Interests

• • Biomedical informatics

  • AMR surveillance

  • Population genomics

  • Microbiology

  • Metagenomics

  • Epidemiology

  • Biostatistics

  • Evolution

  • Genetics

Publications

1.  Specific variants in ftsI reduce carbapenem susceptibility in Pseudomonas aeruginosa

   • Hirokazu Yano, Noboru Nakata, Koji Yahara, Motoyuki Sugai, Yukari Sato 

   • Microbiology Spectrum, in press. 

2. A pluralistic approach to interpreting surveillance data: the likely decline in the occurrence of Invasive Pneumococcal Disease in Japan during the COVID-19 pandemic

   • Reiko Shimbashi, Yuzo Arima, Koji Yahara, Maki Masutani, Ayu Kasamatsu, Munehisa Fukusumi, Toshiki Kajihara, Takeshi Arashiro, Takuri Takahashi, Miyako Otsuka, Yusuke Kobayashi, Katsuhiro Komase, Yuuki Tsuchihashi, Bin Chang, Junko Amemura-Maekawa, Tomimasa Sunagawa, Motoi Suzuki, Yukihiro Akeda

   • Annals of Epidemiology, in press.

3.  Clinical outcomes of flomoxef versus cefmetazole in hospitalized patients with urinary tract infections: combined retrospective analyses of two real-world databases and in vitro data

   • Takahiro Niimura, Mitsuhiro Goda, Satoshi Nakano, Toshiki Kajihara, Koji Yahara, Aki Hirabayashi, Koji Miyata, Marie Ikai, Motoko Shinohara, Yusuke Minato, Masato Suzuki, Keisuke Ishizawa

   • BMC Medicine, in press.

4.  Prospective Multicenter Surveillance of Non–H. pylori Helicobacter Infections during Medical Checkups, Japan

   • Kengo Tokunaga, Emiko Rimbara, Toshihisa Tsukadaira, Katsuhiro Mabe, Koji Yahara, Hidekazu Suzuki, Tadashi Shimoyama, Mitsushige Sugimoto, Tadayoshi Okimoto, Hidenori Matsui, Masato Suzuki, Keigo Shibayama, Hiroyoshi Ota, Kazunari Murakami, and Mototsugu Kato

   • Emerging Infectious Diseases, in press.

5. Staphylococcus aureus ST764-SCCmecII high-risk clone in bloodstream infections revealed through national genomic surveillance integrating clinical data

   • Junzo Hisatsune, Shoko Kutsuno, Yasuhisa Iwao, Kasumi Ishida-Kuroki, Koji Yahara, Norikazu Kitamura, Toshiki Kajihara, Shizuo Kayama, Yo Sugawara, Hiroki Kitagawa, Hiroki Ohge, Tomoyuki Mizukami, JARBS-SA Consortium, Takeshi Takahashi, Fumio Kawano, Motoyuki Sugai

   • Nature Communications, in press.

6. Lipid fingerprinting by MALDI Biotyper Sirius instrument fails to differentiate the three subspecies of the Mycobacterium abscessus complex

   • Mitsunori Yoshida, Hanako Fukano, Koji Yahara, Satoshi Nakano, Takeshi Komine, Masato Suzuki, Azumi Fujinaga, Kohei Doke, Yoshihiko Hoshino

   • Journal of Clinical Microbiology 2025 Apr 9;63(4):e0148424. doi: 10.1128/jcm.01484-24. Epub 2025 Mar 14. 

7. Emergence of the mobile RND-type efflux pump gene cluster tmexCD1-toprJ1 in Klebsiella pneumoniae clinical isolates in Japan

   • Aki Hirabayashi , Hirokazu Yano , Koji Yahara , Sadao Aoki , Yo Sugawara , Toshiki Kajihara , Naomi Shibayama , Shizuo Kayama , Masato Suzuki , Motoyuki Sugai

   • J Antimicrob Chemother. 2025 Jan 3;80(1):192-199. doi: 10.1093/jac/dkae3095. 

8. Enhanced automated detection of outbreaks of a rare antimicrobial-resistant bacterial species

   • Yumiko Hosaka*, Aki Hirabayashi, Adam Clark, Meghan Baker, Motoyuki Sugai, John Stelling, Koji Yahara*

   • PLOS One, 2024 Oct 24;19(10):e0312477.  doi: 10.1371/journal.pone.0312477.

9. Genomic Analysis and Identification of a Novel Superantigen, SargEY, in Staphylococcus argenteus Isolated from Atopic Dermatitis Lesions 

   • Fatkhanuddin Aziz, Junzo Hisatsune, Hisaya Ono, Junko Kajimura, Liansheng Yu, Kanako Masuda, Hiroki Kitagawa, Yusuke Sato'o, Koji Yahara, Mika Yamaoka, Akio Nakane, Hiroshi Kawasaki, Shoko Obata, Ayano Fukushima-Nomura, Yoshihiro Ito, Meiji Aung, Masayuki Amagai, Siti Isrina Salasia, Hiroki Ohge, Yoichiro Kusunoki, and Motoyuki Sugai

   • mSphere, 2024 Jul 30;9(7):e0050524.  doi: 10.1128/msphere.00505-24.

10. Effects of coronavirus disease 2019 on the spread of droplet-transmitted human-to-human bacteria

    • Toshiki Kajihara, Koji Yahara, Taro Kamigaki, Aki Hirabayashi, Yumiko Hosaka, Norikazu Kitamura, Reiko Shimbashi, Motoi Suzuki, Motoyuki Sugai, and Keigo Shibayama

    • Journal of Infection, 2024 Aug;89(2):106201.  doi: 10.1016/j.jinf.2024.106201. 

11. In vitro activity of cefiderocol against carbapenemase-producing and meropenem-non-susceptible gram-negative bacteria collected in the Japan Antimicrobial Resistant Bacterial Surveillance

    • Shizuo Kayama,# Sayoko Kawakami,# Kohei Kondo, Norikazu Kitamura, Liansheng Yu, Wataru Hayashi, Koji Yahara, Yo Sugawara, Motoyuki Sugai#

    • Journal of Global Antimicrobial Resistance, 2024 Sep:38:12-20. doi: 10.1016/j.jgar.2024.05.009. 

12. Shotgun metagenomic analysis of saliva microbiome suggests Mogibacterium as a factor associated with chronic bacterial osteomyelitis

    • Hiroko Yahara, Souichi Yanamoto, Miho Takahashi, Yuji Hamada, Takuya Asaka, Yoshimasa Kitagawa, Kuniyasu Moridera, Kazuma Noguchi, Yutaka Maruoka, Koji Yahara

    • PLoS One, 2024 May 6;19(5):e0302569.  doi: 10.1371/journal.pone.0302569. 

13. Emergence of an IncX3 plasmid co-harbouring the carbapenemase genes blaNDM-5 and blaOXA-181

    • Hui Zuo, Yo Sugawara, Kohei Kondo, Shizuo Kayama, Sayoko Kawakami, Kohei Uechi, Ami Nakano, Koji Yahara, Motoyuki Sugai

    • JAC-Antimicrobial Resistance, 2024 May 13;6(3):dlae073.  doi: 10.1093/jacamr/dlae073.

14. Epistasis, core-genome disharmony, and adaptation in recombining bacteria

    • Aidan Taylor, Koji Yahara, Ben Pascoe, Seungwon Ko, Leonardos Mageiros, Evangelos Mourkas, Jessica Calland, Santeri Puranen, Matthew Hitchings, Keith Jolley, Carolin Kobras, sion bayliss, Nicola J Williams, Arnoud van Vliet, Julian Parkhill, Martin Maiden, Jukka Corander, Laurence Hurst, Daniel Falush, Paul Keim, Xavier Didelot, David Kelly, and Samuel Sheppard

    • mBio, 2024 Jun 12;15(6):e0058124.  doi: 10.1128/mbio.00581-24

15. Development of selective isolation media for detecting Actinomyces and Schaalia genera from oral specimens containing indigenous bacteria 

    • Sadao Aoki, Hiroko Yahara, Ryoma Nakao, Osamu Tsuzukibashi, and Koji Yahara

    • Access Microbiology, 2024 May 10;6(5):000768.v3.  doi: 10.1099/acmi.0.000768.v3.

16. Nationwide genome surveillance of carbapenem-resistant Pseudomonas aeruginosa in Japan 

    • Hirokazu Yano, Wataru Hayashi, Sayoko Kawakami, Sadao Aoki, Eiko Anzai, Hui Zuo, Norikazu Kitamura, Aki Hirabayashi, Toshiki Kajihara, Shizuo Kayama, Yo Sugawara, Koji Yahara, and Motoyuki Sugai 

    • Antimicrobial Agents and Chemotherapy, 2024 May 2;68(5):e0166923. doi: 10.1128/aac.01669-23. 

17. Comparison of disease and economic burden between MRSA infection and MRSA colonization in a university hospital: A retrospective data integration study 

    • Aki Hirabayashi*, Koji Yahara*, Keisuke Oka, Toshiki Kajihara, Teruko Ohkura, Yumiko Hosaka, Keigo Shibayama, Motoyuki Sugai, Tetsuya Yagi*

    • Antimicrobial Resistance & Infection Control, 2024 Feb 29;13(1):27.  doi: 10.1186/s13756-024-01383-8.  

18. Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing

    • Norikazu Kitamura#, Toshiki Kajihara, Camila Gazolla Volpiano, Myo Naung, Guillaume Méric, Aki Hirabayashi, Hirokazu Yano, Masaya Yamamoto, Fumiaki Yoshida, Tsunesaburo Kobayashi, Sari Yamanashi, Tadao Kawamura, Nobuyuki Matsunaga, Jiro Okochi, Motoyuki Sugai, Koji Yahara*# 

    • Microbial Genomics, 2024 Feb;10(2):001180.

19. Antimicrobial use and combination of resistance phenotypes in bacteraemic Escherichia coli in primary care: a study based on Japanese national data in 2018

    • Yumiko Hosaka, Yuichi Muraki, Toshiki Kajihara, Sayoko Kawakami, Aki Hirabayashi, Masahiro Shimojima, Hiroki Ohge, Motoyuki Sugai, Koji Yahara*

    • Journal of Antimicrobial Chemotherapy, 2023 Dec 12:dkad379. doi: 10.1093/jac/dkad379. Online ahead of print 

20. National genomic surveillance integrating standardized quantitative susceptibility testing clarifies antimicrobial resistance in Enterobacterales

    • Shizuo Kayama#*, Koji Yahara#*, Yo Sugawara*, Sayoko Kawakami, Kohei Kondo, Hui Zuo, Shoko Kutsuno, Norikazu Kitamura, Aki Hirabayashi, Toshiki Kajihara, Hitomi Kurosu, Liansheng Yu, Masato Suzuki, Junzo Hisatsune, Motoyuki Sugai*

    • Nature Communications, 2023 Dec 5;14(1):8046. doi: 10.1038/s41467-023-43516-4 

21. Contrasting genes conferring short- and long-term biofilm adaptation in Listeria

    • William Monteith, Ben Pascoe, Evangelos Mourkas, Jack Clark, Maliha Hakim, Matthew D. Hitchings, Noel McCarthy, Koji Yahara​, Hiroshi Asakura, Samuel K. Sheppard

    • Microbial Genomics, 2023 Oct;9(10):001114. doi: 10.1099/mgen.0.001114

22. Oral and rectal colonization of methicillin-resistant Staphylococcus aureus in long-term care facility residents and their association with clinical status

    • Satoru Kusaka, Azusa Haruta, Miki Kawada-Matsuo, Mi Nguyen-Tra Le, Mineka Yoshikawa, Toshiki Kajihara, Koji Yahara, Junzo Hisatsune, Ryota Nomura, Kazuhiro Tsuga, Hiroki Ohge, Motoyuki Sugai, Hitoshi Komatsuzawa

    • Microbiology and Immunology, in press

23. The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

    • Kaisa Thorell, Zilia Y. Muñoz-Ramıŕez, Difei Wang, Santiago Sandoval-Motta, Rajiv Boscolo Agostini, Silvia Ghirotto, Roberto C. Torres, HpGP Research Network, Daniel Falush, M. Constanza Camargo, Charles S. Rabkin

    • Nature Communications, 2023 Dec 11;14(1):8184. doi: 10.1038/s41467-023-43562-y 

24. Genetic and phenotypic characterizations of IncX3 plasmids harboring blaNDM-5 and blaNDM-16b in Japan

    • Hui Zuo, Yo Sugawara, Shizuo Kayama, Sayoko Kawakami, Koji Yahara, and Motoyuki Sugai

    • Microbiology Spectrum, 2023 Dec 12;11(6):e0216723. doi: 10.1128/spectrum.02167-23. Epub 2023 Oct 19 

25. Distribution, trends, and antimicrobial susceptibility of Bacteroides, Clostridium, Fusobacterium, and Prevotella species causing bacteremia in Japan during 2011–2020: A retrospective observational study based on national surveillance data.

    • Toshiki Kajihara, Koji Yahara, Norikazu Kitamura, Aki Hirabayashi, Yumiko Hosaka, and Motoyuki Sugai. 

    • Open Forum Infectious Diseases, 2023 Jul 3;10(7):ofad334. doi: 10.1093/ofid/ofad334

      • selected as an Editors' Choice paper

26. Association between the proportion of laparoscopic approaches for digestive surgeries and the incidence of consequent surgical site infections, 2009-2019: A retrospective observational study based on national surveillance data in Japan

    • Toshiki Kajihara, Koji Yahara, Aki Hirabayashi, Yumiko Hosaka, Norikazu Kitamura, Motoyuki Sugai, Keigo Shibayama

    • PLOS One, 2023 Feb 17;18(2):e0281838. doi: 10.1371/journal.pone.0281838

27. Disinfectant Susceptibility of 3rd-Generation Cephalosporin/Carbapenem-Resistant Gram-Negative Bacteria Isolated from the Oral Cavity of Long-Term Care Facility Residents

    • Azusa Haruta, Miki Kawada-Matsuo, Mi Le, Mineka Yoshikawa, Toshiki Kajihara, Koji Yahara, Norikazu Kitamura, Shoko Kutsuno, Chika Arai, Maho Takeuchi, Yo Sugawara, Junzo Hisatsune, Kazuhiro Tsuga, Hiroki Ohge, Motoyuki Sugai, and Hitoshi Komatsuzawa

    • Applied and Environmental Microbiology, 2023 Jan 31;89(1):e0171222. doi: 10.1128/aem.01712-22

28. Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing

    • Masato Suzuki, Yusuke Hashimoto, Aki Hirabayashi, Koji Yahara, Mitsunori Yoshida, Hanako Fukano, Yoshihiko Hoshino, Keigo Shibayama, and Haruyoshi Tomita

    • Methods Mol Biol. 2023;2632:227-246. doi: 10.1007/978-1-0716-2996-3_16. 

29. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations 

    • Daniel Falush, Harry Thorpe, Elise Tourrette, Koji Yahara, Filipa Vale, Siqi Liu, Monica Oleastro, Teresa Alarcon, Tsachi Perets, Saeid Latifi-Navid, Yoshio Yamaoka, Beatriz Martinez-Gonzalez, Ioannis Karayiannis, Timokratis Karamitros, Dionyssios Sgouras, Wael Elamin, Ben Pascoe, Samuel Sheppard, Jukka Ronkainen, Pertti Aro, Lars Engstrand, Lars Agreus, Sebastian Suerbaum, and Kaisa Thorell 

    • Nature Communications, 2022 Nov 11;13(1):6842. doi: 10.1038/s41467-022-34475-3 

30. Distribution, trends, and antifungal susceptibility of Candida species causing candidemia in Japan, 2010-2019: A retrospective observational study based on national surveillance data

    • Toshiki Kajihara, Koji Yahara, Minoru Nagi, Norikazu Kitamura, Aki Hirabayashi, Yumiko Hosaka, Masahiro Abe, Yoshitsugu Miyazaki, and Motoyuki Sugai

    • Medical Mycology, 2022 Sep 29;60(9):myac071. doi: 10.1093/mmy/myac071.

31. Oral and rectal colonisation by antimicrobial-resistant gram-negative bacteria and their association with death among residents of long-term care facilities: A prospective, multicentre, observational, cohort study

    • Toshiki Kajihara#, Koji Yahara#, Mineka Yoshikawa, Azusa Haruta, Miki Kawada-Matsuo, Mi Nguyen-Tra Le, Chika Araid Maho Takeuchi, Norikazu Kitamura, Yo Sugawara, Junzo Hisatsune, Shizuo Kayama, Kouji Ohta, Kazuhiro Tsuga, Hitoshi Komatsuzawa, Hiroki Ohge, Motoyuki Sugai#

    • Gerontology, 2022 Oct 6;1-12.  doi: 10.1159/000525759

32. Whole blood transcriptome profiling identifies gene expression subnetworks and a key gene characteristic of the rare type of osteomyelitis

    • Hiroko Yahara, Souichi Yanamoto, Miho Takahashi, Yuji Hamada, Haruo Sakamoto, Takuya Asaka, Yoshimasa Kitagawa, Kuniyasu Moridera, Kazuma Noguchi, Masaya Sugiyama, Yutaka Maruoka, Koji Yahara

    • Biochem Biophys Rep. 2022 Aug 27;32:101328. doi: 10.1016/j.bbrep.2022.101328

33. Genomic epidemiology and temperature dependency of hypermucoviscous Klebsiella pneumoniae in Japan

    • Mi Nguyen-Tra Le, Shizuo Kayama, Kelly L. Wyres, Liansheng Yu, Junzo Hisatsune, Masato Suzuki, Koji Yahara, Tsuneko Terachi, Kana Sawa, Shin Takahashi, Toshihiko Okuhara, Kunihiko Kohama, Kathryn E. Holt, Tetsu Mizutani, Hiroki Ohge, Motoyuki Sugai

    • Microbial Genomics, 2022 May;8(5). doi: 10.1099/mgen.0.000827

34. Emergence of blaNDM-5 carrying Klebsiella aerogenes in Japan 

    • Shizuo Kayama, Liansheng Yu, Sayoko Kawakami, Koji Yahara, Junzo Hisatsune, Masaru Yamamoto, Keiko Yamamoto, Makiko Kiyosuke, Yasushi Kibe, Nobuyuki Shimono, and Motoyuki Sugai 

    • Microbiology Spectrum, 2022 Jun 29;10(3):e0222221. doi: 10.1128/spectrum.02222-21.

35. Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter

    • Evangelos Mourkas, Koji Yahara, Sion C. Bayliss, Jessica K. Calland, Håkan Johansson, Leonardos Mageiros, Zilia Y. Muñoz-Ramirez, Grant Futcher, Guillaume Méric#, Matthew D. Hitchings, Santiago Sandoval-Motta, Javier Torres, Keith A. Jolley, Martin C. J. Maiden, Patrik Ellström, Jonas Waldenström, Ben Pascoe, Samuel K. Sheppard

    • eLife, 2022 Feb 22;11:e73552. doi: 10.7554/eLife.73552.

36. Surveillance of multidrug resistance phenotypes in Staphylococcus aureus in Japan and correlation with whole-genome sequence findings

    • Yumiko Hosaka#, Koji Yahara#, Adam Clark, Hiroki Kitagawa, Junzo Hisatsune, Motoyuki Sugai, Keigo Shibayama, John Stelling

    • Journal of Hospital Infection, 2022, May;123:34-42. doi: 10.1016/j.jhin.2022.02.011. Epub 2022 Feb 22 

      • one minute summary in the Wellcome Trust Conference "Applied Bioinformatics and Public Health Microbiology 2023"

37. Genomic differentiation within East Asian Helicobacter pylori

    • Yuanhai You, Kaisa Thorell, Lihua He, Koji Yahara, Yoshio Yamaoka, Jeong- Heon Cha, Kazunari Murakami, Yukako Katsura, TEAMHp, Ichizo Kobayashi#, Daniel Falush#, and Jianzhong Zhang#

    • Microbial Genomics, 2022 Feb;8(2):000676. doi: 10.1099/mgen.0.000676 

38. Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates

    • Vo Phuoc Tuan*, Koji Yahara#*, Ho Dang Quy Dung, Tran Thanh Binh, Pham Huu Tung, Tran Dinh Tri, Ngo Phuong Minh Thuan, Vu Van Khien, Tran Thi Huyen Trang, Bui Hoang Phuc, Evariste Tshibangu-Kabamba,Takashi Matsumoto, Junko Akada, Rumiko Suzuki, Tadayoshi Okimoto, Masaaki Kodama, Kazunari Murakami, Hirokazu Yano, Masaki Fukuyo, Noriko Takahashi, Mototsugu Kato, Shin Nishiumi, Takeshi Azuma, Yoshitoshi Ogura, Tetsuya Hayashi, Atsushi Toyoda, Ichizo Kobayashi#, Yoshio Yamaoka#

    • Microbial Genomics,  2021 Nov;7(11). doi: 10.1099/mgen.0.000680

      • oral presentation in the CHRO2022

39. The use of topical antibiotis based on National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB) Open Data in 2017

    • Tomoko Nakanishi, Ryo Inose, Yoshiki Kusama, Masahiro Ishikane, Toshiki Kajihara, Koji Yahara, Motoyuki Sugai, Hiroki Ohge, Norio Ohmagari, Yuichi Muraki

    • Japanese Journal of Infectious Diseases, 2021 Sep 30. doi: 10.7883/yoken.JJID.2021.450

40. Impact of the COVID-19 pandemic on the surveillance of antimicrobial resistance

    • Aki Hirabayashi#, Toshiki Kajihara#, Koji Yahara#, Keigo Shibayama, and Motoyuki Sugai

    • Journal of Hospital Infection, Nov;117:147-156. doi: 10.1016/j.jhin.2021.09.011. Epub 2021 Sep 22. 

41. Plasmid analysis of NDM metallo-β-lactamase-producing Enterobacterales isolated in Vietnam

    • Aki Hirabayashi, Koji Yahara, Satomi Mitsuhashi, So Nakagawa, Tadashi Imanishi, Van Thi Thu Ha, An Van Nguyen, Son Thai Nguyen, Keigo Shibayama, Masato Suzuki

    • PLOS One, 2021 Jul 28;16(7):e0231119.  doi: 10.1371/journal.pone.0231119. eCollection 2021 

42. On-site genomic epidemiological analysis of antimicrobial-resistant bacteria in Cambodia with portable laboratory equipment

    • Aki Hirabayashi, Hideji Yanagisawa, Hiromizu Takahashi, Koji Yahara, Philipp Boeing, Bethan Wolfenden, Vandarith Nov, Vichet Lorn, Mom Veng, Vuth Ann, Chau Darapheak, Keigo Shibayama, Masato Suzuki

    • Frontiers in Microbiology, 2021 May 13;12:675463.  doi: 10.3389/fmicb.2021.675463. eCollection 2021 

43. Disease burden of bloodstream infections caused by antimicrobial-resistant bacteria: A population-level study, Japan, 2015-2018

    • Shinya Tsuzuki, Nobuaki Matsunaga, Koji Yahara, Keigo Shibayama, Motoyuki Sugai, Norio Ohmagari

    • Int J Infect Dis. 2021 May 13;108:119-124. doi: 10.1016/j.ijid.2021.05.018

44. Association between the frequency of surgeries for video-assisted thoracic surgery and the incidence of consequent surgical site infections: A retrospective observational study based on national surveillance data

    • Toshiki Kajihara, Koji Yahara, Aki Hirabayashi, Hitomi Kurosu, Motoyuki Sugai, and Keigo Shibayama

    • BMC Infect Dis. 2021 Apr 17;21(1):363. doi: 10.1186/s12879-021-06050-6

45. Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae. 

    • Koji Yahara#, Kevin C. Ma, Tatum D. Mortimer, Ken Shimuta, Shu-ichi Nakayama, Aki Hirabayashi, Masato Suzuki, Michio Jinnai, Hitomi Ohya, Toshiro Kuroki, Yuko Watanabe, Mitsuru Yasuda, Takashi Deguchi, Vegard Eldholm, Odile B. Harrison, Martin C. J. Maiden, Yonatan H. Grad, Makoto Ohnishi

    • Genome Medicine, 2021 Mar 30;13(1):51. doi: 10.1186/s13073-021-00860-8  

      • oral presentation in the NgoRS 2022

      • lightning talk in the Wellcome Trust Conference "Applied Bioinformatics and Public Health Microbiology 2021"

46. Genome evolution and the emergence of pathogenicity in avian Escherichia coli. 

    • Leonardos Mageiros, Guillaume Méric, Sion C. Bayliss, Johan Pensar, Ben Pascoe, Evangelos Mourkas, Jessica K. Calland, Koji Yahara, Susan Murray, Thomas S. Wilkinson, Lisa K. Williams, Matthew D. Hitchings, Jonathan Porter, Kirsty Kemmett, Edward J. Feil, Keith A. Jolley, Nicola J. Williams, Jukka Corander & Samuel K. Sheppard 

    • Nature Communications, 2021, 12, 765 (2021). https://doi.org/10.1038/s41467-021-20988-w 

47. Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria. 

    • Koji Yahara#, Masato Suzuki, Aki Hirabayashi, Wataru Suda,  Masahira Hattori, Yutaka Suzuki, Yusuke Okazaki   

    • Nature Communications, 2021, Jan 4;12(1):27. doi: 10.1038/s41467-020-20199-9

      • oral presentation in the Wellcome Trust Conference "Applied Bioinformatics and Public Health Microbiology 2021"

48. Geographical distribution of Enterobacterales with a carbapenemase IMP-6 phenotype and its association with antimicrobial use: an analysis using comprehensive national surveillance data on antimicrobial resistance. 

    • Aki Hirabayashi*#, Koji Yahara*#, Toshiki Kajihara, Motoyuki Sugai, and Keigo Shibayama   

    • PLOS One, 2020 Dec 17;15(12):e0243630. doi: 10.1371/journal.pone.0243630.

49. Shotgun metagenome sequencing identification of a set of genes encoded by Actinomyces associated with medication-related osteonecrosis of the jaw. 

    • Hiroko Yahara*#, Akimitsu Hiraki, Yutaka Maruoka, Aki Hirabayashi, Masato Suzuki, Koji Yahara*#  

    • PLOS One, 2020 Nov 30;15(11):e0241676. doi: 10.1371/journal.pone.0241676

50. Antibiotic treatment regimes as a driver of the global population dynamics of a major gonorrhea lineage. 

    • Magnus N Osnes, Lucy van Dorp, Ola B Brynildsrud, Kristian Alfsnes, Thamarai Schneiders, Kate E Templeton, Koji Yahara, Francois Balloux, Dominique A Caugant, Vegard Eldholm  

    • Molecular Biology and Evolution, 2020, msaa282, https://doi.org/10.1093/molbev/msaa282

51. Improved Penicillin Susceptibility of Streptococcus pneumoniae and Increased Penicillin Consumption in Japan, 2013-18. 

    • Shinya Tsuzuki, Takayuki Akiyama, Nobuaki Matsunaga, Koji Yahara, Keigo Shibayama, Motoyuki Sugai, Norio Ohmagari.  

    • PLOS One,  2020, Oct 22;15(10):e0240655. doi: 10.1371/journal.pone.0240655 

52. Japan Nosocomial Infections Surveillance: current status, international collaboration, and future directions of a comprehensive antimicrobial resistance surveillance system. 

    • Toshiki Kajihara*#, Koji Yahara*#, Aki Hirabayash, Keigo Shibayama, and Motoyuki Sugai#.  

    • Japanese Journal of Infectious Diseases, 2020 Aug 31. doi: 10.7883/yoken.JJID.2020.499 

53. Comparison of de-duplication methods used by WHO Global Antimicrobial Resistance Surveillance System (GLASS) and Japan Nosocomial Infections Surveillance (JANIS) in the surveillance of antimicrobial resistance.  

    • Toshiki Kajihara*#, Koji Yahara*#, Sergey Romualdovich Eremin, Barbara Tornimbene, Visanu Thamlikitkul, John Stelling, Aki Hirabayashi, Eiko Anzai, Satoyo Wakai, Nobuaki Matsunaga, Kayoko Hayakawa, Norio Ohmagari, Motoyuki Sugai, and Keigo Shibayama.  

    • PLoS One, 2020 Jun 26;15(6):e0228234. doi: 10.1371/journal.pone.0228234

      • oral presentation in the Wellcome Trust Conference "Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies 2020"

54. National trend of blood-stream infection attributable deaths caused by Staphylococcus aureus and Escherichia coli in Japan. 

    • Shinya Tsuzuki, Nobuaki Matsunaga, Koji Yahara, Yoshiaki Gu, Kayoko Hayakawa, Aki Hirabayashi, Toshiki Kajihara, Motoyuki Sugai, Keigo Shibayama and Norio Ohmagari. 

    • Journal of Infection and Chemotherapy, 2020 Apr;26(4):367-371

55. A targeted genetic association study of the rare type of osteomyelitis

    • Hiroko Yahara#*, Shoichiro Horita*, Souichi Yanamoto, Yoshimasa Kitagawa, Takuya Asaka, Tetsuya Yoda, Keiichi Morita,, Yasuyuki Michi, Masaaki Takechi, Hiroshi Shimasue, Yutaka Maruoka, Eiji Kondo, Jingo Kusukawa, Hiromasa Tsujiguchi, Takehiro Sato, Takayuki Kannon, Hiroyuki Nakamura, Atsushi Tajima, Kazuyoshi Hosomichi#, Koji Yahara#

    • Journal of Dental Research, 2020 Mar;99(3):271-276. doi: 10.1177/0022034520901519. Epub 2020 Jan 24

56. Analysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species

    • Koji Yahara#, Philippe Lehours, and Filipa F Vale#

    • Microbial Genomics, 2019 Aug;5(8). doi: 10.1099/mgen.0.000282

57. Japan Nosocomial Infections Surveillance (JANIS): from a national antimicrobial resistance (AMR) surveillance system to an international collaboration

    • Koji Yahara, Sirenda Vong, Visanu Thamlikitkul, Rujipas Sirijatuphat, John Stelling, Aki Hirabayashi, Keigo Shibayama, Motoyuki Sugai, and Norifumi Shigemoto.

    • AMR Control, 2019, 46-50. PDF

58. Developing a hybrid antimicrobial resistance surveillance system in India: Needs & challenges 

    • Jasmine Kaur, Arun Sharma, Ajay Singh Dhama, Harish Buttolia, V C Ohri, Kamini Walia, Amitesh Kumar Sharma, Koji Yahara, Rafi Ahmad, Harpreet Singh

    • Indian J Med Res. 2019 Feb;149(2):299-302

59. Automated detection of outbreaks of antimicrobial-resistant bacteria in Japan

    • Atsuko Tsutsui*#, Koji Yahara*#, Adam Clark, Kenichi Fujimoto, Sayoko Kawakami, Hiroki Chikumi, Mitsutaka Iguchi, Tetsuya Yagi, Meghan A. Baker, Thomas O’Brien, John Stelling*

    • Journal of Hospital Infection, 2019 Jun;102(2):226-233. doi: 10.1016/j.jhin.2018.10.005. Epub 2018 Oct 12.

60. Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis

    • Guillaume Méric*, Leonardos Mageiros*, Johan Pensar, Maisem Laabei, Koji Yahara, Ben Pascoe, Nattinee Kittiwan, Phacharaporn Tadee, Virginia Post, Sarah Lamble, Rory Bowden, James Bray, Mario Morgenstern, Keith Jolley, Martin Maiden, Edward Feil, Xavier Didelot, Maria Miragaia, Herminia de Lencastre, T. Fintan Moriarty, Holger Rohde, Ruth Massey, Dietrich Mack, Jukka Corander, and Samuel Sheppard

    • Nature Communications, 2018 Nov 28;9(1):5034. doi: 10.1038/s41467-018-07368-7

61. Evaluating the origin and virulence of a Helicobacter pylori cagA-positive strain isolated from a non-human primate

    • Kana Hashi, Chihiro Imai, Koji Yahara, Kamrunnesa Tahmina, Takeru Hayashi, Takeshi Azuma, Takako Miyabe-Nishiwaki, Hideyuki Sato, Masao Matsuoka, Sachi Niimi, Munehiro Okamoto, Masanori Hatakeyama

    • Scientific Reports, 2018 Oct 29;8(1):15981. doi: 10.1038/s41598-018-34425-4.

62. Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial resistance determinants and lineages

    • Koji Yahara#, Shu-ichi Nakayama, Ken Shimuta, Ken-ichi Lee, Masatomo Morita, Takuya Kawahata, Toshiro Kuroki, Yuko Watanabe, Hitomi Ohya, Mitsuru Yasuda, Takashi Deguchi, Xavier Didelot# and Makoto Ohnishi#, on behalf of Antibiotic-Resistant Gonorrhea Study Group

    • Microbial Genomics. 2018 Aug;4(8). doi: 10.1099/mgen.0.000205. Epub 2018 Jul 31.

63. Investigation of recombination-intense viral groups and their genes in the Earth's virome

    • Jan P. Meier-Kolthoff, Jumpei Uchiyama, Hiroko Yahara, David Paez-Espino, and Koji Yahara#

    • Scientific Reports (2018) 8:11496

64. Macroevolution of gastric Helicobacter species unveils interspecies admixture and time of divergence

    • Annemieke Smet*#, Koji Yahara*#, Mirko Rossi*#, Alfred Tay, Steffen Backert, Ensser Armin, James G. Fox, Bram Flahou, Richard Ducatelle, Freddy Haesebrouck&, Jukka Corander&

    • The ISME journal, 2018 Oct;12(10):2518-2531

65. A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk

    • Elvire Berthenet, Koji Yahara, Kaisa Thorell, Ben Pascoe, Guillaume Meric, Jane M. Mikhail, Lars Engstrand, Helena Enroth, Alain Burette, Francis Megraud, Christine Varon, John C Atherton, Sinead Smith, Thomas S. Wilkinson, Matthew D. Hitchings, Daniel Falush and Samuel K. Sheppard

    • BMC Biology (2018) 16:84

66. Rapid and Easy Detection of Low-Level Resistance to Vancomycin in Methicillin-Resistant Staphylococcus aureus by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry

    • Kota Asakura, Takuya Azechi, Hiroshi Sasano, Hidehito Matsui, Hideaki Hanaki, Motoyasu Miyazaki, Tohru Takata, Miwa Sekine, Tomoiku Takaku, Tomonori Ochiai, Norio Komatsu, Keigo Shibayama, Yuki Katayama*#, Koji Yahara*#.

    • PLoS One, 2018 Mar 9;13(3):e0194212. doi: 10.1371/journal.pone.0194212

67. Genome Sequences of 12 Mycobacteriophages Recovered from Archival Stocks in Japan

    • Jumpei Uchiyama, Keijiro Mizukami, Koji Yahara, Shinichiro Kato, Hironobu Murakami, Tadahiro Nasukawa, Shigenobu Matsuzaki, Masahiro Sakaguchi

    • Genome Announcement. 2018 Jun 21;6(25).

68. Identification of stress responsive genes by studying specific relationships between mRNA and protein abundance

    • Shimpei Morimoto, Koji Yahara#

    • Heliyon, 2018 Mar 8;4(3):e00558. doi: 10.1016/j.heliyon.2018.e00558

    • (featured in Science Trends)

69. Trends and patterns of national antimicrobial consumption in Japan from 2004 to 2016

    • Atsuko Tsutsui, Koji Yahara, and Keigo Shibayama

    • Journal of Infection and Chemotherapy, 2018 Feb 7. pii: S1341-321X(18)30008-4. doi: 10.1016/j.jiac.2018.01.003

70. Molecular characterization of IMP-1-producing Enterobacter cloacae complex isolates in Tokyo

    • Kotaro Aoki, Sohei Harada, Koji Yahara, Yoshikazu Ishii, Daisuke Motooka, Shota Nakamura, Yukihiro Akeda, Tetsuya Iida, Kazunori Tomono, Satoshi Iwata, Kyoji Moriya, and Kazuhiro Tateda

    • Antimicrobial Agents and Chemotherapy, 2018 Feb 23;62(3). pii: e02091-17. doi: 10.1128/AAC.02091-17. Print 2018 Mar.

71. Typhoid Vaccination among Japanese Travelers to South Asia and the Factors Associated with Compliance

    • Kenichiro Yaita, Koji Yahara, Nobuyuki Hamada, Yoshiro Sakai, Jun Iwahashi, Kenji Masunaga, and Hiroshi Watanabe

    • Internal Medicine, 2017 Dec 27. doi: 10.2169/internalmedicine.9405-17

72. Emergence of Resistance Mutations in Salmonella enterica serovar Typhi against Fluoroquinolones

    • Takashi Matono, Masatomo Morita, Koji Yahara, Ken-ichi Lee, Hidemasa Izumiya, Mitsuo Kaku, Makoto Ohnishi

    • Open Forum Infectious Diseases, 2017 Nov 2;4(4):ofx230. doi: 10.1093/ofid/ofx230

73. Complete genome sequence of super biofilm-elaborating Staphylococcus aureus isolated in Japan

    • Liansheng Yu, Junzo Hisatsune, Hideki Hirakawa, Emiri Mizumachi, Atsushi Toyoda, Koji Yahara, Motoyuki Sugai

    • Genome Announcements, 2017 Oct 12;5(41). pii: e01043-17. doi: 10.1128/genomeA.01043-17

74. Integration of DPC and clinical microbiological data in Japan reveals importance of confirming a negative follow-up blood culture in patients with MRSA bacteremia

    • Naoki Miyamoto*, Koji Yahara*#, Rie Horita, Tomomi Yano, Naotaka Tashiro, Daiichi Morii, Atsuko Tsutsui, Kenichiro Yaita, Keigo Shibayama and Hiroshi Watanabe

    • Journal of Infection and Chemotherapy, 2017 Oct;23(10):687-691. doi: 10.1016/j.jiac.2017.07.009

75. Prevalence of slow-growth vancomycin non-susceptibility in Methicillin-resistant Staphylococcus aureus.

    • 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.

    • Antimicrobial Agents and Chemotherapy, 2017 Oct 24;61(11). pii: e00452-17. doi: 10.1128/AAC.00452-17

76. Hepatitis B Vaccination Status among Japanese Travelers

    • Kenichiro Yaita, Koji Yahara, Yoshiro Sakai, Jun Iwahashi, Kenji Masunaga, Nobuyuki Hamada, and Hiroshi Watanabe

    • Kurume Medical Journal,2017 May 8;63(3.4):69-76. doi: 10.2739/kurumemedj.MS00018

77. Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations

    • 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

    • Molecular Ecology, 2017 Sep;26(17):4497-4508

78. Recombination-mediated host-adaptation by avian Staphylococcus aureus

    • 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

    • Genome Biology and Evolution, 2017 Apr 1;9(4):830-842

79. Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas

    • 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

    • PLoS Genetics, 2017, 13(2), e1006546

80. A new subclass of intrinsic aminoglycoside nucleotidyltransferases, ANT(3")-II, is horizontally transferred among Acinetobacter spp. by homologous recombination

    • Gang Zhang, Sébastien O. Leclercq, Jingjing Tian, Chao Wang, Koji Yahara, Guomin Ai, Shuangjiang Liu, and Jie Feng

    • PLoS Genetics, 2017, 13(2), e1006602

81. Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.

    • 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

    • Environmental Microbiology, 2017, 19(1), 361-380

82. A genome-wide association study identifies a horizontally transferred bacterial surface adhesin gene associated with antimicrobial resistant strains

    • Masato Suzuki, Keigo Shibayama, and Koji Yahara#

    • Scientific Reports, 2016, Nov 28;6:37811, doi:10.1038/srep37811

83. Population genomic insights into the emergence, crop-adaptation, and dissemination of Pseudomonas syringae pathogens

    • Caroline L. Monteil, Koji Yahara, David J. Studholme, Leonardos Mageiros, Guillaume Méric, Bryan Swingle, Cindy E. Morris, Boris A. Vinatzer, Samuel K. Sheppard

    • Microbial Genomics, 2016, Oct 21;2(10), doi:10.1099/mgen.0.000089

84. Population evolution of Helicobacter pylori through diversification in DNA methylation and interstrain sequence homogenization

    • Kenji K. Kojima, Yoshikazu Furuta, Koji Yahara, Masaki Fukuyo, Yuh Shiwa, Shin Nishiumi, Masaru Yoshida, Takeshi Azuma, Hirofumi Yoshikawa, and Ichizo Kobayashi

    • Molecular Biology and Evolution, 2016, 33(11) 2848-2859

85. A novel approach to Helicobacter pylori pan-genome analysis for identification of genomic islands

    • Ikuo Uchiyama, Jacob Albritton, Masaki Fukuyo, Kenji K. Kojima, Koji Yahara, Ichizo Kobayashi

    • PLoS One, 2016, 11(8), e0159419

86. Identification of epigenetic biomarkers of lung adenocarcinoma through multi-omics data analysis

    • Chie Kikutake, Koji Yahara#

    • PLoS One, 2016 Apr 4;11(4):e0152918

87. Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

    • Koji Yahara, Yoshikazu Furuta, Shimpei Morimoto, Chie Kikutake, Sho Komukai, Dorota Matelska, Stanisław Dunin-Horkawicz, Janusz Bujnicki, Ikuo Uchiyama, Ichizo Kobayashi

    • DNA Research, 2016 Apr;23(2):135-43.

88. The landscape of realized homologous recombination in pathogenic bacteria

    • Koji Yahara, Xavier Didelot, Keith A Jolley, Ichizo Kobayashi, Martin C. J. Maiden, Samuel K. Sheppard and Daniel Falush

    • Molecular Biology and Evolution, 2016 Feb;33(2):456-71

89. Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds in Campylobacter jejuni

    • 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

    • Environmental Microbiology, 2015 Nov;17(11):4779-89

90. 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

    • Yuko Yonezawa*, Koji Yahara*#, Miho Miura, Fumiyo Hieda, Ryoji Yamakawa, Kenji Masunaga, Yasunori Mishima, and Hiroshi Watanabe

    • Journal of Infection and Chemotherapy, 2015 Dec;21(12):837-41

91. Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis

    • 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

    • Genome Biology and Evolution, 7 (5): 1313-1328 (2015)

92. A definitive haplotype map of structural variations determined by microarray analysis of duplicated haploid genomes.

    • Tomoko Tahira, Koji Yahara, Yoji Kukita, Koichiro Higasa, Kiyoko Kato, Norio Wake, Kenshi Hayashi. 

    • Genomics Data 2: 55-59 (2014)

93. A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter.

    • Guillaume Meric, Koji Yahara, Leonardos Mageiros, Ben Pascoe, Martin C. J. Maiden, Keith A. Jolley, and Samuel K. Sheppard.

    • PLoS One, 9(3): e92798 (2014)

94. Efficient inference of recombination hot regions in bacterial genomes

    • Koji Yahara, Xavier Didelot, M. Azim Ansari, Samuel K. Sheppard and Daniel Falush

    • Molecular Biology and Evolution, 31(6): 1593-1605 (2014)

95. Improvement rate of acute otitis media caused by Haemophilus influenzae at one week is significantly associated with the time to recovery

    • Hisakazu Yano, Yoshitaka Yamazaki, Liang Qin, Naohiro Okitsu, Koji Yahara, Mihoko Irimada, Yoichi Hirakata, Mitsuo Kaku, Toshimitsu Kobayashi, and Hiroshi Watanabe

    • Journal of Clinical Microbiology, 51(11):3542-6 (2013)

96. Chromosome painting in silico in a bacterial species reveals fine population structure 

    • Koji Yahara, Yoshikazu Furuta, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi

    • Molecular Biology and Evolution, 30(6):1454-64 (2013)

97. Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species

    • 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 Biology and Evolution, 4 (5): 628-640 (2012)

98. Evolution of cagA oncogene of Helicobacter pylori through recombination

    • Yoshikazu Furuta, Koji Yahara, Masanori Hatakeyama, Ichizo Kobayashi

    • PLoS One, 6(8): e23499 (2011)

99. Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes

    • Mikihiko Kawai, Yoshikazu Furuta, Koji Yahara, Takeshi Tsuru, Kenshiro Oshima, Naofumi Handa, Noriko Takahashi, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi

    • BMC Microbiology, 11:104 (2011)

100. Chronic kidney disease and subclinical lacunar infarction are associated with frontal lobe dysfunction in community-dwelling elderly subjects: The Sefuri Brain MRI Study

     • Hiroshi Yao, Yoshikazu Miwa, Yuki Takashima, Koji Yahara, Takahiro Mori, Akira Uchino, Takefumi Yuzuriha, Toshiyuki Sasaguri, Manabu Hashimoto.

     • Hypertension Research, 1-6 (2011)

101. Clinical study concerning the relationship between community-acquired pneumonia and viral infection in northern Thailand

     • 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

     • Internal Medicine, 50(9):991-8 (2011)

102. Birth and death of genes linked to chromosomal inversion

     • Yoshikazu Furuta, Mikihiko Kawai, Koji Yahara, Noriko Takahashi, Naofumi Handa, Takeshi Tsuru, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi.

     • Proc. Nat. Acad. Sci. USA, 108: 1501-1506 (2011)

103. Computational identification of discriminating features of pathogenic and symbiotic type III secreted effector proteins

     • Koji Yahara, Ying Jiang, Takashi Yanagawa

     • IPSJ Transaction on Bioinformatics, 3: 95-107 (2010) 

     • errata

104. Comparisons of two control measures of weather stripping in reducing blowing dust and aspergillus during hospital renovations

     • Koji Yahara#, Miho Miura, Kenji Masunaga, Kazuhiro Matsumoto, Toshiyuki Miyao, Chiyoko Tanamachi, Koji Hashimoto, Kimitaka Sagawa, and Hiroshi Watanabe.

     • Journal of Infection and Chemotherapy, 16: 431-435 (2010)

105. A definitive haplotype map as determined by genotyping duplicated haploid genomes finds a predominant haplotype preference at copy number variation events.

     • Yoji Kukita, Koji Yahara, Tomoko Tahira, Koichiro Higasa, Miki Sonoda, Ken Yamamoto, Kiyoko Kato, Norio Wake, and Kenshi Hayashi.

     • The American Journal of Human Genetics, Volume 86, Issue 6, 918-928 (2010)

106. Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer.

     • Koji Yahara, Masaki Fukuyo, Akira Sasaki and Ichizo Kobayashi.

     • Proc. Nat. Acad. Sci. USA, 106: 18861-18866 (2009)

107. Evolution of DNA double-strand break repair by gene conversion: coevolution between a phage and a restriction-modification system.

     • Koji Yahara, Ryota Horie, Ichizo Kobayashi, and Akira Sasaki.

     • Genetics, 176: 513-526 (2007)

108. Genetic addiction: selfish gene's strategy for symbiosis in the genome.

     • Atsushi Mochizuki, Koji Yahara, Ichizo Kobayashi, and Yoh Iwasa.

     • Genetics 172: 1309-1323 (2006)

Awards

1. Research Encouragement Award ("Population genomic studies of microbial recombination, phylogeny and population structure"), Society of Genome Microbiology, Japan, 2019

2. Excellent Poster Presentation Award, MRSA forum, 2017

(presented by Kota Asakura about our paper to which I contributed as a corresponding author)

3. 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))

4. Young Scientist Award ("Population genomic and epidemiological studies on microbes and genes"), Society of Genome Microbiology, Japan, 2014

5. Academic Encouragement Award, Kurume University School of Medicine, 2012

6. Excellent Presentation Award, 2011 (Japanese Foundation of Statistical Science Association)

7. SIGBIO Best Paper Award, 2010 (Special Interest Group on Bioinformatics, Information Processing Society of Japan)

8. 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 (22K10597), 2022-

2. Grant-in-Aid for Scientific Research from MEXT (19H04846), 2019-2021

3. Grant-in-Aid for Scientific Research from MEXT (18K17406), 2018-2024

4. Grant-in-Aid for Scientific Research from MEXT (17H05826), 2017-2019

5. U.S.-Japan Cooperative Medical Sciences Program Collaborative Awards, 2017-2018

6. Grant-in-Aid for Scientific Research from MEXT (15K21554), 2015-2019

7. Ishibashi Foundation Research Grant, 2014

8. JSPS Research Fellowships for Young Scientists (PD), 2012-2014

(Superlative Postdoctoral Research Fellow (SPD) candidate) 

9. Research Grant for Young Scientist, JSTF, 2009 (JSTF; The Science and Technology Foundation of Japan

10. Research Grant for Young Scientist, FOST, 2005 (FOST; foundation for the Fusion Of Science and Technology

Contact by e-mail is welcome: k-yahara at niid.go.jp