press Release (Japanese)
  19. Tsuge T*, Harimoto Y, Hanada K, ,Akagi Y, Kodama M, Akimitsu 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)
  20. 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. 180C865-76. (link)
  21. 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 and Physiology. 2015. 56, 1641-1654. (link) *Press Release (Japanese). This paper is selected PCP award in 2017 prize.
  22. 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 Genetics. 2015. 11(7), e1005361 (link)
  23. 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. (link)
  24. 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. (linkj
  25. 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. 2014. 9, e27848 (link)
  26. 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. 2013. 3(1), 1-10. (link)
  27. 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. 2013. 110, 2395-2400. (link) *Press Release (English, Japanese) *This paper is introduced in RIKEN RISEARCH (2013, May) (English, Japanese)
  28. 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 (link)
  29. 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*. [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 Physiology. Plant Cell and Physiology. 2012. 53, 16-27. (linkj
  30. 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 Journal 2012. 69(1), 154-167. (link)
  31. 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. (link)
  32. 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 and Physiology. 2011. 52, 254-264. (link)
  33. Yonekura-Sakakibara K* and Hanada K. An evolutionary view of functional diversity in family 1 glycosyltransferases. Plant Journal. 2011. 66, 182-193 (link)
  34. Hanada K*, Sawada Y, 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. Molecular Biology and Evolution. 2011. 28(1), 377-382. (link) *Press Release (English, Japanese) *This paper is introduced in RIKEN RISEARCH (2010, Oct) (English, Japanese)
  35. 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. Journal of Plant Research. 2010. 123, 291-298. (link)
  36. Hanada K*, Kuromori T, Myouga F, Toyoda T, Shinozaki K. Increased expression and protein divergence in duplicate genes is associated with morphological diversification. PLoS Genetics 2009. 5, e1000781 (link) *Interview by JST science news (movie) *Press Release (English, Japanese) *This paper is introduced in RIKEN RESEARCH (2010, Feb) (English, Japanese)
  37. 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. 26(3), 399-400 (link)
  38. 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. (link). *This paper is introduced in RIKEN RESEARCH (2010, Feb) (English, Japanese) *This paper is introduced in RIKEN RISEARCH (2010, Oct) (English, Japanese)
  39. 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 and Physiology. 2009. 50, 1249-1259. (link)
  40. Lehti-Shiu MD, Zou C, Hanada K, Shiu SH*. Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes. Plant Physiology. 2009. 150, 12-26. (link)
  41. 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. 106, 2453-2458. (link)
  42. Hanada K, Vallejo V, Nobuta, K, Slotkin K, Lisch D, Meyers BC, Shiu SH, Jiang N*. Functional role of Pack-MULEs in rice inferred from purifying selection and expression profile. Plant CELL. 2009. 21, 25-38. (link)
    *My profile is introduced in Plant CELL *This paper is introduced by Dr. Eckardt in Plant CELL (in Brief)
  43. 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. (link)
  44. 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 Research. 2008. 36, D793-9. ( link)
  45. 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. (link)
  46. 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 Reserch. 2008. 36, D787-92. (link)
  47. 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. 19 (8), 2329-2348. (link)
  48. 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. (link)
  49. 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. Molecular and Biology Evolution. 2007. 24, 2235-2241. (link)
  50. 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. (link)
  51. 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. (link)
  52. 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. ( link)
  53. 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. (link)
  54. 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. Archieve of Virology. 2006. 151, 2269-2276. (link)
  55. Hanada K, Suzuki Y, Nakane T, Hirose O and Gojobori T*. The origin and evolution of porcine reproductive and respiratory syndrome viruses. Molecular Biology and Evolution. 2005. 22, 1024-1031. (link)
  56. 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. Journal of Hepatology. 2005. 42, 47-53. (link)
  57. Imanishi T, ..., Hanada K, et al. (156 co-authors). Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. PLoS Biology. 2004. 2 (6), e162. (link)
  58. 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. Molecular Biology and Evolution. 2004. 21, 1074-1080. (link)
  59. 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. Journal of General Virology. 2003. 84, 647-655. (link)
  60. 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. (link)