Kobayashi Y, Hirakawa H, Shirasawa K, Nishimura K, Fujii K, Oros R, Almanza GR, Nagatoshi Y, Yasui Y, Fujita Y. (2024) Chromosome-level genome assemblies for two quinoa inbred lines from northern and southern highlands of Altiplano where quinoa originated. Front Plant Sci. 2024 Aug 19;15:1434388. doi: 10.3389/fpls.2024.1434388. eCollection 2024.
Nagasaki H, Shirasawa K, Hoshikawa K, Isobe S, Ezura H, Aoki K, Hirakawa H. (2024) Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum). DNA Res. 2024 Jun 7:dsae016. doi: 10.1093/dnares/dsae016.
Yamano K, Haseda A, Iwabuchi K, Osabe T, Sudo Y, Pachakkil B, Tanaka K, Suzuki Y, Toyoda A, Hirakawa H, Onodera Y. (2024) QTL analysis of femaleness in monoecious spinach and fine mapping of a major QTL using an updated version of chromosome-scale pseudomolecules. PLoS One. 19(2):e0296675. doi: 10.1371/journal.pone.0296675. eCollection 2024.
Ichikawa M, Kato N, Toda E, Kashihara M, Ishida Y, Hiei Y, Isobe SN, Shirasawa K, Hirakawa H, Okamoto T, Komari T. (2023) Whole-genome sequence analysis of mutations in rice plants regenerated from zygotes, mature embryos, and immature embryos. Breed Sci. 2023 Jun;73(3):349-353. doi: 10.1270/jsbbs.22100. Epub 2023 Jun 15.A list item
Yokotani N, Hasegawa Y, Kouzai Y, Hirakawa H, Isobe S. (2023) Transcriptome analysis of tomato plants following salicylic acid-induced immunity against Clavibacter michiganensis ssp. Michiganensis. Plant Biotechnology 40, 1-10.
Shirasawa K, Mishima K, Hirakawa H, Hirao T, Tsubomura M, Nagano S, Iki T, Isobe S, Takahashi M. (2023) Haplotype-resolved de novo genome assemblies of four coniferous tree species. Journal of Forest Research, https://doi.org/10.1080/13416979.2023.2267304.
Ichihara H, Yamada M, Kohara M, Hirakawa H, Ghelfi A, Tamura T, Nakaya A, Nakamura Y, Shirasawa S, Yamashita S, Toda Y, Harada D, Fujishiro T, Komaki A, Fawcett JA, Sugihara E, Tabata S, Isobe SN. (2023) Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species. BMC Plant Biol. 2023 Aug 12;23(1):391. doi: 10.1186/s12870-023-04392-8.
Fawcett JA*, Takeshima R, Kikuchi S, Yazaki E, Katsube-Tanaka T, Dong Y, Li M, Hunt HV, Jones MK, Lister DL, Ohsako T, Ogiso-Tanaka E, Fujii K, Hara T, Matsui K, Mizuno N, Nishimura K, Nakazaki T, Saito H, Takeuchi N, Ueno M, Matsumoto D, Norizuki M, Shirasawa K, Li C*, Hirakawa H*, Ota T*, Yasui Y*. (2023) Genome sequencing reveals the genetic architecture of heterostyly and domestication history of common buckwheat. Nature Plants doi: 10.1038/s41477-023-01474-1
Shirasawa K, Moraga R, Ghelfi A, Hirakawa H, Nagasaki H, Ghamkhar K, Barrett BA, Griffiths AG, Isobe SN. (2023) An improved reference genome for Trifolium subterraneum L. provides insight into molecular diversity and intra-specific phylogeny. Front Plant Sci. 2023 Feb 15;14:1103857. doi: 10.3389/fpls.2023.1103857. eCollection 2023.
Kurotani KI, Hirakawa H, Shirasawa K, Tanizawa Y, Nakamura Y, Isobe S, Notaguchi M. (2023) Genome Sequence and Analysis of Nicotiana benthamiana, the Model Plant for Interactions between Organisms. Plant Cell Physiol. 64(2):248-257. 2023 Feb 9:pcac168. doi: 10.1093/pcp/pcac168. Online ahead of print. PMID: 36755428
Kobayashi Y, Shibata TF, Hirakawa H, Nishiyama T, Yamada A, Hasebe M, Shigenobu S, Kawaguchi M. (2023) The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes. DNA Res. 30:dsac053. doi: 10.1093/dnares/dsac053. Online ahead of print. PMID: 36610744
Hasegawa Y, Watanabe T, Otsuka R, Toné S, Kubota S, Hirakawa H. (2023) Genome assembly and transcriptomic analyses of the repeatedly rejuvenating jellyfish Turritopsis dohrnii. DNA Res. 2023 30(1):dsac047. doi: 10.1093/dnares/dsac047. Online ahead of print. PMID: 36519838
Shirasawa K, Arimoto R, Hirakawa H, Ishimorai M, Ghelfi A, Miyasaka M, Endo M, Kawabata S, Isobe SN. (2023) Chromosome-scale genome assembly of Eustoma grandiflorum, the first complete genome sequence in the genus Eustoma. G3 (Bethesda). 13:jkac329. doi: 10.1093/g3journal/jkac329. Online ahead of print. PMID: 36529465
Rai A, Hirakawa H, Rai M, Shimizu Y, Shirasawa K, Kikuchi S, Seki H, Yamazaki M, Toyoda A, Isobe S, Muranaka T, Saito K. (2022) Chromosome-scale genome assembly of Glycyrrhiza uralensis revealed metabolic gene cluster centred specialized metabolites biosynthesis. DNA Res. 29(6):dsac043. doi: 10.1093/dnares/dsac043. PMID: 36535891
Shirasawa K, Hirakawa H, Azuma A, Taniguchi F, Yamamoto T, Sato A, Andrea G, Isobe SN. (2022) De novo whole-genome assembly in an interspecific hybrid table grape, 'Shine Muscat'. DNA Res. 29:dsac040. doi: 10.1093/dnares/dsac040. Online ahead of print. PMID: 36342351
Sumitomo K, Shirasawa K, Isobe S, Hirakawa H, Harata A, Nakano M, Nakano Y, Yagi M, Hisamatsu T, Yamaguchi H, Taniguchi F. (2022) A genome-wide association and fine-mapping study of white rust resistance in hexaploid chrysanthemum cultivars with a wild diploid reference genome. Hortic Res. 9:uhac170. doi: 10.1093/hr/uhac170. eCollection 2022. PMID: 36324641
Mishima K, Hirakawa H, Iki T, Fukuda Y, Hirao T, Tamura A, Takahashi M. (2022) Comprehensive collection of genes and comparative analysis of full-length transcriptome sequences from Japanese larch (Larix kaempferi) and Kuril larch (Larix gmelinii var. japonica). BMC Plant Biol. 22:470. doi: 10.1186/s12870-022-03862-9. PMID: 36192701
Sekine D, Oku S, Nunome T, Hirakawa H, Tsujimura M, Terachi T, Toyoda A, Shigyo M, Sato S, Tsukazaki H. (2022) Development of a genome-wide marker design workflow for onions and its application in target amplicon sequencing-based genotyping. DNA Res. 29:dsac020. doi: 10.1093/dnares/dsac020. PMID: 36007888
Fukai E, Yoshikawa M, Shah N, Sandal N, Miyao A, Ono S, Hirakawa H, Akyol TY, Umehara Y, Nonomura KI, Stougaard J, Hirochika H, Hayashi M, Sato S, Andersen SU, Okazaki K. (2022) Widespread and transgenerational retrotransposon activation in inter- and intra-species recombinant inbred populations of Lotus japonicus. Plant J. 111, 1397-1410. doi: 10.1111/tpj.15896. PMID: 35792830
H. Ichihara, H. Hirakawa, A. Ghelfi, M. Kohara, M. Yamada, T. Tamura, A. Nakaya, Y. Nakamura, S. Shirasawa, E. Sugihara, S. Tabata, S. Isobe (2022) Plant GARDEN: a portal website for accessing plant genome, DNA marker, and SNP information. Acta Horticulturae (1339) 415-418.
Shirasawa K, Chahota R, Hirakawa H, Nagano S, Nagasaki H, Sharma T, Isobe S. (2021) A chromosome-scale draft genome sequence of horsegram (Macrotyloma uniflorum). Gigabyte, 1. https://doi.org/10.46471/gigabyte.30
Sato T, Niwa R, Ezawa T, Sato S, Hirakawa H, Yoshida S, Cheng W, Tawaraya K. (2021) Tracking an Introduced Arbuscular Mycorrhizal Fungus in Allium fistulosum in a Field Condition With or Without Controlling Indigenous Fungi by Soil Fumigation As Well as Evaluation on Plant Phosphorus and Growth. J. Soil Science and Plant Nutrition. 21, 2781–2790.
Yokotani N, Hasegawa Y, Sato M, Hirakawa H, Kouzai Y, Nishizawa Y, Yamamoto E, Naito Y, Isobe S. (2021) Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis-infected tomatoes: a role of salicylic acid in the host response. BMC Plant Biol. 21:476. doi: 10.1186/s12870-021-03251-8. (Oct 19)
Shirasawa K, Kosugi S, Sasaki K, Ghelfi A, Okazaki K, Toyoda A, Hirakawa H, Isobe S. (2021) Genome features of common vetch (Vicia sativa) in natural habitats. Plant Direct. 5:e352. doi: 10.1002/pld3.352. eCollection 2021 (Oct 7)
Nakano M, Hirakawa H, Fukai E, Toyoda A, Kajitani R, Minakuchi Y, Itoh T, Higuchi Y, Kozuka T, Bono H, Shirasawa K, Shiraiwa I, Sumitomo K, Hisamatsu T, Shibata M, Isobe S, Taniguchi K, Kusaba M. (2021) A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum. Commun. Biol. 4:1167. doi: 10.1038/s42003-021-02704-y. (Oct 7)
Sumitomo K, Shirasawa K, Isobe SN, Hirakawa H, Harata A, Kawabe M, Yagi M, Osaka M, Kunihisa M, Taniguchi F. (2021) DNA marker for resistance to Puccinia horiana in chrysanthemum (Chrysanthemum morifolium Ramat.) "Southern Pegasus". Breed. Sci. 71:261-267. doi: 10.1270/jsbbs.20063. (Mar 25)
Shirasawa K, Harada D, Hirakawa H, Isobe S, Kole C. Chromosome-level de novo genome assemblies of over 100 plant species. (2021) Breed. Sci. 71:117-124. doi: 10.1270/jsbbs.20146. (Apr 6)
Fujito S, Akyol TY, Mukae T, Wako T, Yamashita KI, Tsukazaki H, Hirakawa H, Tanaka K, Mine Y, Sato S, Shigyo M. (2021) Construction of a high-density linkage map and graphical representation of the arrangement of transcriptome-based unigene markers on the chromosomes of onion, Allium cepa L. (2021) BMC Genomics. 22:481. doi: 10.1186/s12864-021-07803-y. PMID: 34174821 (Jun 26)
Hirakawa H, Toyoda A, Itoh T, Suzuki Y, Nagano AJ, Sugiyama S, Onodera Y. (2021) A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits. (2021) DNA Res. 28:dsab004. doi: 10.1093/dnares/dsab004. PMID: 34142133 (Jun 25)
Shirasawa K, Sasaki K, Hirakawa H, Isobe S. (2021) Genomic region associated with pod color variation in pea (Pisum sativum). G3 (Bethesda). 11:jkab081. doi: 10.1093/g3journal/jkab081. PMID: 33720317 (May 7)
Yamada Y, Hirakawa H, Hori K, Minakuchi Y, Toyoda A, Shitan N, Sato F. (2021) Comparative analysis using the draft genome sequence of California poppy (Eschscholzia californica) for exploring the candidate genes involved in benzylisoquinoline alkaloid biosynthesis. Biosci. Biotechnol. Biochem. 85:851-859. doi: 10.1093/bbb/zbaa091. PMID: 33589920 (Mar 24)
Rai A, Hirakawa H, Nakabayashi R, Kikuchi S, Hayashi K, Rai M, Tsugawa H, Nakaya T, Mori T, Nagasaki H, Fukushi R, Kusuya Y, Takahashi H, Uchiyama H, Toyoda A, Hikosaka S, Goto E, Saito K, Yamazaki M. (2021) Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis. Nat. Commun. 12:405. doi: 10.1038/s41467-020-20508-2. PMID: 33452249 (Jan 15)
Hiraga Y, Shimada N, Nagashima Y, Suda K, Kanamori T, Ishiguro K, Sato Y, Hirakawa H, Sato S, Akashi T, Tanaka Y, Ohta D, Aoki K, Shibata D, Suzuki H, Kera K. (2021) Identification of a Flavin Monooxygenase-Like Flavonoid 8-Hydroxylase with Gossypetin Synthase Activity from Lotus japonicus. Plant Cell Physiol. 62:411-423. doi: 10.1093/pcp/pcaa171. (Jul 17)
Nashima K, Shirasawa K, Ghelfi A, Hirakawa H, Isobe S, Suyama T, Wada T, Kurokura T, Uemachi T, Azuma M, Akutsu M, Kodama M, Nakazawa Y, Namai K. (2021) Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype. DNA Res. 28(1):dsaa026. doi: 10.1093/dnares/dsaa026. PMID: 33175097 (Jan 19)
Kamal N, Mun T, Reid D, Lin JS, Akyol TY, Sandal N, Asp T, Hirakawa H, Stougaard J, Mayer KFX, Sato S, Andersen SU. (2020) Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence. DNA Res. 2020 Jun 1;27(3):dsaa015. doi: 10.1093/dnares/dsaa015. PMID: 32658273 Free PMC article.
Asamizu E, Shirasawa K, Hirakawa H, Iwahori H. (2020) Root-knot nematode genetic diversity associated with host compatibility to sweetpotato cultivars. Mol Plant Pathol. 2020 Aug;21(8):1088-1098. doi: 10.1111/mpp.12961. Epub 2020 Jun 17. PMID: 32558191 Free PMC article.
Shirasawa K, Hirakawa H, Fukino N, Kitashiba H, Isobe S. (2020) Genome sequence and analysis of a Japanese radish (Raphanus sativus) cultivar named 'Sakurajima Daikon' possessing giant root. Apr 1;27(2):dsaa010. doi: 10.1093/dnares/dsaa010. PMID: 32426809 Free PMC article.
Pham KD, Shida Y, Miyata A, Takamizawa T, Suzuki Y, Ara S, Yamazaki H, Masaki K, Mori K, Aburatani S, Hirakawa H, Tashiro K, Kuhara S, Takaku H, Ogasawara W. (2020) Effect of light on carotenoid and lipid production in the oleaginous yeast Rhodosporidium toruloides. (2020) Biosci Biotechnol Biochem. 2020 Mar 19:1-12. doi: 10.1080/09168451.2020.1740581. [Epub ahead of print] PMID: 32189572
Yagi M, Shirasawa K、Hirakawa H, Isobe S, Matsuno J, Uno Y, Tanase K, Onozaki T, Yamaguchi H. (2020) QTL analysis for flowering time in carnation (Dianthus caryophyllus L.), Scientia Horticulturae, 267, Feb 2020, 109053. (2020 Feb)
Akagi T, Shirasawa K, Nagasaki H, Hirakawa H, Tao R, Comai L, Henry IM. (2020) The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. PLoS Genet. (2020) 16(2):e1008566. doi: 10.1371/journal.pgen.1008566. [Epub ahead of print]
Kobayashi H, Shirasawa K, Fukino N, Hirakawa H, Akanuma T, Kitashiba H. (2020) Identification of genome-wide SNPs among geographically diverse radish accessions. DNA Res. 2020 Feb 17. pii: dsaa001. doi: 10.1093/dnares/dsaa001. [Epub ahead of print]
Matsutani M, Matsumoto N, Hirakawa H, Shiwa Y, Yoshikawa H, Okamoto-Kainuma A, Ishikawa M, Kataoka N, Yakushi T, Matsushita K. (2020) Comparative genomic analysis of closely related Acetobacter pasteurianus strains provides evidence of horizontal gene transfer and reveals factors necessary for thermotolerance. J Bacteriol. 2020 Feb 3. pii: JB.00553-19. doi: 10.1128/JB.00553-19. [Epub ahead of print]
Shirasawa K, Yakushiji H, Nishimura R, Morita T, Jikumaru S, Ikegami H, Toyoda A, Hirakawa H, Isobe S. (2020) The Ficus erecta genome towards Ceratocystis canker resistance breeding in common fig (F. carica). Plant J. 102(6):1313-1322. (2020 Jan 24)
Shimoda Y, Nishigaya Y, Yamaya-Ito H, Inagaki N, Umehara Y, Hirakawa H, Sato S, Yamazaki T, Hayashi M. (2020) The rhizobial autotransporter determines the symbiotic nitrogen fixation activity of Lotus japonicus in a host-specific manner. Proc Natl Acad Sci U S A. 117:1806-1815. (2020 Jan 21)
Hirao T, Matsunaga K, Hirakawa H, Shirasawa K, Isoda K, Mishima K, Tamura M, Watanabe A. (2019) Construction of genetic linkage map and identification of a novel major locus for resistance to pine wood nematode in Japanese black pine (Pinus thunbergii). BMC Plant Biol. 19:424. (2019 Oct 15)
Sumitomo K, Shirasawa K, Isobe S, Hirakawa H, Hisamatsu T, Nakano Y, Yagi M, Ohmiya A. (2019) Genome-wide association study overcomes the genome complexity in autohexaploid chrysanthemum and tags SNP markers onto the flower color genes. Sci Rep. 9:13947. (2019 Sep 26)
Nakano M, Taniguchi K, Masuda Y, Kozuka T, Aruga Y, Han J, Motohara K, Nakata M, Sumitomo K, Hisamatsu T, Nakano Y, Yagi M, Hirakawa H, Isobe SN, Shirasawa K, Nagashima Y, Na H, Chen L, Liang G, Chen R, Kusaba M. (2019) A pure line derived from a self-compatible Chrysanthemum seticuspe mutant as a model strain in the genus Chrysanthemum. Plant Sci. 287:110174. doi: 10.1016/j.plantsci.2019.110174. Epub 2019 Jun 28. (2019 Oct)
Isobe S, Shirasawa K, Hirakawa H (2019) Current status in whole genome sequencing and analysis of Ipomoea spp. Plant Cell Rep. 38:1365-1371. (2019 Aug 29)
Shirasawa K, Esumi T, Hirakawa H, Tanaka H, Itai A, Ghelfi A, Nagasaki H, Isobe S. (2019) Phased genome sequence of an interspecific hybrid flowering cherry, 'Somei-Yoshino' (Cerasus × yedoensis). DNA Res. 26, 379-389 (2019 Jul 23)
Imai A, Ohtani M, Nara A, Tsukakoshi A, Narita A, Hirakawa H, Sato S, Suganuma N. (2019) The Lotus japonicus nucleoporin GLE1 is involved in symbiotic association with rhizobia. Physiol Plant. doi: 10.1111/ppl.12996. (2019 May 22)
Ghelfi A, Shirasawa K, Hirakawa H, Isobe S. (2019) Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants. Bioinformatics. 35, 4427-4429. (2019 May 15)
Okazaki Y, Takahata S, Hirakawa H, Suzuki Y, Onodera Y. (2019) Molecular evidence for recent divergence of X- and Y-linked gene pairs in Spinacia oleracea L. PLoS One. 14:e0214949. (2019 Apr 9)
Abdelrahman M, Hirata S, Sawada Y, Hirai MY, Sato S, Hirakawa H, Mine Y, Tanaka K, Shigyo M. (2019) Widely targeted metabolome and transcriptome landscapes of Allium fistulosum-A. cepa chromosome addition lines revealed a flavonoid hot spot on chromosome 5A. Sci Rep. 9:3541. (2019 Mar 5)
Hirakawa H., Sumitomo K., Hisamatsu T., Nagano S., Shirasawa K., Higuchi Y., Kusaba M., Koshioka M., Nakano Y., Yagi M., Yamaguchi H., Taniguchi K., Nakano M., Isobe S.N. (2019) De novo whole-genome assembly in Chrysanthemum seticuspe, a model species of Chrysanthemums, and its application to genetic and gene discovery analysis. DNA Res. 26, 195-203. (2019 Jun 1)
Matsutani M., Hirakawa H., Sriherfyna F.H., Yakushi T., Matsushita K. (2019) Diversity of NADH dehydrogenases in acetic acid bacteria: adaptation to modify their phenotype through gene expansions and losses and neo-functionalization. Microbiology. 165, 287-291. (2019 Mar)
Akyol T.Y., Niwa R., Hirakawa H., Maruyama H., Sato T., Suzuki T., Fukunaga A., Sato T., Yoshida S., Tawaraya K., Saito M., Ezawa T., Sato S. (2018) Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields. Microbes Environ. 34, 23-32. (2019 Mar 30)
Kuwahara Y., Nakajima D., Shinpo S., Nakamura M., Kawano N., Kawahara N., Yamazaki M., Saito K., Suzuki H., Hirakawa H. (2019) Identification of potential genes involved in triterpenoid saponins biosynthesis in Gleditsia sinensis by transcriptome and metabolome analyses. J. Nat. Med. 73, 369-380. (2019 Mar)
Niwa R., Koyama T., Sato T., Adachi K., Tawaraya K., Sato S., Hirakawa H., Yoshida S., Ezawa T. (2018) Dissection of niche competition between introduced and indigenous arbuscular mycorrhizal fungi with respect to soybean yield responses. Sci Rep. 8, 7419.
Li H., Tsuchimoto S., Harada K., Yamasaki M., Sakai H., Wada N., Alipour A., Sasai T., Tsunekawa A., Tsujimoto H., Ando T., Tomemori H., Sato S., Hirakawa H., Pecina-Quintero V., Zamarripa A., Fukui K. (2018) Association Study of Seed-Yield Related Traits for Jatropha curcas L. in Mexico, Trop. Agr. Develop. 62, 68-77.
Hori K., Yamada Y., Purwanto R., Minakuchi Y., Toyoda A., Hirakawa H., Sato F. (2018) Mining of the Uncharacterized Cytochrome P450 Genes Involved in Alkaloid Biosynthesis in California Poppy Using a Draft Genome Sequence. Plant Cell Physiol. 59, 222-233.
Kudoh T., Takahashi M., Osabe T., Toyoda A., Hirakawa H., Suzuki Y., Ohmido N., Onodera Y. (2018) Molecular insights into the non-recombining nature of the spinach male-determining region. Mol Genet Genomics. 293, 557-568.
Nakamura N., Hirakawa H., Sato S., Otagaki S., Matsumoto S., Tabata S., Tanaka Y. (2018) Genome structure of Rosa multiflora, a wild ancestor of cultivated roses. DNA Res. 25, 113-121.
Yu L, Hisatsune J, Hirakawa H, Mizumachi E, Toyoda A, Yahara K, Sugai M. (2017) Complete Genome Sequence of Super Biofilm-Elaborating Staphylococcus aureus Isolated in Japan. Genome Announc. 2017 Oct 12;5(41). pii: e01043-17. doi: 10.1128/genomeA.01043-17.
Li H, Tsuchimoto S, Harada K, Yamasaki M, Sakai H, Wada N, Alipour A, Sasai T, Tsunekawa A, Tsujimoto H, Ando T, Tomemori H, Sato S, Hirakawa H, Quintero VP, Zamarripa A, Santos P, Hegazy A, Ali AM, Fukui K. (2017) Genetic Tracing of Jatropha curcas L. from Its Mesoamerican Origin to the World. Front Plant Sci. 2017 Sep 7;8:1539. doi: 10.3389/fpls.2017.01539. eCollection 2017.
Kaur P, Appels R, Bayer PE, Keeble-Gagnere G, Wang J, Hirakawa H, Shirasawa K, Vercoe P, Stefanova K, Durmic Z, Nichols P, Revell C, Isobe SN, Edwards D, Erskine W. (2017) Climate Clever Clovers: New Paradigm to Reduce the Environmental Footprint of Ruminants by Breeding Low Methanogenic Forages Utilizing Haplotype Variation. Front Plant Sci. 2017 Sep 5;8:1463. doi: 10.3389/fpls.2017.01463. eCollection 2017
Sato'o Y, Hisatsune J, Hirakawa H, Ono HK, Omoe K, Sugai M. (2017) Complete Sequence of a Staphylococcus aureus Clonal Complex 81 Strain, the Dominant Lineage in Food Poisoning Outbreaks in Japan. Genome Announc. 2017 Aug 24;5(34). pii: e00853-17. doi: 10.1128/genomeA.00853-17.
Abdelrahman M, El-Sayed M, Sato S, Hirakawa H, Ito SI, Tanaka K, Mine Y, Sugiyama N, Suzuki M, Yamauchi N, Shigyo M. (2017) RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum-A. cepa monosomic addition lines. PLoS One. 2017 Aug 11;12(8):e0181784. doi: 10.1371/journal.pone.0181784. eCollection 2017.
Shirasawa K., Isuzugawa K., Ikenaga M., Saito Y., Yamamoto T., Hirakawa H., Isobe S. (2017) The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. DNA Research, 24:499-508.
Okada N., Tanimura A., Hirakawa H., Takashima M., Ogawa J., Shima J. (2017) Draft genome sequences of the xylose-fermenting yeast Scheffersomyces shehatae NBRC 1983T and a thermotolerant isolate of S. shehatae ATY839 (JCM 18690). Genome Announc. 5, pii: e00347-17.
Nagano S., Shirasawa K., Hirakawa H., Maeda F., Ishikawa M., Isobe S.N. (2017) Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa). BMC Genomics. 18, 374.
Isobe S., Shirasawa K., Hirakawa H. (2017) Challenges to genome sequence dissection in sweetpotato. Breed Sci., 67, 35-40.
Ishiguro K., Higashino S., Hirakawa H., Sato S., Aizawa Y. (2017) Establishment of a genome-wide and quantitative protocol for assessment of transcriptional activity at human retrotransposon L1 antisense promoters. Genes Genet Syst. doi: 10.1266/ggs.16-00053.
Shirasawa K., Tanaka M., Takahata Y., Ma D., Cao Q., Liu Q., Zhai H., Kwak S.S., Cheol Jeong J., Yoon U.H., Lee H.U., Hirakawa H., Isobe S. (2017) A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas). Sci Rep., 7:44207.
Matsutani M., Nantapong N., Murata R., Paisrisan P., Hirakawa H., Kataoka N., Yakushi T., Matsushita K. (2017) Complete genome sequencing of newly isolated thermotolerant Corynebacterium glutamicum N24 provides a new insights into its thermotolerant phenotype. J Biotechnol., 247, 29-33.
Yu L., Hisatsune J., Hayashi I., Tatsukawa N., Sato'o Y., Mizumachi E., Kato F., Hirakawa H., Pier G.B., Sugai M. (2017) A novel repressor of the ica locus discovered in clinically isolated super-biofilm-elaborating Staphylococcus aureus. MBio., 8, e02282-16.
Makita Y., Ng K.K., Veera Singham G., Kawashima M., Hirakawa H., Sato S., Othman A.S., Matsui M. (2017) Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis. DNA Research, 24, 159-167.
Nakaya A., Ichihara H., Asamizu E., Shirasawa S., Nakamura Y., Tabata S., Hirakawa H. (2017) Plant Genome DataBase Japan (PGDBj). Methods Mol. Biol., 1533, 45-77.
Shirasawa K., Kuwata C., Watanabe M., Fukami M., Hirakawa H., Isobe S. (2016) Target amplicon sequencing for genotyping genome-wide single nucleotide polymorphisms identified by whole-genome resequencing in peanut. Plant Genome, 9, doi: 10.3835/plantgenome2016.06.0052.
Shimomura A., Naka A., Miyazaki N., Moriuchi S., Arima S., Sato S., Hirakawa H., Hayashi M., Maymon M., Hirsch A.M., Suzuki A. (2016) Blue light perception by both roots and rhizobia inhibits nodule formation in Lotus japonicus. Mol. Plant Microbe Interact., 29, 786-796.
Shimoda Y., Hirakawa H., Sato S., Saeki K., Hayashi M. (2016) Whole-genome sequence of the nitrogen-fixing symbiotic Rhizobium Mesorhizobium loti strain TONO. Genome Announc., 4, pii: e01016-16.
Matsutani M., Hirakawa H., Hiraoka E., Theeragool G., Yakushi T., Matsushita K. (2016) Complete genome sequencing and comparative genomic analysis of the thermotolerant acetic acid bacterium, Acetobacter pasteurianus SKU1108, provide a new insight into thermotolerance. Microbes Environ., 31, 395-400.
Takahata S., Yago T., Iwabuchi K., Hirakawa H., Suzuki Y., Onodera Y. (2016) Comparison of spinach sex chromosomes with sugar beet autosomes reveals extensive synteny and low recombination at the male-determining locus. J Hered., 107, 679-685.
Hirakawa H., Kaur P., Shirasawa K., Nichols P., Nagano S., Appels R., Erskine W., Isobe S.N. (2016) Draft genome sequence of subterranean clover, a reference for genus Trifolium. Sci Rep., 6:30358.
Yasui Y., Hirakawa H., Oikawa T., Toyoshima M., Matsuzaki C., Ueno M., Mizuno N., Nagatoshi Y., Imamura T., Miyago M., Tanaka K., Mise K., Tanaka T., Mizukoshi H., Mori M., Fujita Y. (2016) Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties. DNA Research, 23, 535-546.
Goto T., Hirakawa H., Morita Y., Tomida J., Sato J., Matsumura Y., Mitani A., Niwano Y., Takeuchi K., Kubota H., Kawamura Y. (2016) Complete genome sequence of Moraxella osloensis strain KMC41, a producer of 4-methyl-3-hexenoic acid, a major malodor compound in laundry. Genome Announc., 4, e00705-16.
Shah N., Hirakawa H., Kusakabe S., Sandal N., Stougaard J., Schierup M.H., Sato S., Andersen S.U. (2016) High-resolution genetic maps of Lotus japonicus and L. burttii based on re-sequencing of recombinant inbred lines. DNA Research, 23, 487–494.
Małolepszy A., Mun T., Sandal N., Gupta V., Dubin M., Urbański D., Shah N., Bachmann A., Fukai E., Hirakawa H., Tabata S., Nadzieja M., Markmann K., Su J., Umehara Y., Soyano T., Miyahara A., Sato S., Hayashi M., Stougaard J., Andersen S.U. (2016) The LORE1 insertion mutant resource. Plant J., 88, 306-317.
Yasui Y., Hirakawa H., Ueno M., Matsui K., Katsube-Tanaka T., Yang S.J., Aii J., Sato S., Mori M. (2016) Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes. DNA Research, 23, 215-224. (equally contributed)
Shirasawa K., Hirakawa H., Isobe S. (2016) Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato. DNA Research, 23, 145-153.
Tanaka H., Hirakawa H., Kosugi S., Nakayama S., Ono A., Watanabe A., Hashiguchi M., Gondo T., Ishigaki G., Muguerza M., Shimizu K., Sawamura N., Inoue T., Shigeki Y., Ohno N., Tabata S., Akashi R., Sato S. (2016) Sequencing and comparative analyses of the genomes of zoysiagrasses. DNA Research, 23, 171-180. (equally contributed)
Tanaka H., Hirakawa H., Muguerza M., Hashiguchi M., Tabata S., Akashi R., Sato S. The Complete chloroplast genome sequence of Zoysia matrella (L.) Merr. Crop Science, 56, 1206-1212.
Shirasawa K., Hirakawa H., Nunome T., Tabata S., Isobe S. (2016) Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato. Plant Biotechnol. J., 14, 51-60.
Yamamoto E., Matsunaga H., Onogi A., Kajiya-Kanegae H., Minamikawa M., Suzuki A., Shirasawa K., Hirakawa H., Nunome T., Yamaguchi H., Miyatake K., Ohyama A., Iwata H., Fukuoka H. (2016) A simulation-based breeding design that uses whole-genome prediction in tomato. Scientific Reports, 6:19454.
Abdelrahman M., Sawada Y., Nakabayashi R., Sato S., Hirakawa H., El-Sayed M., Hirai M.Y., Saito K., Yamauchi N., Shigyo M. (2015) Integrating transcriptome and target metabolome variability in doubled haploids of Allium cepa for abiotic stress protection. Molecular Breeding, 35:195
Goto T., Nagano K., Hirakawa H., Tanaka K., Yoshimura F. (2015) Draft genome sequence of Porphyromonas gingivalis strain Ando expressing a 53-kilodalton-type fimbrilin variant of Mfa1 fimbriae. Genome Announcements, 5, 3.
Shimada S., Makita Y., Kuriyama-Kondou T., Kawashima M., Mochizuki Y., Hirakawa H., Sato S., Toyoda T., Matsui M. (2015) Functional and expression analyses of transcripts based on full-length cDNAs of Sorghum bicolor. DNA Research, 22, 485-493.
Kawai M., Higashiura N., Hayasaki K., Okamoto N., Takami A., Hirakawa H., Matsushita K., Azuma Y. (2015) Complete genome and gene expression analyses of Asaia bogorensis reveal unique responses to culture with mammalian cells as a potential opportunistic human pathogen. DNA Research, 22, 357-366.
Kosugi S., Hirakawa H., Tabata S. (2015) GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments. Bioinformatics, 31, 3733-3741.
Hirakawa H., Okada Y., Tabuchi H., Shirasawa K., Watanabe A., Tsuruoka H., Minami C., Nakayama S., Sasamoto S., Kohara M., Kishida Y., Fujishiro T., Kato M., Nanri K., Komaki A., Yoshinaga M., Takahata Y., Tanaka M., Tabata S., Isobe S.N. (2015) Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. DNA Research, 22, 171-179.
Nishikawa H., Iijima T., Kajitani R., Yamaguchi J., Ando T., Suzuki Y., Sugano S., Fujiyama A., Kosugi S., Hirakawa H., Tabata S., Ozaki K., Morimoto H., Ihara K., Obara M., Hori H., Itoh T., Fujiwara H. (2015) A genetic mechanism for female-limited Batesian mimicry in Papilio butterfly. Nature Genetics, 47, 405-409.
Tsukazaki H., Yaguchi S., Sato S., Hirakawa H., Katayose Y., Kanamori H., Kurita K., Itoh T., Kumagai M., Mizuno S., Hamada M., Fukuoka H., Yamashita K., McCallum J.A., Shigyo M., Wako T. (2015) Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum). Molecular Breeding, 35:55
Hara H., Yokosuka T., Hirakawa H., Ishihara C., Yasukawa S., Yamazaki M., Koseki H., Yoshida H., Saito T. (2015) Clustering of CARMA1 through SH3-GUK domain interactions is required for its activation of NF-κB signalling. Nature Communications, 6:5555.
Chungopast S., Hirakawa H., Sato S., Handa Y., Saito K., Kawaguchi M., Tajima S., Nomura M. (2014) Transcriptomic profiles of nodule senescence in Lotus japonicus and Mesorhizobium loti symbiosis. Plant Biotechnology, 31, 345-349.
Shirasawa K., Hand M.L., Henderson S.T., Okada T., Johnson S.D., Taylor J.M., Spriggs A., Siddons H., Hirakawa H., Isobe S., Tabata S., Koltunow AM. (2014) A reference genetic linkage map of apomictic Hieracium species based on expressed markers derived from developing ovule transcripts. Ann. Bot., 115, 567-580.
Kayama S., Shigemoto N., Kuwahara R., Oshima K., Hirakawa H., Hisatsune J., Jové T., Nishio H., Yamasaki K., Wada Y., Ueshimo T., Miura T., Sueda T., Onodera M., Yokozaki M., Hattori M., Ohge H., Sugai M. (2014) The complete nucleotide sequence of the IncN plasmid encoding IMP-6 and CTX-M-2 from the emerging carbapenem-resistant Enterobacteriaceae in Japan. Antimicrob. Agents Chemother., 59, 1356-1359.
Shirasawa K., Isobe S., Tabata S., Hirakawa H. (2014) Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants. Breed. Sci., 64, 264-271.
El-Rodeny W., Kimura M., Hirakawa H., Sabah A., Shirasawa K., Sato S., Tabata S., Sasamoto S., Watanabe A., Kawashima K., Kato M., Wada T., Tsuruoka H., Takahashi C., Minami C., Nanri K., Nakayama S., Kohara M., Yamada M., Kishida Y., Fujishiro T., Isobe S. (2014) Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba). Breed. Sci., 64, 252-263.
Soyano T., Hirakawa H., Sato S., Hayashi M., Kawaguchi M. (2014) NODULE INCEPTION creates a long-distance negative feedback loop involved in homeostatic regulation of nodule organ production. Proc. Natl. Acad. Sci. USA. 111, 14607-14612.
Hirakawa H., Shirasawa K., Miyatake K., Nunome T., Negoro S., Ohyama A., Yamaguchi H., Sato S., Isobe S., Tabata S., Fukuoka H. (2014) Draft genome sequence of eggplant (Solanum melongena L.): the representative Solanum species indigenous to the old world. DNA Research, 21, 649-660.
Chankaew S., Isemura T., Isobe S., Kaga A., Tomooka N., Somta P., Hirakawa H., Shirasawa K., Vaughan D.A., Srinives P. (2014) Detection of genome donor species of neglected tetraploid crop Vigna reflexo-pilosa (Créole Bean), and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis). PLoS One, 9:e104990.
Ariizumi T., Kishimoto S., Kakami R., Maoka T., Hirakawa H., Suzuki Y., Ozeki Y., Shirasawa K., Bernillon S., Okabe Y., Moing A., Asamizu E., Rothan C., Ohmiya A., Ezura H. (2014) Identification of the carotenoid modifying gene PALE YELLOW PETAL 1 as an essential factor in xanthophyll esterification and yellow flower pigmentation in tomato (Solanum lycopersicum). Plant J., 79, 453-465.
Matsutani M., Fukushima K., Kayama C., Arimitsu M., Hirakawa H., Toyama H., Adachi O., Yakushi T., Matsushita K. (2014) Replacement of a terminal cytochrome c oxidase by ubiquinol oxidase during the evolution of acetic acid bacteria. Biochim. Biophys. Acta., 1837, 1810-1820.
Suzaki T., Ito M., Yoro E., Sato S., Hirakawa H., Takeda N., Kawaguchi M. (2014) Endoreduplication-mediated initiation of symbiotic organ development in Lotus japonicus. Development. 141, 2441-2445.
Kitashiba H., Li F., Hirakawa H., Kawanabe T., Zou Z., Hasegawa Y., Tonosaki K., Shirasawa S., Fukushima A., Yokoi S., Takahata Y., Kakizaki T., Ishida M., Okamoto S., Sakamoto K., Shirasawa K., Tabata S., Nishio T. (2014) Draft sequences of the radish (Raphanus sativus L.) genome. DNA Research, 21, 481-490.
Tuncel A., Kawaguchi J., Ihara Y., Matsusaka H., Nishi A., Nakamura T., Kuhara S., Hirakawa H., Nakamura Y., Cakir B., Nagamine A., Okita T.W., Hwang S.K., Satoh H. (2014) The rice endosperm ADP-glucose pyrophosphorylase large subunit is essential for optimal catalysis and allosteric regulation of the heterotetrameric enzyme. Plant Cell Physiol., 55, 1169-1183.
Asamizu E., Ichihara H., Nakaya A., Nakamura Y., Hirakawa H., Ishii T., Tamura T., Fukami-Kobayashi K., Nakajima Y., Tabata S. (2014) Plant Genome DataBase Japan (PGDBj): A portal website for the integration of plant genome-related databases. Plant Cell Physiol., 55:e8.
Sato S., Hirakawa H., Tsuchimoto S., Sakai H., Shibagaki N., Matsunaga S., Fukui K., Tabata S. (2013) Genome structure of Jatropha curcas L. Jatropha, Challenges for a New Energy Crop, 563-576.
Yagi M., Kosugi S., Hirakawa H., Ohmiya A., Tanase K., Harada T., Kishimoto K., Nakayama M., Ichimura K., Onozaki T., Yamaguchi H., Sasaki N., Miyahara T., Nishizaki Y., Ozeki Y., Nakamura N., Suzuki T., Tanaka Y., Sato S., Shirasawa K., Isobe S., Miyamura Y., Watanabe A., Nakayama S., Kishida Y., Kohara M., Tabata S. (2014) Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). DNA Research, 21, 231-241.
Higashiura N., Hadano H., Hirakawa H., Matsutani M., Takebe S., Matsushita K., Azuma Y. (2013) Draft genomic DNA sequence of the facultatively methylotrophic bacterium Acidomonas methanolica type strain MB58. FEMS Microbiol. Lett., 351, 9–13.
Hirakawa H., Shirasawa K., Kosugi S., Tashiro K., Nakayama S., Yamada M., Kohara M., Watanabe A., Kishida Y., Fujishiro T., Tsuruoka H., Minami C., Sasamoto S., Kato M., Nanri K., Komaki A., Yanagi T., Guoxin Q., Maeda F., Ishikawa M., Kuhara S., Sato S., Tabata S., Isobe SN. (2013) Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. DNA Research, 21,169-181.
Yoshikawa K., Shimada M., Kuwahara T., Hirakawa H., Kurita N., Sato H., Utsunomiya T., Iwata T., Miyatani T., Higashijima J., Kashihara H., Takasu C., Matsumoto N., Nakayama-Imaohji H. (2013) Effect of Kampo medicine "Dai-kenchu-to" on microbiome in the intestine of the rats with fast stress. J. Med. Invest., 60, 221-227.
Yagi M., Yamamoto T., Isobe S., Hirakawa H., Tabata S., Tanase K., Yamaguchi H., Onozaki T. (2013) Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.). BMC Genomics. 14:734.
Hisatsune J., Hirakawa H., Yamaguchi T., Fudaba Y., Oshima K., Hattori M., Kato F., Kayama S., Sugai M. (2013) Emergence of Staphylococcus aureus carrying multiple drug resistance genes on a plasmid encoding exfoliative toxin B. Antimicrob Agents Chemother., 57, 6131-6140.
Matsutani M., Ogawa M., Takaoka N., Hanaoka N., Toh H., Yamashita A., Oshima K., Hirakawa H., Kuhara S., Suzuki H., Hattori M., Kishimoto T., Ando S., Azuma Y., Shirai M. (2013) Complete genomic DNA sequence of the east Asian spotted fever disease agent Rickettsia japonica. PLoS One, 8, e71861.
Kobayashi K., Hayashi I., Kouda S., Kato F., Fujiwara T., Kayama S., Hirakawa H., Itaha H., Ohge H., Gotoh N., Usui T., Matsubara A., Sugai M. (2013) Identification and characterization of a novel aac(6')-Iag associated with the bla IMP-1-Integron in a multidrug-resistant Pseudomonas aeruginosa. PLoS One. 8, e70557.
Shirasawa K., Fukuoka H., Matsunaga H., Kobayashi Y., Kobayashi I., Hirakawa H., Isobe S., Tabata S. (2013) Genome-Wide Association Studies Using Single Nucleotide Polymorphism Markers Developed by Re-Sequencing of the Genomes of Cultivated Tomato. DNA Research, 20, 593-603.
Nakamura Y., Mori K., Saitoh K., Oshima K., Mekuchi M., Sugaya T., Shigenobu Y., Ojima N., Muta S., Fujiwara A., Yasuike M., Oohara I., Hirakawa H., Chowdhury V.S., Kobayashi T., Nakajima K., Sano M., Wada T., Tashiro K., Ikeo K., Hattori M., Kuhara S., Gojobori T., Inouye K. (2013) Evolutionary changes of multiple visual pigment genes in the complete genome of Pacific bluefin tuna. Proc. Natl. Acad. Sci. USA., 110, 11061-11066.
Ichimura M., Uchida K., Nakayama-Imaohji H., Hirakawa H., Tada T., Morita H., Yasutomo K., Okazaki K., Kuwahara T. (2014) Mariner-based transposon mutagenesis for Bacteroides species. J. Basic Microbiol., 54, 558-567.
Kasai-Maita H., Hirakawa H., Nakamura Y., Kaneko T., Miki K., Maruya J., Okazaki S., Tabata S., Saeki K., Sato S. (2013) Commonalities and Differences among Symbiosis Islands of Three Mesorhizobium loti Strains., Microbes Environ., 28, 275-278.
Ohtani K., Hirakawa H., Paredes-Sabja D., Tashiro K., Kuhara S., Sarker M.R., Shimizu T. (2013) Unique regulatory mechanism of sporulation and enterotoxin production in Clostridium perfringens. J. Bacteriol., 195, 2931-2936.
Porciuncula J.D., Furukawa, T., Mori, K., Shida, Y., Hirakawa, H., Tashiro, K., Kuhara, S., Nakagawa, S., Morikawa, Y., Ogasawara, W. (2013) Single Nucleotide Polymorphism Analysis of a Trichoderma reesei Hyper-Cellulolytic Mutant Developed in Japan. Biosci Biotechnol Biochem., 77, 534-543.
Hirakawa H., Shirasawa K., Ohyama A., Fukuoka H., Aoki K., Rothan C., Sato S., Isobe S., Tabata S. (2013) Genome-wide SNP genotyping to infer the effects on gene functions in tomato. DNA research, 20, 221-233
Wakimoto S., Nakayama-Imaohji H., Ichimura M., Morita H., Hirakawa H., Hayashi T., Yasutomo K., Kuwahara T. (2013) PhoB regulates the survival of Bacteroides fragilis in peritoneal abscesses. PLoS One, 8, e53829.
Shirasawa K., Bertioli D.J., Varshney R.K., Moretzsohn M.C., Leal-Bertioli S.C., Thudi M., Pandey M.K., Rami J.F., Foncéka D., Gowda M.V., Qin H., Guo B., Hong Y., Liang X., Hirakawa H., Tabata S., Isobe S. (2013) Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Research, 20, 173-184.
Asamizu E., Shirasawa K., Hirakawa H., Sato S., Tabata S., Yano K., Ariizumi T., Shibata D., Ezura H. (2012) Mapping of Micro-Tom BAC-end sequences to the reference tomato genome reveals possible genome rearrangements and polymorphisms. Int. J. Plant Genomics., 2012:437026.
Isobe S., Hirakawa H., Sato S., Maeda F., Ishikawa M., Mori T., Yamamoto Y., Shirasawa K., Kimura M., Fukami M., Hashizume F., Tsuji A., Sasamoto S., Kato M., Nanri K., Tsuruoka H., Minami C., Takahashi C., Wada T., Ono A., Kawashima K., Nakazaki N., Kishida Y., Kohara M., Nakayama S., Yamada M., Fujishiro T., Watanabe A., Tabata S. (2013) Construction of an integrated high density SSR linkage map in cultivated strawberry (Fragaria × axananassa) and its applicability. DNA research, 20, 79-92.
Aikawa Y., Hirakawa H., Lee S. (2012) Spatiotemporal regulation of the ubiquitinated cargo-binding activity of Rabex-5 in the endocytic pathway. J. Biol. Chem., 287, 40586-40597.
Shirakawa K., Hirakawa H. (2013) DNA marker applications to molecular genetics and genomics in tomato. Breeding Sci., 63, 21-30.
Takeno A., Okamoto A., Tori K., Oshima K., Hirakawa H., Toh H., Agata N., Yamada K., Ogasawara N., Hayashi T., Shimizu T., Kuhara S., Hattori M., Ohta M. (2012) Complete genome sequence of Bacillus cereus NC7401, which produces high levels of the emetic toxin cereulide. J. Bacteriol., 194, 4767-4768.
Hirakawa H., Tsuchimoto S., Sakai H., Nakayama S., Fujishiro T., Kishida Y., Kohara M., Watanabe A., Yamada M., Aizu T., Toyoda A., Fujiyama A., Tabata S., Fukui K., Sato S. (2012) Upgraded genomic information of Jatropha curcas L. Plant Biotechnology, 29, 123-130.
Tanase K., Nishitani C., Hirakawa H., Isobe S., Tabata S., Ohmiya A., Onozaki T. (2012) Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology. BMC Genomics, 13, 292.
Goto T., Ogura Y., Hirakawa H., Tomida J., Morita Y., Akaike T., Hayashi T., Kawamura Y. (2012) Complete genome sequence of Helicobacter cinaedi strain PAGU611, isolated in a case of human bacteremia. J. Bacteriol., 194, 3744-3745.
Koilkonda P., Sato S., Tabata S., Shirasawa K., Hirakawa H., Sakai H., Sasamoto S., Watanabe A., Wada T., Kishida Y., Tsuruoka H., Fujishiro T., Yamada M., Kohara M., Suzuki S., Hasegawa M., Kiyoshima H., Isobe S. (2012) Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp. Mol Breed. 30, 125-138.
Isobe SN., Hisano H., Sato S., Hirakawa H., Okumura K., Shirasawa K., Sasamoto S., Watanabe A., Wada T., Kishida Y., Tsuruoka H., Fujishiro T., Yamada M., Kohara M., Tabata S. (2012) Comparative Genetic Mapping and Discovery of Linkage Disequilibrium Across Linkage Groups in White Clover (Trifolium repens L.). G3 (Bethesda), 2, 607-617.
Sato S., Tabata S., Hirakawa H., Asamizu E., Shirasawa K., Isobe S., Kaneko T., Nakamura Y., Shibata D., Aoki K., Egholm M., Knight J., Li C., Shuang Y., Xu X., Pan S., Cheng S., Liu X., Ren Y., Wang J., Albiero A., Dal Pero F., Todesco S., Van Eck J., Buels RM., Bombarely A., Gosselin JR., Huang M., Leto JA., Menda N., Strickler S., Mao L., Gao S., Tecle IY., York T., Zheng Y., Vrebalov JT., Lee J., Zhong S., Mueller LA., Stiekema WJ., Ribeca P., Alioto T., Yang W., Huang S., Du Y., Zhang Z., Gao J., Guo Y., Wang X., Li Y., He J., Li C., Cheng Z., Zuo J., Wang X., Ren J., Zhao J., Yan L., Jiang H., Wang B., Li H., Li Z., Fu F., Chen B., Han B., Feng Q., Fan D., Ling H., Xue Y., Wang Y., Ling H., Xue Y., Ware D., McCombie W., Lippman ZB., Chia JM., Jiang K., Pasternak S., Gelley L., Kramer M., Anderson LK., Chang SB., Royer SM., Shearer LA., Stack SM., Chang SB., Rose JK., Xu Y., Eannetta N., Matas AJ., McQuinn R., Tanksley SD., Camara F., Guigó R., Rombauts S., Fawcett J., Van de Peer Y., Zamir D., Liang C., Spannagl M., Gundlach H., Bruggmann R., Mayer K., Jia Z., Zhang J., Ye Z., Bishop GJ., Butcher S., Lopez-Cobollo R., Buchan D., Filippis I., Abbott J., Dixit R., Singh M., Singh A., Pal JK., Pandit A., Singh PK., Mahato AK., Dogra V., Gaikwad K., Sharma TR., Mohapatra T., Singh NK., Causse M., Rothan C., Schiex T., Noirot C., Bellec A., Klopp C., Berges H., Mariette J., Frasse P., Vautrin S., Zouine M., Latché A., Rousseau C., Regad F., Pech JC., Philippot M., Mondher JC., Bouzayen M., Pericard P., Osorio S., del Carmen AF., Monforte A., Granell A., Fernandez-Muñoz R., Conte M., Lichtenstein G., Carrari F., De Bellis G., Fuligni F., Peano C., Grandillo S., Termolino P., Pietrella M., Fantini E., Falcone G., Fiore A., Giuliano G., Lopez L., Facella P., Lopez L., Perrotta G., Daddiego L., Bryan G, Orozco M., Girona J., Orozco M., Pastor X., Torrents D., van Schriek MG., Feron RM., van Oeveren J., de Heer P., daPonte L., Jacobs-Oomen S., Cariaso M., Prins M., van Eijk MJ., Janssen A., van Haaren MJ., Jo SH., Kim J., Kwon SY., Kim S., Koo DH., Lee S., Hur CG., Clouser C., Rico A., Hallab A., Gebhardt C., Klee K., Jöcker A., Warfsmann J., Göbel U., Kawamura S., Yano K., Sherman JD., Fukuoka H., Negoro S., Sarita U., Kawamura S., Yano K., Sherman JD., Fukuoka H., Negoro S., Bhutty S., Chowdhury P., Chattopadhyay D., Datema E., Smit S., Schijlen EG., van de Belt J., van Haarst JC., Peters SA., van Staveren MJ., Henkens MH., Mooyman PJ., Hesselink T., van Ham RC., Jiang G., Droege M., Choi D., Kang BC., Kim BD., Park M., Kim S., Yeom SI., Lee YH., Choi YD., Li G., Gao J., Liu Y., Huang S., Fernandez-Pedrosa V., Collado C., Zuñiga S., Wang G., Cade R., Dietrich RA., Rogers J., Knapp S., Fei Z., White RA., Thannhauser TW., Giovannoni JJ., Botella MA., Gilbert L., Gonzalez R., Goicoechea JL., Yu Y., Kudrna D., Collura K., Wissotski M., Wing R., Schoof H., Meyers BC., Gurazada AB., Green PJ., Mathur S., Vyas S., Solanke AU., Kumar R., Gupta V., Sharma AK., Khurana P., Khurana JP., Tyagi AK., Dalmay T., Mohorianu I., Walts B., Chamala S., Barbazuk W., Li J., Hui Guo TH., Wang Y., Zhang D., Paterson AH., Wang X., Tang H., Barone A., Chiusano ML., Ercolano MR., D'Agostino N., Di Filippo M., Traini A., Sanseverino W., Frusciante L., Bonington S., Seymour GB., Elharam M., Fu Y., Hua A., Kenton S., Lewis J., Lin S., Najar F., Lai H., Qin B., Qu C., Shi R., White D., White J., Xing Y., Yang K., Yi J., Yao Z., Zhou L., Roe BA., Vezzi A., D'Angelo M., Zimbello R., Schiavon R., Caniato E., Rigobello C., Campagna D., Vitulo N., Valle G., Nelson DR., De Paoli E., Szinay D., de Jong HH., Bai Y., Visser RG., Klein RM., Beasley H., Helen S., McLaren K., Nicholson C., Riddle C., Gianese G., Schiex T. (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635-641.
Shirasawa K., Koilkonda P., Aoki K., Hirakawa H., Tabata S., Watanabe M., Hasegawa M., Kiyoshima H., Suzuki S., Kuwata C., Naito Y., Kuboyama T., Nakaya A., Sasamoto S., Watanabe A., Kato M., Kawashima K., Kishida Y., Kohara M., Kurabayashi A., Takahashi C., Tsuruoka H., Wada T., Isobe S. (2012) In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biol.,12, 80.
Okubo T., Tsukui T., Maita H., Okamoto S., Oshima K., Fujisawa T., Saito A., Futamata H., Hattori R., Shimomura Y., Haruta S., Morimoto S., Wang Y., Sakai Y., Hattori M., Aizawa S., Nagashima KVP., Masuda S., Hattori T., Yamashita A., Bao Z., Hayatsu M., Kajiya-Kanegae H., Yoshinaga I., Sakamoto K., Toyota K., Nakao M., Kohara M., Anda M., Niwa R., Jung-Hwan P., Sameshima-Saito R., Tokuda S., Yamamoto S., Yamamoto S., Yokoyama T., Akutsu T., Nakamura Y., Nakahira-Yanaka Y., Takada-Hoshino Y., Hirakawa H., Mitsui H., Terasawa K., Itakura M., Sato S., Ikeda-Ohtsubo W., Sakakura N., Kaminuma E., Minamisawa K. (2012) Complete Genome Sequence of Bradyrhizobium sp. S23321: Insights into Symbiosis Evolution in Soil Oligotrophs. Microbes and Enviroments, 27, 306-315.
Shirasawa K., Hirakawa H., Tabata S., Hasegawa M., Kiyoshima H., Suzuki S., Sasamoto S., Watanabe A., Fujishiro T., Isobe S. (2012) Characterization of active miniature inverted-repeat transposable elements in the peanut genome. Theor. Appl. Genet. 124, 1429-1438.
Hirakawa H., Nakamura Y., Kaneko T., Isobe S., Sakai H., Kato T., Hibino T., Sasamoto S., Watanabe A., Yamada M., Nakayama S., Fujishiro T., Kishida Y., Kohara M., Tabata S., Sato S. (2011) Survey of the genetic information carried in the genome of Eucalyptus camaldulensis. Plant biotechnology, 28, 471-480.
Kaneko T., Maita H., Hirakawa H., Uchiike N., Minamisawa K., Watanabe A., Sato S. (2011) Complete genome sequence of the soybean symbiont Bradyrhizobium japonicum strain USDA6T. Genes, 2, 763-787.
Matsutani M., Hirakawa H., Saichana N., Soemphol W., Yakushi T., Matsushita K. (2011) Genome-wide phylogenetic analysis of differences in thermotolerance among closely related Acetobacter pasteurianus strains. Microbiology. 158, 229-239.
Fukai E., Soyano T., Umehara Y., Nakayama S., Hirakawa H., Tabata S., Sato S., Hayashi M. (2011) Establishment of a Lotus japonicus gene tagging population using the exon-targeting endogenous retrotransposon LORE1. Plant J. 69, 720-730.
The Brassica rapa Genome Sequencing Project Consortium, Wang X., Wang H., Wang J., Sun R., Wu J., Liu S., Bai Y., Mun JH., Bancroft I., Cheng F., Huang S., Li X., Hua W., Wang J., Wang X., Freeling M., Pires JC., Paterson AH., Chalhoub B., Wang B., Hayward A., Sharpe AG., Park BS., Weisshaar B., Liu B., Li B., Liu B., Tong C., Song C., Duran C., Peng C., Geng C., Koh C., Lin C., Edwards D., Mu D., Shen D., Soumpourou E., Li F., Fraser F., Conant G., Lassalle G., King GJ., Bonnema G., Tang H., Wang H., Belcram H., Zhou H., Hirakawa H., Abe H., Guo H., Wang H., Jin H., Parkin IA., Batley J., Kim JS., Just J., Li J., Xu J., Deng J., Kim JA., Li J., Yu J., Meng J., Wang J., Min J., Poulain J., Wang J., Hatakeyama K., Wu K., Wang L., Fang L., Trick M., Links MG., Zhao M., Jin M., Ramchiary N., Drou N., Berkman PJ., Cai Q., Huang Q., Li R., Tabata S., Cheng S., Zhang S., Zhang S., Huang S., Sato S., Sun S., Kwon SJ., Choi SR., Lee TH., Fan W., Zhao X., Tan X., Xu X., Wang Y., Qiu Y., Yin Y., Li Y., Du Y., Liao Y., Lim Y., Narusaka Y., Wang Y, Wang Z., Li Z., Wang Z., Xiong Z., Zhang Z. (2011) The genome of the mesopolyploid crop species Brassica rapa. Nature genetics, 43, 1035-1039.
Kuwahara T, Ogura Y, Oshima K, Kurokawa K, Ooka T, Hirakawa H, Itoh T, Nakayama-Imaohji H, Ichimura M, Itoh K, Ishifune C, Maekawa Y, Yasutomo K, Hattori M, Hayashi T. (2011) The Lifestyle of the Segmented Filamentous Bacterium: A Non-Culturable Gut-Associated Immunostimulating Microbe Inferred by Whole-Genome Sequencing. DNA Research. 18, 291-303
Shirasawa K., Oyama M., Hirakawa H., Sato S., Tabata S., Fujioka T. Kimizuka-Takagi C., Sasamoto S., Watanabe A., Kato M., Kishida Y., Kohara M., Takahashi C., Tsuruoka H., Wada T., Sakai T., Isobe S. (2011) An EST-SSR Linkage Map of Raphanus sativus and Comparative Genomics of the Brassicaceae. DNA Research. 18, 221-232.
Asada M., Hirakawa H., Kuhara S. (2011) Classification of Bacteria Based on the Biases of Terminal Amino Acid Residues. Protein J. 30, 290-297.
Matsutani M., Hirakawa H., Nishikura M., Soemphol W., Ali I.A., Yakushi T., Matsushita K. (2011) Increased number of Arginine-based salt bridges contributes to the thermotolerance of thermotolerant acetic acid bacteria, Acetobacter tropicalis SKU1100. Biochem. Biophys. Res. Commun. 409, 120-124.
Matsutani M., Hirakawa, H., Yakushi T., Matsushita K. (2011) Genome-wide phylogenetic analysis of Gluconobacter, Acetobacter, and Gluconacetobacter. FEMS Microbiology Letters, 315, 122-128.
Sato S., Hirakawa H., Isobe S., Watanabe A., Kato M., Kawashima K., Minami C., Muraki A., Nakazaki N., Takahashi C., Nakayama S., Kishida Y., Kohara M., Yamada M., Tsuruoka H., Sasamoto S., Tabata S., Aizu T., Toyoda A., Shin-I T., Minakuchi Y., Kohara Y., Fujiyama A., Tsuchimoto S., Kajiyama S., Makigano E., Ohmido N., Shibagaki N., Cartagena J.A., Wada N., Kohinata T., Atefeh A., Yuasa S., Matsunaga S., Fukui K. (2011) Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. DNA Research, 18, 65-76.
Shirasawa K., Isobe S., Hirakawa H., Asamizu E., Fukuoka H., Rothan C., Sasamoto S., Fujishiro T., Kishida Y., Kohara M., Tsuruoka H., Wada T., Nakamura Y., Sato S., Tabata S. (2010) SNP discovery and linkage map construction in cultivated tomato. DNA Research, 17, 381-391.
Kim S., Hirakawa H., Muta S., Kuhara S. (2010) Identification and Classification of a Two-Component System Based on Domain Structures in Bacteria and Differences in Domain Structure between Gram-Positive and Gram-Negative Bacteria. Biosci Biotechnol Biochem., 74, 716-720.
Yasukochi Y., Maruyama O., Mahajan M.C., Padden C., Euskirchen G.M., Schulz V., Hirakawa H., Kuhara S., Pan X.H., Newburger P.E., Snyder M., Weissman S.M. (2010) X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils. Proc Natl Acad Sci U. S. A., 107, 3704-3709.
Sato K., Naito M., Yukitake H., Hirakawa H., Shoji M., Mcbride M., Rhodes R., Nakayama K. (2010) A protein secretion system linked to bacteroidete gliding motility and pathogenesis. Proc. Natl. Acad. Sci. U.S.A., 107, 276-281.
Ohtani K., Hirakawa H., Tashiro K., Yoshizawa S., Kuhara S., Shimizu T. (2010) Identification of a two-component VirR/VirS regulon in Clostridium perfringens. Anaerobe, 16, 258-264.
Nakayama-Imaohji H., Hirakawa H., Ichimura M., Wakimoto S., Kuhara S., Hayashi T., Kuwahara T. (2009) Identification of the site-specific DNA invertase responsible for the phase variation of SusC/SusD family outer membrane proteins in Bacteroides fragilis. J. Bacteriol., 191, 6003-6011.
Azuma Y., Hosoyama A., Matsutani M., Furuya N., Horikawa H., Harada T., Hirakawa H., Kuhara S., Matsushita K., Fujita N., Shirai M. (2009) Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus. Nucleic Acids Res., 37, 5768-5783.
Qin T., Iida K., Hirakawa H., Shiota S., Nakayama H., Yoshida S. (2009) Conjugative plasmid pLD-TEX-KL promotes growth of host bacterium Legionella dumoffii at low temperatures. Arch Microbiol., 191, 543-551.
Hirakawa H., Akita H., Fujiwara T., Sugai M., Kuhara S. (2009) Structural insight into the binding mode between the targeting domain of ALE-1 (92AA) and pentaglycine of peptidoglycan. Protein Eng Des Sel., 22, 385-391.
Hirakawa H., Ochi A., Kawahara Y., Kawamura S., Torikata T., Kuhara S. (2008) Catalytic reaction mechanism of goose egg-white lysozyme by molecular modeling of enzyme-substrate complex. J. Biochem., 144, 753-761.
Maruyama O., Hirakawa H., Iwayanagi T., Ishida Y., Takeda S., Otomo J., Kuhara S. (2008) Evaluating protein sequence signatures inferred from protein-protein interaction data by gene ontology annotations. The IEEE International conference on Bioinformatics and Biomedicine 2008 (BIBM2008), 417-420.
Naito M., Hirakawa H., Yamashita A., Ohara N., Shoji M., Yukitake H., Nakayama K., Toh H., Yoshimura F., Kuhara S., Hattori M., Hayashi T., Nakayama K. (2008) Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis. DNA research, 15, 215-25.
Kawamura S., Ohkuma M., Chijiiwa Y., Kohno D., Nakagawa H., Hirakawa H., Kuhara S., Torikata T. (2008) Role of disulfide bonds in goose-type lysozyme. FEBS J., 275, 2818-2830.
Moriyama K, Ando C, Tashiro K, Kuhara S, Okamura S, Nakano S, Takagi Y, Miki T, Nakashima Y, Hirakawa H. (2008) Polymerase chain reaction detection of bacterial 16S rRNA gene in human blood. Microbiol Immunol., 52, 375-382.
Miura K., Toh H., Hirakawa H., Sugii M., Murata M., Nakai K., Tashiro K., Kuhara S., Azuma Y., Shirai M. (2008) Genome-wide analysis of Chlamydophila pneumoniae gene expression at the late stage of infection. DNA research, 15, 83-91.
Goto T., Yamashita A., Hirakawa H., Matsutani M., Todo K., Ohshima K., Toh H., Miyamoto K., Kuhara S., Hattori M., Shimizu T., Akimoto S. (2008) Complete genome sequence of Finegoldia magna. DNA Research, 15, 39-47.
Qin T., Hirakawa H., Iida K., Oshima K., Hattori M., Tashiro K., Kuhara S., Yoshida S. (2007) Complete nucleotide sequence of pLD-TEX-KL, a 66-kb plasmid of Legionella dumoffii TEX-KL strain. Plasmid, 58, 261-268.
Katekaew S., Torikata T., Hirakawa H., Kuhara S., Araki T. (2007) Enzymatic properties of newly found green turtle egg white ribonuclease. Protein J., 26, 75-85.
Kayano M., Konishi S., Hirakawa H., Kuhara S. (2006) Functional principal component analysis via regularized basis expansion and its application. J. Appl. Statist., 35, 1-16.
Hirakawa H., Kawahara Y., Ochi A., Muta S., Kawamura S., Torikata T., Kuhara S. (2006) Construction of enzyme-substrate complexes between hen egg-white lysozyme and N-acetyl-D-glucosamine hexamer by systematic conformational search and molecular dynamics simulation. J. Biochem., 140, 221-227.
Azuma Y., Hirakawa H., Yamashita A., Cai Y., Rahman M.A., Suzuki H., Mitaku S., Toh H., Goto S., Murakami T., Sugi K., Hayashi H., Fukushi H., Hattori M., Kuhara S., Shirai M. (2006) Genome sequence of the cat pathogen, Chlamydophila felis. DNA research, 13, 15-23. (equally contributed)
Kuroda M., Yamashita A., Hirakawa H., Kumano M., Morikawa K., Higashide M., Maruyama A., Inose Y., Matoba K., Toh H., Kuhara S., Hattori M., Ohta T. (2005) Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection. Proc. Natl. Acad. Sci. U.S.A., 102, 13272-13277.
Oba T., Nomiyama S., Hirakawa H., Tashiro K., Kuhara S. (2005) Asp578 in LEU4p is one of the key residues for leucine feedback inhibition release in sake yeast. Biosci. Biotechnol. Biochem., 2005, 69, 1270-1273.
Yamamoto K., Rutherford S.A., Rajagopalan M., Hirakawa H., Kuhara S., Banno Y., Fujii H., Madiraju M.V.V.S. (2004) Heterogeneity of dnaB locus of Mycobacterium avium-intracellulare complex. J. Fac. Agr., Kyushu Univ., 49, 375-381.
Araki T., Seki S., Hirakawa H., Chijiiwa Y., Kawamura S., Kuhara S., Torikata T. (2004) Bare-faced curassow lysozyme carrying amino acid substitutions at subsites E and F shows a change in activity against chitooligosaccharide caused by a local conformational change. J. Biochem., 136, 485-493.
Kuwahara T., Yamashita A., Hirakawa H., Nakayama H., Toh H., Okada N., Kuhara S., Hattori M., Hayashi T., Ohnishi Y. (2004) Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc. Natl. Acad. Sci. U. S. A., 101, 14919-14924.
Ohta T., Hirakawa H., Morikawa K., Maruyama A., Inose Y., Yamashita A., Ohshima K., Kuroda M., Hattori M., Hiramatsu K., Kuhara S., Hayashi H. (2004) Nucleotide substitutions in Staphylococcus aureus strains, Mu50, Mu3 and N315. DNA Research, 11, 51-56.
Ametani A., Sakurai T., Katakura Y., Kuhara S., Hirakawa H., Hosoi T., Dosako S., Kaminogawa S. (2003) Amino acid residue substitution at T-cell determinant-flanking sites in beta-lactoglobulin modulates antigen presentation to T cells through subtle conformational change. Biosci. Biotechnol. Biochem., 67, 1507-1514.
Nomiyama H., Egami K., Tanase S., Miura R., Hirakawa H., Kuhara S., Ogasawara J., Morishita S., Yoshie O., Kusuda J., Hashimoto K. (2003) Comparative DNA sequence analysis of mouse and human CC chemokine gene clusters. J. Interferon Cytokine Res., 23, 37-45.
Suzukawa K., Yamagami T., Ohnuma T., Hirakawa H., Kuhara S., Aso Y., Ishiguro M. (2003) Mutational analysis of amino acid residues involved in catalytic activity of the family 18 chitinase from the tulip bulbs. Biosci. Biotechnol. Biochem., 67, 341-346.
Shimizu T., Ohtani K., Hirakawa H., Ohshima K., Yamashita A., Shiba T., Ogasawara N., Hattori M., Kuhara S., Hayashi H. (2002) Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc. Natl. Acad. Sci. U.S.A., 99, 996-1001.
Kuroda M., Ohta T., Uchiyama I., Baba T., Yuzawa H., Kobayashi I., Cui L., Oguchi A., Aoki K., Nagai Y., Lian J., Ito T., Kanamori M., Matsumaru H., Maruyama A., Murakami H., Hosoyama A., Mizutani-Ui Y., Takahashi N.K., Sawano T., Inoue R., Kaito C., Sekimizu K., Hirakawa H., Kuhara S., Goto S., Yabuzaki J., Kanehisa M., Yamashita A., Oshima K., Furuya K., Yoshino C., Shiba T., Hattori M., Ogasawara N., Hayashi H., Hiramatsu K. (2001) Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet, 357, 1225-1240.
Shirai M., Hirakawa H., Ouchi K., Tabuchi M., Kishi F., Kimoto M., Takeuchi H., Nishida J., Shibata K., Fujinaga R., Yoneda H., Matsushima H., Tanaka C., Furukawa S., Miura K., Nakazawa A., Ishii K., Shiba T., Hattori M., Kuhara S., Nakazawa T. (2000) Comparison of outer membrane protein genes omp and pmp in the whole genome sequences of Chlamydia pneumoniae isolates from Japan and the United States. J. Infect. Dis., 181, S524-S527.
Shirai M., Hirakawa H., Kimoto M., Tabuchi M., Kishi F., Ouchi K., Shiba T., Ishii K., Hattori M., Kuhara S., Nakazawa T. (2000) Comparison of whole genome sequences of Chlamydia pneumoniae J138 from Japan and CWL029 from USA. Nucleic Acids Res., 28, 2311-2314.
Hirakawa H., Muta S., Kuhara S. (1999) The hydrophobic cores of proteins predicted by wavelet analysis. Bioinformatics, 15, 141-148.
Hirakawa H., Kuhara S. (1997) Prediction of hydrophobic cores of proteins using wavelet analysis. Genome Inform. Ser. Workshop Genome Inform., 61-70.