Publication

Article

1. Fumihito Miura, Miki Miura, Yukiko Shibata, Yoshikazu Furuta, Keisuke Miyamura, Yuki Ino, Asmaa M.A. Bayoumi, Utako Oba, Takashi Ito.
   Identification, expression, and purification of DNA cytosine 5-methyltransferases with short recognition sequences.
   BMC biotechnology, 22, 33 (2022). [PubMed][Journal][bioRxiv]


2. Ryoya Tsujikawa, Jeewan Thapa, Torahiko Okubo, Shinji Nakamura, Saicheng Zhang, Yoshikazu Furuta, Hideaki Higashi, Hiroyuki Yamaguchi.
   Chlamydia trachomatis L2/434/Bu favors hypoxia for its growth in human lymphoid Jurkat cells while maintaining production of proinflammatory cytokines.
   Curr. Microbiol., 79(9):265 (2022). [PubMed][Journal]


3. Jeewan Thapa, Gen Yoshiiri, Koki Ito, Torahiko Okubo, Shinji Nakamura, Yoshikazu Furuta, Hideaki Higashi, Hiroyuki Yamaguchi.
   Chlamydia trachomatis requires functional host-cell mitochondria and NADPH oxidase 4/p38MAPK signaling for growth in normoxia.
   Front. Cell. Infect. Microbiol., 12:902492 (2022). [PubMed][Journal]


4. Ken Natsuga, Yoshikazu Furuta, Shota Takashima, Takuma Nohara, Hsin-Yu Huang, Satoru Shinkuma, Hideki Nakamura, Yousuke Katsuda, Hideaki Higashi, Chao-Kai Hsu, Satoshi Fukushima, Hideyuki Ujiie.
   Cas9-guided haplotyping of three truncation variants in autosomal recessive disease.
   Human Mutat., 43(7): 877-881 (2022). [PubMed][Journal]


5. Yoshikazu Furuta*, Fumihito Miura, Takahiro Ichise, Shouta M M Nakayama, Yoshinori Ikenaka, Tuvshinzaya Zorigt, Mai Tsujinouchi, Mayumi Ishizuka, Takashi Ito, Hideaki Higashi. (*: Corresponding author)
   A GCDGC-specific DNA (cytosine-5) methyltransferase that methylates the GCWGC sequence on both strands and the GCSGC sequence on one strand.
   PLoS ONE, 17(3): e0265225 (2022). [PubMed][Journal]


6. Yoshikazu Furuta*, Mai Tsujinouchi, Misheck Shawa, Tuvshinzaya Zorigt, Yuya Miyajima, Atmika Paudel, Satowa Suzuki, Hideaki Higashi. (*: Corresponding author)
   Complete genome sequences of 24 strains of Bacillus cereus isolated from nosocomial infection and bacteremia cases in Japan.
   Microbiol. Resour. Announc., 11(4): e01203-21 (2022). [PubMed][Journal]


7. Ken Natsuga*, Yoshikazu Furuta*, Shota Takashima, Takuma Nohara, Hideyuki Kosumi, Yosuke Mai, Hideaki Higashi, Hideyuki Ujiie. (*: Co-first and Co-corresponding)
   Detection of revertant mosaicism in epidermolysis bullosa through Cas9-targeted long-read sequencing.
   Human Mutat., 43(4): 529-536 (2022). [PubMed][Journal]


8. Misheck Shawa, Yoshikazu Furuta, Atmika Paudel, O'Brian Kabunda, Evans Mulenga, Maron Mubanga, Harvey Kamboyi, Tuvshinzaya Zorigt, Herman Chambaro, Manyando Simbotwe, Bernard Hang'ombe, Hideaki Higashi.
   Clonal relationship between multidrug-resistant Escherichia coli ST69 from poultry and humans in Lusaka, Zambia.
   FEMS Microbiol Lett., 368(21-24): fnac004 (2022). [PubMed][Journal]


9. Michael A. Lobritz, Ian W. Andrews, Dana Braff, Caroline B.M. Porter, Arnaud Gutierrez, Yoshikazu Furuta, Louis B.G. Cortes, Thomas Ferrante, Sarah C. Bening, Felix Wong, Charley Gruber, Christopher W. Bakerlee, Guillaume Lambert, Graham C. Walker, Daniel J. Dwyer, James J. Collins.
   Increased energy demand from anabolic-catabolic processes drives β-lactam antibiotic lethality.
   Cell Chem. Biol., 29(2): 276-286.e4 (2022). [PubMed][Journal]


10. Tuvshinzaya Zorigt, Satoshi Ito, Norikazu Isoda, Yoshikazu Furuta, Misheck Shawa, Natsagdorj Norov, Baasansuren Lkham, Jargalsaikhan Enkhtuya, Hideaki Higashi.
    Risk factors and spatio-temporal patterns of livestock anthrax in Khuvsgul Province, Mongolia.
    PLoS ONE, 16(11): e0260299 (2021). [PubMed][Journal]


11. Tuvshinzaya Zorigt, Yoshikazu Furuta, Manyando Simbotwe, Akihiro Ochi, Mai Tsujinouchi, Misheck Shawa, Tomoko Shimizu, Norikazu Isoda, Jargalsaikhan Enkhtuya, Hideaki Higashi.
    Development of ELISA based on Bacillus anthracis capsule biosynthesis protein CapA for naturally acquired antibodies against anthrax.
    PLoS ONE, 16(10): e0258317 (2021). [PubMed][Journal]


12. Yoshikazu Furuta*, Cheng Cheng, Tuvshinzaya Zorigt, Atmika Paudel, Shun Izumi, Mai Tsujinouchi, Tomoko Shimizu, Wim G. Meijer, Hideaki Higashi. (*: Corresponding author)
    Direct regulons of AtxA, the master virulence regulator of Bacillus anthracis.
    mSystems, 6(4): e00291-21 (2021). [PubMed][Journal]


13. Atmika Paudel, Yoshikazu Furuta, Hideaki Higashi.
    Silkworm model for Bacillus anthracis infection and virulence determination.
    Virulence, 12(1): 2285-2295 (2021). [PubMed][Journal]


14. Misheck Shawa, Yoshikazu Furuta, Gillan Mulenga, Maron Mubanga, Evans Mulenga, Tuvshinzaya Zorigt, Christone Kaile, Manyando Simbotwe, Atmika Paudel, Bernard Hang'ombe, Hideaki Higashi.
    Novel chromosomal insertions of ISEcp1-bla_CTX-M-15 and diverse antimicrobial resistance genes in Zambian clinical isolates of Enterobacter cloacae and Escherichia coli.
    Antimicrob. Resist. Infect. Control, 10(1): 79 (2021). [PubMed][Journal]


15. Miho Okude, Junji Matsuo, Tomohiro Yamazaki, Kentaro Saito, Yoshikazu Furuta, Shinji Nakamura, Jeewan Thapa, Torahiko Okubo, Hideaki Higashi, Hiroyuki Yamaguchi.
    Distribution of amoebal endosymbiotic environmental chlamydia Neochlamydia S13 via amoebal cytokinesis.
    Microbiol. Immunol., 65(3): 115-124 (2021). [PubMed][Journal]


16. Hirokazu Yano, Md. Zobaidul Alam, Emiko Rimbara, Tomoko F. Shibata, Masaki Fukuyo, Yoshikazu Furuta, Tomoaki Nishiyama, Shuji Shigenobu, Mitsuyasu Hasebe, Atsushi Toyoda, Yutaka Suzuki, Sumio Sugano, Keigo Shibayama, Ichizo Kobayashi.
    Networking and Specificity-Changing DNA Methyltransferases in Helicobacter pylori.
    Front. Microbiol., 11: 1628 (2020). [PubMed][Journal]


17. Yoshihiko Suzuki, Suguru Nishijima, Yoshikazu Furuta, Jun Yoshimura, Wataru Suda, Kenshiro Oshima, Masahira Hattori, Shinichi Morishita.
    Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut.
    Microbiome, 7: 119 (2019). [PubMed][Journal]


18. Manyando Simbotwe, Evans Mulenga, Yoshikazu Furuta, Geoffrey Munkombwe Muuka, Bernard Mudenda Hang'ombe, Hideaki Higashi.
    Geographic distribution of cattle anthrax in Western Zambia.
    Jpn. J. Vet. Res., 67(2): 195-202 (2019). [Journal]


19. Reiko Akamatsu, Masato Suzuki, Keiji Okinaka, Teppei Sasahara, Kunikazu Yamane, Satowa Suzuki, Daisuke Fujikura, Yoshikazu Furuta, Naomi Ohnishi, Minoru Esaki, Keigo Shibayama, Hideaki Higashi.
    Novel sequence type in Bacillus cereus strains associated with nosocomial infections and bacteremia, Japan.
    Emerg. Infect. Dis., 25(5): 883-890 (2019). [PubMed][Journal]


20. Kochi Toyomane, Yoshikazu Furuta, Daisuke Fujikura, Hideaki Higashi.
    Upstream sequence-dependent suppression and AtxA-dependent activation of protective antigens in Bacillus anthracis.
    Peer J, e6718 (2019). [PubMed][Journal]


21. Cynthia Zaman, Takako Osaki, Yoshikazu Furuta, Fuhito Hojo, Hideo Yonezawa, Mutsuko Konno, Satoshi Kurata, Tomoko Hanawa, Shigeru Kamiya.
    Enhanced infectivity of strains of Helicobacter pylori isolated from children compared with parental strains.
    J. Med. Microbiol., 68: 633-641 (2019). [PubMed][Journal]


22. Yoshikazu Furuta, Hayato Harima, Emiko Ito, Fumito Maruyama, Naomi Ohnishi, Ken Osaki, Hirohito Ogawa, David Squarre, Bernard Mudenda Hang'ombe, Hideaki Higashi.
    Loss of bacitracin resistance due to a large genomic deletion among Bacillus anthracis strains.
    mSystems, 3(5): e00182-18 (2018). [PubMed][Journal]


23. Manyando Simbotwe, Daisuke Fujikura, Miyuki Ohnuma, Ryosuke Omori, Yoshikazu Furuta, Geoffrey M. Muuka, Bernard M. Hang’ombe, Hideaki Higashi.
    Development and application of a Bacillus anthracis protective antigen domain-1 in-house ELISA for the detection of anti-protective antigen antibodies in cattle in Zambia.
    PLoS ONE, 13(10): e0205986 (2018). [PubMed][Journal]


24. Melissa Takahashi, Xiao Tan, Aaron J. Dy, Dana Braff, Reid T. Akana, Yoshikazu Furuta, Nina Donghia, Ashwin Ananthakrishnan, James J. Collins.
    A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers.
    Nat. Commun., 9: 3347 (2018). [PubMed][Journal]


25. Noriko Takahashi, Charley C. Gruber, Jason H. Yang, Xiaobo Liu, Dana Braff, Chittampalli Yashaswini, Sakkarin Bhubhanil, Yoshikazu Furuta, Silvana Andreescu, James J. Collins, Graham C. Walker.
    Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality.
    Proc. Nat. Acad. Sci. USA, 114(34): 9164-9169 (2017). [PubMed][Journal]


26. Yingbiao Zhang, Tomoyuki Matsuzaka, Hirokazu Yano, Yoshikazu Furuta, Toshiaki Nakano, Ken Ishikawa, Masaki Fukuyo, Noriko Takahashi, Yutaka Suzuki, Sumio Sugano, Hiroshi Ide, Ichizo Kobayashi.
    Restriction glycosylases: involvement of endonuclease activities in the restriction process.
    Nucleic Acids Res., 45(3): 1392-1403 (2017). [PubMed][Journal]


27. Keith Pardee, Shimyn Slomovic, Peter Q. Nguyen, Jeong Wook Lee, Nina Donghia, Devin Burrill, Tom Ferrante, Fern R. McSorley, Yoshikazu Furuta, Andyna Vernet, Michael Lewandowski, Christopher N. Boddy, Neel S. Joshi, James J. Collins.
    Portable, On-Demand Biomolecular Manufacturing.
    Cell, 167(1): 248-259, e12 (2016). [PubMed][Journal]


28. Kenji K. Kojima*, Yoshikazu Furuta*, Koji Yahara, Masaki Fukuyo, Yuh Shiwa, Shin Nishiumi, Masaru Yoshida, Takeshi Azuma, Hirofumi Yoshikawa, Ichizo Kobayashi. (*: Co-first)
    Population evolution of Helicobacter pylori through diversification in DNA methylation and interstrain sequence homogenization.
    Mol. Biol. Evol., 33(11): 2848-2859 (2016). [PubMed][Journal]


29. Koji Yahara, Yoshikazu Furuta, Shinpei Morimoto, Chie Kikutake, Sho Komukai, Dorota Matelska, Stanisław Dunin-Horkawicz, Janusz M. Bujnicki, Ikuo Uchiyama, Ichizo Kobayashi.
    Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori.
    DNA Research, 23(2): 135-143 (2016). [PubMed][Journal]


30. Yoshikazu Furuta, Mutsuko Konno, Takako Osaki, Hideo Yonezawa, Taichiro Ishige, Misaki Imai, Yuh Shiwa, Mari Shibata-Hatta, Yu Kanesaki, Hirofumi Yoshikawa, Shigeru Kamiya, Ichizo Kobayashi.
    Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection.
    PLoS ONE, 10(5): e0127197 (2015). [PubMed][Journal]


31. Masaki Fukuyo, Toshiaki Nakano, Yingbiao Zhang, Yoshikazu Furuta, Ken Ishikawa, Miki Watanabe-Matsui, Hirokazu Yano, Takeshi Hamakawa, Hiroshi Ide, Ichizo Kobayashi.
    Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities.
    Nucleic Acids Res., 43(5): 2841-2852 (2015). [PubMed][Journal]


32. Yoshikazu Furuta, Hiroe Namba-Fukuyo, Tomoko F. Shibata, Tomoaki Nishiyama, Shuji Shigenobu, Yutaka Suzuki, Sumio Sugano, Mitsuyasu Hasebe, Ichizo Kobayashi.
    Methylome diversification through changes in DNA methyltransferase sequence specificity.
    PLoS Genet., 10(4): e1004272 (2014). [PubMed][Journal]


33. Ken-ichi Miyazono, Yoshikazu Furuta, Miki Watanabe-Matsui, Takuya Miyakawa, Tomoko Ito, Ichizo Kobayashi, Masaru Tanokura.
    A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi.
    Nat. Commun., 5: 3178 (2014). [PubMed][Journal]


34. 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.
    Mol. Biol. Evol., 30(6): 1454-1464 (2013). [PubMed][Journal]


35. Yoshikazu Furuta, Ichizo Kobayashi.
    Movement of DNA sequence recognition domains between non-orthologous proteins.
    Nucleic Acids Res., 40(18): 9218-9232 (2012). [PubMed][Journal]


36. 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 Biol. Evol., 4(5): 628-640 (2012). [PubMed][Journal]


37. Kyungtaek Lim, Yoshikazu Furuta, Ichizo Kobayashi.
    Large variations in bacterial ribosomal RNA genes.
    Mol. Biol. Evol., 29(10): 2937-2948 (2012). [PubMed][Journal]


38. Yoshikazu Furuta, Koji Yahara, Masanori Hatakeyama, Ichizo Kobayashi.
    Evolution of cagA oncogene of Helicobacter pylori through recombination.
    PLoS ONE, 6(8): e23499 (2011). [PubMed][Journal]


39. 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 Microbiol., 11:104 (2011). [PubMed][Journal]


40. Yoshikazu Furuta, Mikihiko Kawai, Ikuo Uchiyama, Ichizo Kobayashi.
    Domain movement within a gene: a novel evolutionary mechanism for protein diversification.
    PLoS ONE, 6(4): e18819 (2011). [PubMed][Journal]


41. Yoshikazu Furuta*, Mikihiko Kawai*, Koji Yahara, Noriko Takahashi, Naofumi Handa, Takeshi Tsuru, Kenshiro Oshima, Masaru Yoshida, Takeshi Azuma, Masahira Hattori, Ikuo Uchiyama, Ichizo Kobayashi. (*: Co-first)
    Birth and death of genes linked to chromosomal inversion.
    Proc. Nat. Acad. Sci. USA, 108: 1501-1506 (2011). [PubMed][Journal]
    Picked up in Research Highlights, Nature, 469: 135 (2011).


42. Feroz Khan, Yoshikazu Furuta, Mikihiko Kawai, Katarzyna Kaminska, Ken Ishikawa, Janusz Bujnicki, Ichizo Kobayashi.
    A putative mobile genetic element carrying a novel Type IIF restriction-modification system (PluTI).
    Nucleic Acids Res., 38: 3019-3030 (2010). [PubMed][Journal]


43. Yoshikazu Furuta, Kentaro Abe, Ichizo Kobayashi.
    Genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements.
    Nucleic Acids Res., 38: 2428-2443 (2010). [PubMed][Journal]

Review, Methods, Commentary

1. Yoshikazu Furuta.
   Detection of DNA Modification Using Nanopore Sequencers.
   In: Arakawa, K. (eds). Nanopore Sequencing.. Methods in Molecular Biology, vol 2632, Humana, New York, NY, 79-90 (2023). [Book]


2. Yoshikazu Furuta, Ichizo Kobayashi.
   Restriction-modification systems as mobile epigenetic elements.
   In: Adam Roberts and Peter Mullany editors. Bacterial Integrative Mobile Genetic Elements. Landes Bioscience, 85-103 (2013). [NCBI bookshelf]


3. Yoshikazu Furuta, Ichizo Kobayashi.
   Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution.
   Mobile Genetic Elements, 2: 292-296 (2012). [PubMed][Journal]

See also My Citations (Google Scholar)

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Presentation

1. Yoshikazu Furuta, Cheng Cheng, Tuvshinzaya Zorigt, Atmika Paudel, Shun Izumi, Mai Tsujinouchi, Tomoko Shimizu, Wim G Meijer, Hideaki Higashi
   Direct regulons of AtxA, the master virulence regulator of Bacillus anthracis.
   The 19th Awaji International Forum on Infection and Immunity, S3-4, September 28st 2021, Sapporo (Online), Japan (oral)


2. Yoshikazu Furuta, Hayato Harima, Emiko Ito, Fumito Maruyama, Naomi Ohnishi, Ken Osaki, Hirohito Ogawa, David Squarre, Bernard Mudenda Hang'ombe, Hideaki Higashi
   Large genomic deletion conferring bacitracin susceptibility on Bacillus anthracis.
   ASM Microbe 2019, EEB-478, June 21st 2019, San Francisco, USA (poster)


3. Yoshikazu Furuta, Hayato Harima, Emiko Ito, Fumito Maruyama, Naomi Ohnishi, Ken Osaki, Hirohito Ogawa, David Squarre, Bernard Mudenda Hang'ombe, Hideaki Higashi
   Large genomic deletion conferring bacitracin susceptibility on Bacillus anthracis.
   The 17th Awaji International Forum on Infection and Immunity, P-34, September 6th 2018, Hyogo, Japan (poster)


4. Yoshikazu Furuta
   Diversity of bacterial epigenome and its contribution to evolution.
   The 12th International Workshop on Advanced Genomics, June 27th 2017, Tokyo, Japan (oral (invited))


5. Yoshikazu Furuta, Ichizo Kobayashi
   Epigenome evolution—Two mechanisms in alteration of DNA sequence recognition domains in restriction-modification systems.
   Bacteria, Archaea & Phages, 141, August 24th 2012, Cold Spring Harbor, New York, US (oral)


6. Yoshikazu Furuta, Mikihiko Kawai, Koji Yahara, Takeshi Tsuru, Noriko Takahashi, Naofumi Handa, Kenshiro Oshima, Masahira Hattori, Masaru Yoshida, Takeshi Azuma, Ikuo Uchiyama, Ichizo Kobayashi
   Novel genome rearrangement mechanisms detected by Helicobacter pylori genome comparison.
   International Union of Microbiological Societies 2011 Congress, BR30-3, September 9th 2011, Sapporo, Japan (oral (invited) and poster)


7. Yoshikazu Furuta, Koji Yahara, Masanori Hatakeyama, Ichizo Kobayashi.
   Evolution of cagA oncogene of Helicobacter pylori through recombination: analysis of all known cagA variants at the DNA sequence level with the single nucleotide resolution.
   16th International Workshop on Campylobacter, Helicobacter, and Related Organisms, A121, August 29th 2011, Vancouver, Canada (poster)


8. Yoshikazu Furuta, Mikihiko Kawai, Koji Yahara, Takeshi Tsuru, Noriko Takahashi, Naofumi Handa, Kenshiro Oshima, Masahira Hattori, Masaru Yoshida, Takeshi Azuma, Ikuo Uchiyama, Ichizo Kobayashi
   Novel genome rearrangement mechanisms detected by H. pylori genome comparison.
   Annual Meeting of the Society for Molecular Biology and Evolution 2011, 84, July 28th 2011, Kyoto, Japan (poster)


9. Yoshikazu Furuta, Mikihiko Kawai, Koji Yahara, Takeshi Tsuru, Noriko Takahashi, Naofumi Handa, Kenshiro Oshima, Masahira Hattori, Masaru Yoshida, Takeshi Azuma, Ikuo Uchiyama, Ichizo Kobayashi
   Genome rearrangements revealed through comparison of four complete genomes of Japanese Helicobacter pylori.
   XXIIIrd International Workshop on Helicobacter and related bacteria in chronic digestive inflammation and gastric cancer, W7.2, September 18th 2010, Rotterdam, The Netherlands (oral)


10. Yoshikazu Furuta, Mikihiko Kawai, Koji Yahara, Takeshi Tsuru, Noriko Takahashi, Naofumi Handa, Kenshiro Oshima, Masahira Hattori, Masaru Yoshida, Takeshi Azuma, Ikuo Uchiyama, Ichizo Kobayashi
    Comparison of four complete genomes of Japanese Helicobacter pylori: Genome rearrangements and genomic islands.
    Infectious Disease Genomics & Global Health 2010, 32, September 13th 2010, Hinxton, UK (poster)

Display option: Yoshikazu Furuta, Furuta Y

Publication

Article

1. Miura F, Miura M, Shibata Y, Furuta Y, Miyamura K, Ino Y, Bayoumi AMA, Oba U, Ito T.
   Identification, expression, and purification of DNA cytosine 5-methyltransferases with short recognition sequences.
   BMC biotechnology, 22, 33 (2022). [PubMed][Journal][bioRxiv]


2. Tsujikawa R, Thapa J, Okubo T, Nakamura S, Zhang S, Furuta Y, Higashi H, Yamaguchi H.
   Chlamydia trachomatis L2/434/Bu favors hypoxia for its growth in human lymphoid Jurkat cells while maintaining production of proinflammatory cytokines.
   Curr. Microbiol., 79(9):265 (2022). [PubMed][Journal]


3. Thapa J, Yoshiiri G, Ito K, Okubo T, Nakamura S, Furuta Y, Higashi H, Yamaguchi H.
   Chlamydia trachomatis requires functional host-cell mitochondria and NADPH oxidase 4/p38MAPK signaling for growth in normoxia.
   Front. Cell. Infect. Microbiol., 12:902492 (2022). [PubMed][Journal]


4. Natsuga K, Furuta Y, Takashima S, Nohara T, Huang HY, Shinkuma S, Nakamura H, Katsuda Y, Higashi H, Hsu CK, Fukushima S, Ujiie H.
   Cas9-guided haplotyping of three truncation variants in autosomal recessive disease.
   Human Mutat., 43(7): 877-881 (2022). [PubMed][Journal]


5. Furuta Y*, Miura F, Ichise T, Nakayama SMM, Ikenaka Y, Zorigt T, Tsujinouchi M, Ishizuka M, Ito T, Higashi H. (*: Corresponding author)
   A GCDGC-specific DNA (cytosine-5) methyltransferase that methylates the GCWGC sequence on both strands and the GCSGC sequence on one strand.
   PLoS ONE, 17(3): e0265225 (2022). [PubMed][Journal]


6. Furuta Y*, Tsujinouchi M, Shawa M, Zorigt T, Miyajima Y, Paudel A, Suzuki S, Higashi H. (*: Corresponding author)
   Complete genome sequences of 24 strains of Bacillus cereus isolated from nosocomial infection and bacteremia cases in Japan.
   Microbiol. Resour. Announc., 11(4): e01203-21 (2022). [PubMed][Journal]


7. Natsuga K*, Furuta Y*, Takashima S, Nohara T, Kosumi H, Mai Y, Higashi H, Ujiie H. (*: Co-first and Co-corresponding)
   Detection of revertant mosaicism in epidermolysis bullosa through Cas9-targeted long-read sequencing.
   Human Mutat., 43(4): 529-536 (2022). [PubMed][Journal]


8. Shawa M, Furuta Y, Paudel A, Kabunda O, Mulenga E, Mubanga M, Kamboyi H, Zorigt T, Chambaro H, Simbotwe M, Hang'ombe B, Higashi H.
   Clonal relationship between multidrug-resistant Escherichia coli ST69 from poultry and humans in Lusaka, Zambia.
   FEMS Microbiol Lett., 368(21-24): fnac004 (2022). [PubMed][Journal]


9. Lobritz MA, Andrews IW, Braff D, Porter CBM, Gutierrez A, Furuta Y, Cortes LBG, Ferrante T, Bening SC, Wong F, Gruber C, Bakerlee CW, Lambert G, Walker GC, Dwyer DJ, Collins JJ.
   Increased energy demand from anabolic-catabolic processes drives β-lactam antibiotic lethality.
   Cell Chem. Biol., 29(2): 276-286.e4 (2022). [PubMed][Journal]


10. Zorigt T, Ito S, Isoda N, Furuta Y, Shawa M, Norov N, Lkham B, Enkhtuya J, Higashi H.
    Risk factors and spatio-temporal patterns of livestock anthrax in Khuvsgul Province, Mongolia.
    PLoS ONE, 16(11): e0260299 (2021). [PubMed][Journal]


11. Zorigt T, Furuta Y, Simbotwe M, Ochi A, Tsujinouchi M, Shawa M, Shimizu T, Isoda N, Enkhtuya J, Higashi H.
    Development of ELISA based on Bacillus anthracis capsule biosynthesis protein CapA for naturally acquired antibodies against anthrax.
    PLoS ONE, 16(10): e0258317 (2021). [PubMed][Journal]


12. Furuta Y*, Cheng C, Zorigt T, Paudel A, Izumi S, Tsujinouchi M, Shimizu T, Meijer WG, Higashi H. (*: Corresponding author)
    Direct regulons of AtxA, the master virulence regulator of Bacillus anthracis.
    mSystems, 6(4): e00291-21 (2021). [PubMed][Journal]


13. Paudel A, Furuta Y, Higashi H.
    Silkworm model for Bacillus anthracis infection and virulence determination.
    Virulence, 12(1): 2285-2295 (2021). [PubMed][Journal]


14. Shawa M, Furuta Y, Mulenga G, Mubanga M, Mulenga E, Zorigt T, Kaile C, Simbotwe M, Paudel A, Hang'ombe BM, Higashi H.
    Novel chromosomal insertions of ISEcp1-bla_CTX-M-15 and diverse antimicrobial resistance genes in Zambian clinical isolates of Enterobacter cloacae and Escherichia coli.
    Antimicrob. Resist. Infect. Control., 10(1): 79 (2021). [PubMed][Journal]


15. Okude M, Matsuo J, Yamazaki T, Saito K, Furuta Y, Nakamura S, Thapa J, Okubo T, Higashi H, Yamaguchi H.
    Distribution of amoebal endosymbiotic environmental chlamydia Neochlamydia S13 via amoebal cytokinesis.
    Microbiol. Immunol., 65(3): 115-124 (2021). [PubMed][Journal]


16. Yano H, Alam MZ, Rimbara E, Shibata TF, Fukuyo M, Furuta Y, Nishiyama T, Shigenobu S, Hasebe M, Toyoda A, Suzuki Y, Sugano S, Shibayama K, Kobayashi I.
    Networking and Specificity-Changing DNA Methyltransferases in Helicobacter pylori.
    Front. Microbiol., 11: 1628 (2020). [PubMed][Journal]


17. Suzuki Y, Nishijima S, Furuta Y, Yoshimura J, Suda W, Oshima K, Hattori M, Morishita S.
    Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut.
    Microbiome, 7: 119 (2019). [PubMed][Journal]


18. Simbotwe M, Mulenga E, Furuta Y, Muuka GM, Hang'ombe BM, Higashi H.
    Geographic distribution of cattle anthrax in Western Zambia.
    Jpn. J. Vet. Res., 67(2): 195-202 (2019). [Journal]


19. Akamatsu R, Suzuki M, Okinaka K, Sasahara T, Yamane K, Suzuki S, Fujikura D, Furuta Y, Ohnishi N, Esaki M, Shibayama K, Higashi H.
    Novel sequence type in Bacillus cereus strains associated with nosocomial infections and bacteremia, Japan.
    Emerg. Infect. Dis., 25(5): 883-890 (2019). [PubMed][Journal]


20. Toyomane K, Furuta Y, Fujikura D, Higashi H.
    Upstream sequence-dependent suppression and AtxA-dependent activation of protective antigens in Bacillus anthracis.
    Peer J, e6718 (2019). [PubMed][Journal]


21. Zaman C, Osaki T, Furuta Y, Hojo F, Yonezawa H, Konno M, Kurata S, Hanawa T, Kamiya S.
    Enhanced infectivity of strains of Helicobacter pylori isolated from children compared with parental strains.
    J. Med. Microbiol., 68: 633-641 (2019). [PubMed][Journal]


22. Furuta Y, Harima H, Ito E, Maruyama F, Ohnishi N, Osaki K, Ogawa H, Squarre D, Hang'ombe BM, Higashi H.
    Loss of bacitracin resistance due to a large genomic deletion among Bacillus anthracis strains.
    mSystems, 3(5): e00182-18 (2018). [PubMed][Journal]


23. Simbotwe M, Fujikura D, Ohnuma M, Omori R, Furuta Y, Muuka GM, Hang’ombe BM, Higashi H.
    Development and application of a Bacillus anthracis protective antigen domain-1 in-house ELISA for the detection of anti-protective antigen antibodies in cattle in Zambia.
    PLoS ONE, 13(10): e0205986 (2018). [PubMed][Journal]


24. Takahashi M, Tan X, Dy AJ, Braff D, Akana RT, Furuta Y, Donghia N, Ananthakrishnan A, Collins JJ.
    A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers.
    Nat. Commun., 9: 3347 (2018). [PubMed][Journal]


25. Takahashi N, Gruber CC, Yang JH, Liu X, Braff D, Yashaswini C, Bhubhanil S, Furuta Y, Andreescu S, Collins JJ, Walker GC.
    Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality.
    Proc. Nat. Acad. Sci. USA, 114(34): 9164-9169 (2017). [PubMed][Journal]


26. Zhang Y, Matsuzaka T, Yano H, Furuta Y, Nakano T, Ishikawa K, Fukuyo M, Takahashi N, Suzuki Y, Sugano S, Ide H, Kobayashi I.
    Restriction glycosylases: involvement of endonuclease activities in the restriction process.
    Nucleic Acids Res., 45(3): 1392-1403 (2017). [PubMed][Journal]


27. Pardee K, Slomovic S, Nguyen PQ, Lee JW, Donghia N, Burrill D, Ferrante T, McSorley FR, Furuta Y, Vernet A, Lewandowski M, Boddy CN, Joshi NS, Collins JJ.
    Portable, On-Demand Biomolecular Manufacturing.
    Cell, 167(1): 248-259, e12 (2016). [PubMed][Journal]


28. Kojima KK*, Furuta Y*, Yahara K, Fukuyo M, Shiwa Y, Nishiumi S, Yoshida M, Azuma T, Yoshikawa H, Kobayashi I. (*: Co-first)
    Population evolution of Helicobacter pylori through diversification in DNA methylation and interstrain sequence homogenization.
    Mol. Biol. Evol., 33(11): 2848-2859 (2016). [PubMed][Journal]


29. Yahara K, Furuta Y, Morimoto S, Kikutake C, Komukai S, Matelska D, Dunin-Horkawicz S, Bujnicki JM, Uchiyama I, Kobayashi I.
    Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori.
    DNA Research, 23(2): 135-143 (2016). [PubMed][Journal]


30. Furuta Y, Konno M, Osaki T, Yonezawa H, Ishige T, Imai M, Shiwa Y, Shibata-Hatta M, Kanesaki Y, Yoshikawa H, Kamiya S, Kobayashi I.
    Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection.
    PLoS ONE, 10(5): e0127197 (2015). [PubMed][Journal]


31. Fukuyo M, Nakano T, Zhang Y, Furuta Y, Ishikawa K, Watanabe-Matsui M, Yano H, Hamakawa T, Ide H, Kobayashi I.
    Restriction-modification system with methyl-inhibited base excision and abasic-site cleavage activities.
    Nucleic Acids Res., 43(5): 2841-2852 (2015). [PubMed][Journal]


32. Furuta Y, Namba-Fukuyo H, Shibata TF, Nishiyama T, Shigenobu S, Suzuki Y, Sugano S, Hasebe M, Kobayashi I.
    Methylome diversification through changes in DNA methyltransferase sequence specificity.
    PLoS Genet., 10(4): e1004272 (2014). [PubMed][Journal]


33. Miyazono K, Furuta Y, Watanabe-Matsui M, Miyakawa T, Ito T, Kobayashi I, Tanokura M.
    A sequence-specific DNA glycosylase mediates restriction-modification in Pyrococcus abyssi.
    Nat. Commun., 5: 3178 (2014). [PubMed][Journal]


34. Yahara K, Furuta Y, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I.
    Chromosome painting in silico in a bacterial species reveals fine population structure.
    Mol. Biol. Evol., 30(6): 1454-1464 (2013). [PubMed][Journal]


35. Furuta Y, Kobayashi I.
    Movement of DNA sequence recognition domains between non-orthologous proteins.
    Nucleic Acids Res., 40(18): 9218-9232 (2012). [PubMed][Journal]


36. Yahara K, Kawai M, Furuta Y, Takahashi N, Handa N, Tsuru T, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I.
    Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species.
    Genome Biol. Evol., 4(5): 628-640 (2012). [PubMed][Journal]


37. Lim K, Furuta Y, Kobayashi I.
    Large variations in bacterial ribosomal RNA genes.
    Mol. Biol. Evol., 29(10): 2937-2948 (2012). [PubMed][Journal]


38. Furuta Y, Yahara K, Hatakeyama M, Kobayashi I.
    Evolution of cagA oncogene of Helicobacter pylori through recombination.
    PLoS ONE, 6(8): e23499 (2011). [PubMed][Journal]


39. Kawai M, Furuta Y, Yahara K, Tsuru T, Oshima K, Handa N, Takahashi N, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I.
    Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes.
    BMC Microbiol., 11:104 (2011). [PubMed][Journal]


40. Furuta Y, Kawai M, Uchiyama I, Kobayashi I.
    Domain movement within a gene: a novel evolutionary mechanism for protein diversification.
    PLoS ONE, 6(4): e18819 (2011). [PubMed][Journal]


41. Furuta Y*, Kawai M*, Yahara K, Takahashi N, Handa N, Tsuru T, Oshima K, Yoshida M, Azuma T, Hattori M, Uchiyama I, Kobayashi I. (*: Co-first)
    Birth and death of genes linked to chromosomal inversion.
    Proc. Nat. Acad. Sci. USA, 108: 1501-1506 (2011). [PubMed][Journal]
    Picked up in Research Highlights, Nature, 469: 135 (2011).


42. Khan F, Furuta Y, Kawai M, Kaminska K, Ishikawa K, Bujnicki J, Kobayashi I.
    A putative mobile genetic element carrying a novel Type IIF restriction-modification system (PluTI).
    Nucleic Acids Res., 38: 3019-3030 (2010). [PubMed][Journal]


43. Furuta Y, Abe K, Kobayashi I.
    Genome comparison and context analysis reveals putative mobile forms of restriction-modification systems and related rearrangements.
    Nucleic Acids Res., 38: 2428-2443 (2010). [PubMed][Journal]

Review, Commentary

1. Furuta Y.
   Detection of DNA Modification Using Nanopore Sequencers.
   In: Arakawa, K. (eds). Nanopore Sequencing.. Methods in Molecular Biology, vol 2632, Humana, New York, NY, 79-90 (2023). [Book]


2. Furuta Y, Kobayashi I.
   Restriction-modification systems as mobile epigenetic elements.
   In: Adam Roberts and Peter Mullany editors. Bacterial Integrative Mobile Genetic Elements. Landes Bioscience, 85-103 (2013). [NCBI bookshelf]


3. Furuta Y, Kobayashi I.
   Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution.
   Mobile Genetic Elements, 2: 292-296 (2012). [PubMed][Journal]

See also My Citations (Google Scholar)

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Presentation

1. Furuta Y, Cheng C, Zorigt T, Paudel A, Izumi S, Tsujinouchi M, Shimizu T, Meijer WG, Higashi H
   Direct regulons of AtxA, the master virulence regulator of Bacillus anthracis.
   The 19th Awaji International Forum on Infection and Immunity, S3-4, September 28st 2021, Sapporo (Online), Japan (oral)


2. Furuta Y, Harima H, Ito E, Maruyama F, Ohnishi N, Osaki K, Ogawa H, Squarre D, Hang'ombe BM, Higashi H
   Large genomic deletion conferring bacitracin susceptibility on Bacillus anthracis.
   ASM Microbe 2019, EEB-478, June 21st 2019, San Francisco, USA (poster)


3. Furuta Y, Harima H, Ito E, Maruyama F, Ohnishi N, Osaki K, Ogawa H, Squarre D, Hang'ombe BM, Higashi H
   Large genomic deletion conferring bacitracin susceptibility on Bacillus anthracis.
   The 17th Awaji International Forum on Infection and Immunity, P-34, September 6th 2018, Hyogo, Japan (poster)


4. Furuta Y
   Diversity of bacterial epigenome and its contribution to evolution.
   The 12th International Workshop on Advanced Genomics, June 27th 2017, Tokyo, Japan (oral (invited))


5. Furuta Y, Kobayashi I
   Epigenome evolution—Two mechanisms in alteration of DNA sequence recognition domains in restriction-modification systems.
   Bacteria, Archaea & Phages, 141, August 24th 2012, Cold Spring Harbor, New York, US (oral)


6. Furuta Y, Kawai M, Yahara K, Tsuru T, Takahashi N, Handa N, Oshima K, Hattori M, Yoshida M, Azuma T, Uchiyama I, Kobayashi I
   Novel genome rearrangement mechanisms detected by Helicobacter pylori genome comparison.
   International Union of Microbiological Societies 2011 Congress, BR30-3, September 9th 2011, Sapporo, Japan (oral (invited) and poster)


7. Furuta Y, Yahara K, Hatakeyama M, Kobayashi I.
   Evolution of cagA oncogene of Helicobacter pylori through recombination: analysis of all known cagA variants at the DNA sequence level with the single nucleotide resolution.
   16th International Workshop on Campylobacter, Helicobacter, and Related Organisms, A121, August 29th 2011, Vancouver, Canada (poster)


8. Furuta Y, Kawai M, Yahara K, Tsuru T, Takahashi N, Handa N, Oshima K, Hattori M, Yoshida M, Azuma T, Uchiyama I, Kobayashi I
   Novel genome rearrangement mechanisms detected by H. pylori genome comparison.
   Annual Meeting of the Society for Molecular Biology and Evolution 2011, 84, July 28th 2011, Kyoto, Japan (poster)


9. Furuta Y, Kawai M, Yahara K, Tsuru T, Takahashi N, Handa N, Oshima K, Hattori M, Yoshida M, Azuma T, Uchiyama I, Kobayashi I
   Genome rearrangements revealed through comparison of four complete genomes of Japanese Helicobacter pylori.
   XXIIIrd International Workshop on Helicobacter and related bacteria in chronic digestive inflammation and gastric cancer, W7.2, September 18th 2010, Rotterdam, The Netherlands (oral)


10. Furuta Y, Kawai M, Yahara K, Tsuru T, Takahashi N, Handa N, Oshima K, Hattori M, Yoshida M, Azuma T, Uchiyama I, Kobayashi I
    Comparison of four complete genomes of Japanese Helicobacter pylori: Genome rearrangements and genomic islands.
    Infectious Disease Genomics & Global Health 2010, 32, September 13th 2010, Hinxton, UK (poster)

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