Koji Yahara's research page


 Interests

  • Bioinformatics
  • Biostatistics
  • Infectious diseases
  • Population genomics
  • Epidemiology
  • Evolution
  • Genetics

Publications

  1. Naoki Miyamoto*, Koji Yahara*#, Rie Horita, Tomomi Yano, Naotaka Tashiro, Daiichi Morii, Atsuko Tsutsui, Kenichiro Yaita, Keigo Shibayama and Hiroshi Watanabe
    Integration of DPC and clinical microbiological data in Japan reveals importance of confirming a negative follow-up blood culture in patients with MRSA bacteremia
    Journal of Infection and Chemotherapy, in press

  2. Yuki Katayama, Takuya Azechi, Motoyasu Miyamoto, Touru Takada, Miwa Sekine, Hidehito Matsui, Hideaki Hanaki, Koji Yahara, Hiroshi Sasano, Kota Asakura, Tomoiku Takaku, Tomonori Ochiai, Norio Komatsu and Henry F. Chambers.
    Prevalence of slow-growth vancomycin non-susceptibility in Methicillin-resistant Staphylococcus aureus.
    Antimicrobial Agents and Chemotherapy, in press

  3. Ben Pascoe, Guillaume Méric, Koji Yahara, Helen Wimaralathna, Susan Murray, Matthew D. Hitchings, Emma L. Sproston, Catherine D. Carrillo, Eduardo N. Taboada, Kerry K. Cooper, Steven Huynh, Alison J. Cody, Keith A. Jolley, Martin C. J. Maiden, Noel D. McCarthy, Xavier Didelot, Craig T. Parker and Samuel K. Sheppard
    Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations
    Molecular Ecology, 2017 Sep;26(17):4497-4508

  4. Susan Murray*, Ben Pascoe*, Guillaume Méric, Leonardos Mageiros, Koji Yahara,, Matthew D. Hitchings, Yasmin Friedmann, Llinos G. Harris, Thomas S. Wilkinson, Fraser J. Gormley, Sarah Wendlandt, Stefan Schwarz, Dietrich Mack, James E. Bray, Sarah Lamble, Rory Bowden, Keith A. Jolley, Martin C. J. Maiden, J. Ross Fitzgerald, Samuel K. Sheppard
    Recombination-mediated host-adaptation by avian Staphylococcus aureus
    Genome Biology and Evolution, 2017 Apr 1;9(4):830-842

  5. Kaisa Thorell*, Koji Yahara*, Elvire Berthenet, Daniel J Lawson, Jane Mikhail, Ikuko Kato, Alfonso Tenorio Mendez, Cosmeri Rizzato, Maria Mercedes Bravo, Rumiko Suzuki, Yoshio Yamaoka, Javier Torres, Samuel K Sheppard, and Daniel Falush
    Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas
    PLoS Genetics, 2017, 13(2), e1006546

  6. Gang Zhang, Sébastien O. Leclercq, Jingjing Tian, Chao Wang, Koji Yahara, Guomin Ai, Shuangjiang Liu, and Jie Feng
    A new subclass of intrinsic aminoglycoside nucleotidyltransferases, ANT(3")-II, is horizontally transferred among Acinetobacter spp. by homologous recombination
    PLoS Genetics, 2017, 13(2), e1006602

  7. Koji Yahara*, Guillaume Méric*, Aidan J. Taylor, Stefan P. W. de Vries, Susan Murray, Ben  Pascoe,  Leonardos  Mageiros,  Alicia  Torralbo,  Ana  Vidal,  Anne  Ridley,  Sho Komukai, Helen Wimalarathna, Alison J. Cody, Frances M. Colles, Noel McCarthy,  David Harris, James E. Bray, Keith A. Jolley, Martin C. J. Maiden, Stephen D. Bentley, Julian Parkhill, Christopher D. Bayliss, Andrew Grant, Duncan Maskell, Xavier Didelot, David J. Kelly, Samuel K. Sheppard
    Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.
    Environmental Microbiology, 2017, 19(1), 361-380

  8. Masato Suzuki, Keigo Shibayama, and Koji Yahara#
    A genome-wide association study identifies a horizontally transferred bacterial surface adhesin gene associated with antimicrobial resistant strains
    Scientifc Reports, 2016, Nov 28;6:37811, doi:10.1038/srep37811

  9. Caroline L. Monteil, Koji Yahara, David J. Studholme, Leonardos Mageiros, Guillaume Méric, Bryan Swingle, Cindy E. Morris, Boris A. Vinatzer, Samuel K. Sheppard
    Population genomic insights into the emergence, crop-adaptation, and dissemination of Pseudomonas syringae pathogens
    Microbial Genomics, 2016, Oct 21;2(10), doi:10.1099/mgen.0.000089

  10. Kenji K. Kojima, Yoshikazu Furuta, Koji Yahara, Masaki Fukuyo, Yuh Shiwa, Shin Nishiumi, Masaru Yoshida, Takeshi Azuma, Hirofumi Yoshikawa, and Ichizo Kobayashi
    Population evolution of Helicobacter pylori through diversification in DNA methylation and interstrain sequence homogenization
    Molecular Biology and Evolution, 2016, 33(11) 2848-2859

  11. Ikuo Uchiyama, Jacob Albritton, Masaki Fukuyo, Kenji K. Kojima, Koji Yahara, Ichizo Kobayashi
    A novel approach to Helicobacter pylori pan-genome analysis for identification of genomic islands
    PLoS One, 2016, 11(8), e0159419

  12. Chie Kikutake, Koji Yahara#
    Identification of epigenetic biomarkers of lung adenocarcinoma through multi-omics data analysis
    PLoS One, 2016 Apr 4;11(4):e0152918

  13. Koji Yahara, Yoshikazu Furuta, Shimpei Morimoto, Chie Kikutake, Sho Komukai, Dorota Matelska, Stanisław Dunin-Horkawicz, Janusz Bujnicki, Ikuo Uchiyama, Ichizo Kobayashi
    Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori
    DNA Research, 2016 Apr;23(2):135-43.

  14. Koji Yahara, Xavier Didelot, Keith A Jolley, Ichizo Kobayashi, Martin C. J. Maiden, Samuel K. Sheppard and Daniel Falush
    The landscape of realized homologous recombination in pathogenic bacteria
    Molecular Biology and Evolution, 2016 Feb;33(2):456-71

  15. Ben Pascoe, Guillaume Méric, Susan Murray, Koji Yahara, Leonardos Mageiros, Ryan Bowen, Nathan H. Jones, Rose E. Jeeves, Hilary M. Lappin-Scott, Hiroshi Asakura, Samuel K. Sheppard
    Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds in Campylobacter jejuni
    Environmental Microbiology, 2015 Nov;17(11):4779-89

  16. Yuko Yonezawa*, Koji Yahara*#, Miho Miura, Fumiyo Hieda, Ryoji Yamakawa, Kenji Masunaga, Yasunori Mishima, and Hiroshi Watanabe
    Risk factors for and circumstances of needlestick and sharps injuries of doctors in operating rooms: a study focusing on surgeries using general anesthesia at Kurume University Hospital, Japan
    Journal of Infection and Chemotherapy, 2015 Dec;21(12):837-41

  17. Guillaume Méric, Maria Miragaia, Mark de Been, Koji Yahara, Ben Pascoe, Leonardos Mageiros, Jane Mikhail, Llinos G. Harris, Thomas S. Wilkinson, Joana Rolo, Sarah Lamble, James E. Bray, Keith A. Jolley, William P. Hanage, Rory Bowden, Martin C. J. Maiden, Dietrich Mack, Hermínia de Lencastre, Edward J. Feil, Jukka Corander, Samuel K. Sheppard
    Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis
    Genome Biology and Evolution, 7 (5): 1313-1328 (2015)

  18. Tomoko Tahira, Koji Yahara, Yoji Kukita, Koichiro Higasa, Kiyoko Kato, Norio Wake, Kenshi Hayashi. A definitive haplotype map of structural variations determined by microarray analysis of duplicated haploid genomes.
    Genomics Data 2: 55-59 (2014)

  19. Guillaume Meric, Koji Yahara, Leonardos Mageiros, Ben Pascoe, Martin C. J. Maiden, Keith A. Jolley, and Samuel K. Sheppard.
    A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter.
    PLoS One, 9(3): e92798 (2014)

  20. Koji Yahara, Xavier Didelot, M. Azim Ansari, Samuel K. Sheppard and Daniel Falush
    Efficient inference of recombination hot regions in bacterial genomes
    Molecular Biology and Evolution, 31(6): 1593-1605 (2014)

  21. Hisakazu Yano, Yoshitaka Yamazaki, Liang Qin, Naohiro Okitsu, Koji Yahara, Mihoko Irimada, Yoichi Hirakata, Mitsuo Kaku, Toshimitsu Kobayashi, and Hiroshi Watanabe
    Improvement rate of acute otitis media caused by Haemophilus influenzae at one week is significantly associated with the time to recovery
    Journal of Clinical Microbiology, 51(11):3542-6 (2013)

  22. Koji Yahara, Yoshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi
    Chromosome painting in silico in a bacterial species reveals fine population structure 
    Molecular Biology and Evolution, 30(6):1454-64 (2013)

  23. Koji Yahara, Mikihiko Kawai, Yoshikazu Furuta, Noriko Takahashi, Naofumi Handa, Takeshi Tsuru, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi
    Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species
    Genome Biology and Evolution, 4 (5): 628-640 (2012)

  24. Yoshikazu Furuta, Koji Yahara, Masanori Hatakeyama, Ichizo Kobayashi
    Evolution of cagA oncogene of Helicobacter pylori through recombination
    PLoS One
    , 6(8): e23499 (2011)

  25. Mikihiko Kawai, Yoshikazu Furuta, Koji Yahara, Takeshi Tsuru, Kenshiro Oshima, Naofumi Handa, Noriko Takahashi, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi
    Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes
    BMC Microbiology
    , 11:104 (2011)

  26. Hiroshi Yao, Yoshikazu Miwa, Yuki Takashima, Koji Yahara, Takahiro Mori, Akira Uchino, Takefumi Yuzuriha, Toshiyuki Sasaguri, Manabu Hashimoto.
    Chronic kidney disease and subclinical lacunar infarction are associated with frontal lobe dysfunction in community-dwelling elderly subjects: The Sefuri Brain MRI Study
    Hypertension Research, 1-6 (2011)

  27. Koyu Hara, Koji Yahara, Kenji Gotoh, Yoko Nakazono, Takahito Kashiwagi, Yoshihiro Imamura, Nobuyuki Hamada, Weerayut Kositsakulchai, Tippaya Sanchai, Banyong Khantawa, Prasit Tharavichitkul, Niwat Maneekarn, Thira Sirisanthana, and Hiroshi Watanabe
    Clinical study concerning the relationship between community-acquired pneumonia and viral infection in northern Thailand
    Internal Medicine,
    50(9):991-8 (2011)

  28. Yoshikazu Furuta, Mikihiko Kawai, Koji Yahara, Noriko Takahashi,
    Naofumi Handa, Takeshi Tsuru, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma,
    Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi.
    Birth and death of genes linked to chromosomal inversion
    Proc. Nat. Acad. Sci. USA, 108: 1501-1506 (2011)

  29. Koji Yahara, Ying Jiang, Takashi Yanagawa
    Computational identification of discriminating features of pathogenic and symbiotic type III secreted effector proteins
    IPSJ Transaction on Bioinformatics, 3: 95-107 (2010) errata

  30. Koji Yahara#, Miho Miura, Kenji Masunaga, Kazuhiro Matsumoto, Toshiyuki Miyao, Chiyoko Tanamachi, Koji Hashimoto, Kimitaka Sagawa, and Hiroshi Watanabe.
    Comparisons of two control measures of weather stripping in reducing blowing dust and aspergillus during hospital renovations
    Journal of Infection and Chemotherapy, 16: 431-435 (2010)

  31. Yoji Kukita, Koji Yahara, Tomoko Tahira, Koichiro Higasa, Miki Sonoda, Ken Yamamoto, Kiyoko Kato, Norio Wake, and Kenshi Hayashi.
    A definitive haplotype map as determined by genotyping duplicated haploid genomes finds a predominant haplotype preference at copy number variation events.
    The American Journal of Human Genetics, Volume 86, Issue 6, 918-928 (2010)

  32. Koji Yahara, Masaki Fukuyo, Akira Sasaki and Ichizo Kobayashi.
    Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer.
    Proc. Nat. Acad. Sci. USA, 106: 18861-18866 (2009)

  33. Koji Yahara, Ryota Horie, Ichizo Kobayashi, and Akira Sasaki.
    Evolution of DNA double-strand break repair by gene conversion:
    coevolution between a phage and a restriction-modification system.
    Genetics, 176: 513-526 (2007)

  34. Atsushi Mochizuki, Koji Yahara, Ichizo Kobayashi, and Yoh Iwasa.
    Genetic addiction: selfish gene's strategy for symbiosis in the genome.
    Genetics 172: 1309-1323 (2006)


Awards

  1. Excellent Study Award, Japanese Society for Infection Prevention and Control, 2016
    (to a former master course student Yuko Yonezawa, and our paper Yonezawa, Yahara et al (2015))
  2. Young Scientist Award, Society of Genome Microbiology, Japan, 2014
  3. Academic Encouragement Award, Kurume University School of Medicine, 2012
  4. Excellent Presentation Award, 2011 (Japanese Foundation of Statistical Science Association)
  5. SIGBIO Best Paper Award, 2010 (Special Interest Group on Bioinformatics, Information Processing Society of Japan)
  6. SIGBIO Best Student Presentation Award, 2010 (Special Interest Group on Bioinformatics, Information Processing Society of Japan)

Grant and Scholarships

  1. Grant-in-Aid for Scientific Research from MEXT (15K21554), 2015-
  2. Ishibashi Foundation Research Grant, 2014
  3. JSPS Research Fellowships for Young Scientists (PD), 2012-2014
    (Superlative Postdoctoral Research Fellow (SPD) candidate) 
  4. Research Grant for Young Scientist, JSTF, 2009 (JSTF; The Science and Technology Foundation of Japan
  5. Research Grant for Young Scientist, FOST, 2005 (FOST; foundation for the Fusion Of Science and Technology