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日本語文献(研究室メンバーによる)

(〜2012年4月)
  1. 南波宏枝、小林一三:日本のピロリ菌は世界のピロリ菌とどう違うのでしょうか. Helicobacter Research, 2012年8月号（8月1日発行）
  2. 小林一三: 遺伝子にハマって進化する. Carl Zimmer （カール・ジンマー）著、長谷川真理子監訳「進化」、岩波書店, 刊行中, (2012)
  3. Ritesh Kumar、Desirazu N. Rao （リテシ・クマール、デシラズ・N・ラオ）著、福世真樹、小林一三 訳: ピロリ菌の制限修飾系: 埋もれた財宝。細胞工学, Vol.31, No.4: 480-484 (2012)
  4. 古田芳一、小林一三:タンパク質のドメイン間での配列の移動(DoMo): 新しい遺伝子多様化機構とエピゲノム単位の進化。細胞工学, Vol.31, No.4: 474-479 (2012)
  5. 古田芳一: cagA 発癌遺伝子の構造多様性と進化。細胞工学, Vol.31, No.3: 364-369 (2012)
  6. 古田芳一、河合幹彦、内山郁夫、小林一三: ピロリ菌エピジェネティックス遺伝子の東西比較から発見された「遺伝子内ドメイン移動によるタンパク多様化」。日本ヘリコバクター学会誌、Vol.13, No.2: 36-39 (2012)
  7. 小林一三、古田芳一、河合幹彦: 遺伝子の誕生と崩壊の新しい仕組み：逆位を伴う重複. 細胞工学、Vol.31, No.1:90-97 (2011)
  8. 小林一三: ピロリ菌日本系統ゲノム: 超悪玉（？）発癌細菌の素顔. Helicobacter Research, 2011年12月号 (Vol.15 No.6: 38-46)
  9. 小林一三: ピロリ菌の全ゲノム解読からわかること．Helicobacter Research, 2010年8月号 (Vol.14 No.4: 265-272)
  10. 半田直史: 相同組換え初期反応に重要なリセクション。生化学第82巻, 第2号: 126-130 (2010)
  11. 小林一三、河合幹彦、矢原耕史、古田芳一、鶴剛史、高橋規子、半田直史、吉田優、大島健志朗、内山郁夫、東健、服部正平: 日本分離ピロリ菌４株の全ゲノム解読と種内比較解析についてのプログレス・レポート。日本ヘリコバクター学会誌Vol.11, No.2: 31-38 (2010)
  12. 矢原耕史、小林一三: 超利己的遺伝子の自律的進化: ホーミング・エンドヌクレアーゼ遺伝子は閉じた集団でどう生き延びるか。 細胞工学、Vol.29, No.2: 190-195 (2010)
  13. 小林一三、半田直史、河合幹彦，高橋規子、福田江里：ゲノムDNA二重鎖切断とその修復 の高感度検出法の開発。宇宙利用シンポジウム (Proceedings of the twenty-fifth Space Utilization Symposium.) Space Utilization Research, 25: 39-41 (2009)
  14. 小林一三: 近縁複数全ゲノム配列比較によるゲノム進化ダイナミクスの解明. 実験医学増刊号「生命研究への応用と開発が進むバイオデータベースとソフトウェア最前線」 森下真一、阿久津達也編、pp.216-219, 2008
  15. 石川健、小林一三: 制限酵素が回文構造を切断することが多い理由. 日本医事新報、刊行中
  16. 小林一三、半田直史: 組換え酵素、今堀和友　山川民夫 監修　 大島泰郎、鈴木紘一、脊山洋右、新井洋由、石浦章一、大隈良典、岸本健雄、正木春彦、山本一夫（編） 生化学辞典　第4版、p.380. 東京化学同人, 2007
  17. 河合幹彦，小林一三: 近縁ゲノム比較によるゲノム再編進化過程の解析. 生物の科学遺伝 別冊No.21「日本の遺伝学の潮流」 pp.282-289. NTS, 2007
  18. 半田直史: RecBCD酵素の精製法　タンパク質実験マニュアル（胡桃坂編）　朝倉書店: 22-31, 2006.
  19. 矢原耕史、小林一三: 有害遺伝子なしでは生き残れなくなったゲノム. 伏見譲、 西垣功一（編）「進化・情報・かたち --- “生命知”のパースペクティブ」、pp.79-99. 培風館、 2006.
  20. 小林一三: ゲノムはなぜ変わるのか：原核生物を中心に. 斎藤成也・佐藤矩行 （編）、シリーズ「進化学」第２巻「遺伝子とゲノムの進化」、岩波書店、2006.
  21. 半田直史: ゲノムを維持する組換え酵素の一分子生化学　蛋白核酸酵素　Vol.50 No.11 1429-1435 2005.
  22. 広瀬彩、小林一三: バクテリオファージ・ラムダ。石川統、黒岩常祥、永田和宏（編）、細胞生物学事典、朝倉書店、pp.342-345. 2005
  23. 小林一三、石川健: 制限酵素修飾酵素遺伝子の自己増殖の発見。海洋、号外33号、128-136, 2003.
  24. 小林一三: メイナードスミス博士京都賞受賞記念ワークショップ講演：ゲームの場としてのゲノム --- あるいは、遺伝子はなぜ愛し合うのか？　遺伝、56, 70-76, 2002.
  25. 小林一三:　ゲノム比較：ゲノムを造り替えていた制限酵素修飾酵素遺伝子. 榊佳之、小原雄治、大木操、金久実、高木利久、菅野純夫、小笠原直毅（編）、蛋白質核酸酵素、臨時増刊号「ゲノムサイエンスの新たなる挑戦」46：2393-2399、2001.
  26. 小林一三:　なぜ微生物実験進化か？　SHINKA, 10、31-34、2000.
  27. 小林一三:　ゲノムはなぜ変わるのか？　利己的な動く遺伝子たちのコミュニティーとしてのゲノム.　科学、70: 335-345, 2000.　
  28. 小林一三:　制限酵素は病原体である --- 制限修飾遺伝子の“動く遺伝子“としての活動とゲノムの防御と多型.　細胞工学、18: 1846-1857, 1999.　
  29. 半田直史、小林一三:　ゲノムにとっての自己と非自己.　臨床免疫,　31: 222-227. 1999.
  30. 内藤泰宏、小林一三: 相同組換え法による遺伝子導入. 遺伝子治療開発研究ハンドブック. エヌ・ティー・エス.　日本遺伝子治療学会. 310-321, 1999.
  31. 半田直史、小林一三:　「利己的な遺伝子」にプログラムされる死. 遺伝　52: 61-67, 1998.
  32. 小林一三:　反「利己的遺伝子」戦略としての性.　遺伝、52: 27-33, 1998.　
  33. 半田直史、小林一三:　死をプログラムする利己的遺伝子. 最新医学　52: 2057-2064, 1997.
  34. 半田直史、小林一三:　死をプログラムする細菌の遺伝子. バイオクリニカ　12: 352-355, 1997.
  35. 半田直史、小林一三:　相同組換えの機序と遺伝子治療への応用. 治療学　31: 429-433, 1997.
  36. 小林一三: プログラムされた遺伝子の死.　科学、66: 362-371, 1996.
  37. 小林一三: “利己的な遺伝子”単位としての制限酵素メチル化酵素系. 細胞工学、 14: 1015-1022,　1995.

Publications in English by Ichizo Kobayashi and Colleagues

Last modified on 05/14/2012

  1. Naofumi Handa, Liang Yang, Mark S. Dillingham, Ichizo Kobayashi, Dale B. Wigley, Stephen C. Kowalczykowski. Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, χ, by RecBCD enzyme. Proc. Nat. Acad. Sci. USA, accepted.
  2. 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]
  3. Kyungtaek Lim, Yoshikazu Furuta, Ichizo Kobayashi. Large variations in bacterial ribosomal RNA genes. Mol. Biol. Evol., epub ahead of print. [PubMed][Journal]
    Recommended by Faculty of 1000.
  4. Masaki Fukuyo, Akira Sasaki, Ichizo Kobayashi. Success of a suicidal defense strategy against infection in a structured habitat. Scientific Reports, 2: 238 (2012). [PubMed][Journal]
  5. 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, in press (2012). [NCBI bookshelf]
  6. 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]
  7. Yoko Asakura, Hiroyuki Kojima, Ichizo Kobayashi. Evolutionary Genome Engineering using a Restriction-modification System. Nucleic Acids Research, 39(20): 9034-9046 (2011). [PubMed][Journal]
  8. 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). [PubMed][Journal]
  9. 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]
  10. Iwona Mruk*, Yaoping Liu*, Liying Ge, Ichizo Kobayashi. Antisense RNA associated with biological regulation of a restriction-modification system. Nucleic Acids Research, 39(13): 5622-5632 (2011). (*: Equal contribution) [PubMed][Journal]
  11. Ken Ishikawa, Naofumi Handa, Lauren Sears, Elisabeth Raleigh, Ichizo Kobayashi. Cleavage of a model DNA replication fork by a methyl-specific endonuclease. Nucleic Acids Research, 39(13): 5489-5498 (2011).[PubMed][Journal]
  12. Noriko Takahashi, Seishi Ohashi, Marat R. Sadykov, Yoko Mizutani-Ui, Ichizo Kobayashi. IS-linked Movement of a Restriction-modification System. PLoS ONE, 6: e16554 (2011). [PubMed][Journal]
  13. 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)(*: Equal contribution). [PubMed][Journal]
  14. Feroz Khan and Ichizo Kobayashi. Routes of DNA cleavage by Type II restriction enzymes. American Journal of Biochemistry and Molecular Biology, 1: 20-29 (2011). [Journal]
  15. Ken Ishikawa, Eri Fukuda, Ichizo Kobayashi. Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems. DNA Research, 17:325-342 (2010).[PubMed][Journal]
  16. 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]
  17. 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]
  18. Youhei Fujitani, Junji Kawai, Ichizo Kobayashi. Random-Walk Mechanism in the Genetic Recombination. In Advances in Computational Biology (series: Advances in Experimental Medicine and Biology), Springer, 680: 275-282 (2010). [PubMed]
  19. 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). [PubMed][Journal]
  20. Ichizo Kobayashi and Naofumi Handa. DNA Double-strand Breaks and their Consequences in Bacteria. In Encyclopedia of Life Sciences, John Wiley & Sons, Ltd Chichester, December 2009 [DOI:10.1002/9780470015902.a0000576.pub2]
  21. Naofumi Handa, Ichiro Amitani, Nathan Gumlaw, Steven J Sandler and Stephen C. Kowalczykowski. Single-molecule analysis of a red fluorescent RecA protein reveals a defect in nucleoprotein filament nucleation that relates to its reduced biological functions. Journal of Biological Chemistry, 284: 18664-18673 (2009). [PubMed][Journal]
  22. Naofumi Handa, Asao Ichige and Ichizo Kobayashi. Contribution of RecFOR machinery of homologous recombination to cell survival after loss of a restriction-modification gene complex. Microbiology, 155: 2320-2332 (2009). [PubMed][Journal]
  23. Miki Watanabe-Matsui, Ken-ichi Miyazono, Masaru Tanokura, Tatsuya Sawasaki, Yaeta Endo, Ichizo Kobayashi. Cell-free protein synthesis for structure determination by X-ray crystallography. In Cell-free Expression Systems (Series: Methods in Molecular Biology) Editors: Yaeta Endo, Kazuyuki Takai, Takuya Ueda. Humana Press, pp.149-160 .
  24. Naofumi Handa, Katsumi Morimatsu, Susan T. Lovett, and Stephen C. Kowalczykowski. Reconstitution of Initial Steps of Double-strand DNA Break Repair by the RecF pathway of E. coli. Genes and Development, 23: 1234-1245 (2009). [PubMed][Journal]
  25. Ichizo Kobayashi, Naofumi Handa, Mikihiko Kawai, Noriko Takahashi, Eri Fukuda. Sensitive detection of DNA double-strand breakage and its repair. Proceedings of the twenty-fifth Space Utilization Symposium. Space Utilization Research, 25: 39-41 (2009)
  26. Ken Ishikawa, Naofumi Handa, Ichizo Kobayashi. Cleavage of a model DNA replication fork by a Type I restriction endonuclease, Nucleic Acids Research, 37(11):3531-3544 (2009). [PubMed][Journal]
  27. Yoko Asakura, Ichizo Kobayashi. From Damaged Genome to Cell Surface: Transcriptome Changes during Bacterial Cell Death Triggered by Loss of a Restriction-modification Gene Complex, Nucleic Acids Research, 37(9):3021-31 (2009). [PubMed][Journal]
  28. Eri Fukuda, Katarzyna H Kaminska, Janusz M Bujnicki and Ichizo Kobayashi. Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases. Genome Biology, 9:R163 (2008). [PubMed][Journal]
  29. Katarzyna H Kaminska*, Mikihiko Kawai*, Michal Boniecki, Ichizo Kobayashi, Janusz M Bujnicki. Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site. BMC Structural Biology, 8:48 (2008). (*: Equal contribution) [PubMed][Journal]
  30. Takeshi Tsuru, Ichizo Kobayashi. Multiple genome comparison within a bacterial species reveals a unit of evolution spanning two adjacent genes in a tandem paralog cluster. Molecular biology and evolution, 25: 2457-2473 (2008). [PubMed][Journal]
  31. Satona Ohno*, Naohumi Handa*, Miki Watanabe-Matsui, Noriko Takahashi, Ichizo Kobayashi. Maintenance forced by a restriction-modification system can be modulated by a region in its modification enzyme not essential for the methyltransferase activity. Journal of Bacteriology, 190: 2039-2049 (2008). (*: Equal contribution)[PubMed][Journal]
  32. Yaoping Liu, Ichizo Kobayashi. Negative regulation of EcoRI restriction enzyme gene associated with intragenic reverse promoters. Journal of Bacteriology, 189: 6928-6935 (2007).[PubMed][Journal]
  33. Yaoping Liu, Asao Ichige and Ichizo Kobayashi. Regulation of the EcoRI restriction-modification system: identification of ecoRIM gene promoters and their upstream negative regulators in the ecoRIR gene. Gene, 400: 140-149 (2007).[PubMed][Journal]
  34. 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). [PubMed] [Journal]
  35. Ken-ichi Miyazono*, Miki Watanabe*, Jan Kosinski, Ken Ishikawa, Masayuki Kamo, Tatsuya Sawasaki, Koji Nagata, Janusz M. Bujnicki, Yaeta Endo, Masaru Tanokura, Ichizo Kobayashi. Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Research, 35: 1908-1918 (2007). (*: Equal contribution)[PubMed] [Journal]
  36. Ichizo Kobayashi, Ken Ishikawa, and Miki Watanabe, Chromatin as anti-restriction adaptation: a hypothesis based on restriction enzymes of a novel structure. Proceedings of International Symposium on Extremophiles and Their Applications, 205: 167-174 (2007). [Abstract]
  37. Miki Watanabe, Naofumi Handa, Harumi Yuzawa and Ichizo Kobayashi. Hyperthermophilic DNA methyltransferase, M.PabI, from Pyrococcus abyssi. Proceedings of International Symposium on Extremophiles and Their Applications, 205: 161-166 (2007). [Abstract]
  38. Naofumi Handa and Stephen C. Kowalczykowski. A RecA mutant, RecA730, suppresses the recombination deficiency of the RecBC1004D-Chi* interaction in vitro and in vivo. J Mol Biol, 365(5): 1314-25 (2007). [PubMed] [Journal]
  39. Mikihiko Kawai, Keiichiro Nakao, Ikuo Uchiyama and Ichizo Kobayashi. How genomes rearrange: Genome comparison within bacteria Neisseria suggests roles for mobile elements in formation of complex genome polymorphisms. Gene, 383: 52-63 (2006). [PubMed] [Journal]
  40. Ikuo Uchiyama, Toshio Higuchi, Ichizo Kobayashi, CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes. BMC Bioinformatics, 7: 472 (2006). [PubMed] [Journal]
  41. Miki Watanabe, Harumi Yuzawa, Naofumi Handa, and Ichizo Kobayashi, Hyperthermophilic DNA methyltransferase M.PabI from the archaeon Pyrococcus abyssi. Applied and Environmental Microbiology, 72: 5367-75 (2006). [PubMed] [Journal]
  42. Frederic Chedin, Naofumi Handa, Mark S. Dillingham, and Stephen C. Kowalczykowski, The AddAB helicase/nuclease forms a stable complex with its cognate c sequence during translocation, Journal of Biological Chemistry, 281: 18610-18617 (2006). [PubMed] [Journal]
  43. Takeshi Tsuru, Mikihiko Kawai, Yoko Mizutani-Ui, Ikuo Uchiyama, Ichizo Kobayashi, Evolution of paralogous genes: reconstruction of genome rearrangements through comparison of multiple genomes within Staphylococcus aureus. Molecular Biology and Evolution, 23: 1269-1285 (2006). [PubMed] [Journal]
  44. 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). [PubMed] [Journal]
  45. Mikihiko Kawai, Ikuo Uchiyama and Ichizo Kobayashi. Genome comparison in silico in Neisseria suggests integration of filamentous bacteriophages by their own transposase, DNA Research, 12: 389-401 (2005). [PubMed] [Journal]
  46. Asami Ino, Yasuhiro Naito, Hiroyuki Mizuguchi, Naofumi Handa, Takao Hayakawa and Ichizo Kobayashi. A trial of somatic gene targeting in vivo with an adenovirus vector. Genetic Vaccines and Therapy, 3: 8 (2005). [PubMed] [Journal]
  47. Naofumi Handa and Ichizo Kobayashi. Type III restriction is alleviated by bacteriophage (RecE) homologous recombination function but enhanced by bacterial (RecBCD) function. Journal of Bacteriology, 187: 7362-7373 (2005). [PubMed] [Journal]
  48. Asao Ichige and Ichizo Kobayashi. Stability of EcoRI Restriction-Modification Enzymes In Vivo Differentiates the EcoRI Restriction-Modification System from Other Postsegregational Cell Killing Systems. Journal of Bacteriology, 187: 6612-6621 (2005). [PubMed] [Journal]
  49. Ken Ishikawa, Miki Watanabe, Toshihiro Kuroita, Ikuo Uchiyama, Janusz M. Bujnicki, Bunsei Kawakami, Masaru Tanokura and Ichizo Kobayashi. Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5’GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi. Nucleic Acids Research, 33: e112 (2005). [PubMed] [Journal]
  50. Satyendra Gautam, Arun Sharma, Ichizo Kobayashi. Programmed Cell Death in Microorganisms. In Survival and Death in Bacteria. M. Yamada, Ed. (Research Signpost, Kerala), pp.1-43 (2005).
  51. Naofumi Handa, Piero R. Bianco, Ronald J. Baskin and Stephen C. Kowalczykowski. Direct Visualization of RecBCD Movement Reveals Cotranslocation of the RecD Motor after chi Recognition. Mol Cell. 17:745-750, (2005). [PubMed] [Journal]
  52. Asami Ino, Seiji Yamamoto, Yasufumi Kaneda and Ichizo Kobayashi. Somatic gene targeting with RNA/DNA chimeric oligonucleotides: an analysis with a sensitive reporter mouse system. Journal of Gene Medicine , 6: 1272-1280 (2004). [PubMed] [Journal]
  53. Ichizo Kobayashi. Death as a principle of symbiosis of genetic elements in a genome - restriction enzymes, chromosomes, and mitochondria. Endocytobiosis and Cell Research, 15: 36-44 (2004). [Journal]
  54. Ichizo Kobayashi. Genetic addiction - a principle in symbiosis of genes in a genome. In Plasmid Biology. G. Phillips and B. Funnell, Eds. (ASM Press, Washington, D.C.), pp.105-144 (2004).
  55. Ichizo Kobayashi. Restriction-modification systems as minimal forms of life. In Restriction endonucleases. A. Pingoud (ed.) (Springer-Verlag, Berlin), pp.19-62 (2004). [PDF(1.4MB)]
  56. Maria Spies, Piero R. Bianco, Mark S. Dillingham, Naofumi Handa, Ronald J. Baskin and Stephen C. Kowalczykowski. A molecular throttle: the recombination hotspot chi controls DNA translocation by the RecBCD helicase. Cell. 114: 647-654, 2003. [PubMed] [Journal]
  57. Kohji Kusano, Yasuo Asami, Ayumi Fujita, Masaru Tanokura and Ichizo Kobayashi. Type I restriction enzyme with RecA protein promotes illegitimate recombination. Plasmid, 50: 202-212 (2003). [PubMed] [Journal]
  58. Naofumi Handa and Ichizo Kobayashi. Accumulation of large non-circular forms of the chromosome in recombination-defective mutants of Escherichia coli. BMC Molecular Biology, 4: 5 (2003). [PubMed] [Journal]
  59. Yuki Katayama, Fumihiko Takeuchi, Teruyo Ito, Xiao Xue Ma, Yoko Ui-Mizutani, Ichizo Kobayashi and Keiichi Hiramatsu. Identification in a Methicillin-Susceptible Staphylococcus hominis of an Active Primordial Mobile Genetic Element for the Staphylococcal Cassette Chromosome mec of Methicillin-Resistant Staphylococcus aureus. J. Bacteriol., 185: 2711-2722 (2003). [PubMed] [Journal]
  60. Richard J. Roberts, Marlene Belfort, Timothy Bestor, Ashok S. Bhagwat, Thomas A. Bickle, Jurate Bitinaite, Robert M. Blumenthal, Sergey Kh. Degtyarev, David T. F. Dryden, Kevin Dybvig, Keith Firman, Elizaveta S. Gromova, Richard I. Gumport, Stephen E. Halford, Stanley Hattman, Joseph Heitman, David P. Hornby, Arvydas Janulaitis, Albert Jeltsch, Jytte Josephsen, Antal Kiss, Todd R. Klaenhammer, Ichizo Kobayashi, Huimin Kong, Detlev H. Kruger, Sanford Lacks, Martin G. Marinus, Michiko Miyahara, Richard D. Morgan, Noreen E. Murray, Valakunja Nagaraja, Andrzej Piekarowicz, Alfred Pingoud, Elisabeth Raleigh, Desirazu N. Rao, Norbert Reich, Vladimir E. Repin, Eric U. Selker, Pang-Chui Shaw, Daniel C. Stein, Barry L. Stoddard, Waclaw Szybalski, Thomas A. Trautner, James L. Van Etten, Jorge M.B. Vitor, Geoffrey G. Wilson and Shuang-yong Xu. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res., 31: 1805-1812 (2003). [PubMed] [Journal]
  61. Marat Sadykov, Yasuo Asami, Hironori Niki, Naofumi Handa, Mitsuhiro Itaya, Masaru Tanokura and Ichizo Kobayashi. Multiplication of a restriction modification gene complex. Mol. Microbiol., 48: 417-427 (2003). [PubMed] [Journal]
  62. Ichizo Kobayashi. Life cycle of restriction-modification systems, powers in genome evolution. In Genome Science --- Towards a new paradigm? H. Yoshikawa, N. Ogasawara, N. Satoh, Eds. (Elsevier Science, Amsterdam), pp. 191-202 (2003).
  63. Noriko Takahashi, Hiroshi Yoshikura and Ichizo Kobayashi. An Escherichia coli strain, BJ5183, that shows highly efficient conservative (two-progeny) DNA double-strand break repair of restriction breaks. Gene, 303: 89-97 (2003). [PubMed] [Journal]
  64. Youhei Fujitani and Ichizo Kobayashi. Asymmetric Random Walk in a Reaction Intermediate of Homologous Recombination. J. Theor. Biol., 220: 359-370 (2003). [PubMed] [Journal]
  65. Noriko Takahashi, Yasuhiro Naito, Naofumi Handa and Ichizo Kobayashi. A DNA methyltransferase can protect the genome from post-disturbance attack by a restriction-modification gene complex. J. Bacteriol., 184: 6100-6108 (2002). [PubMed] [Journal]
  66. Youhei Fujitani, Shintaro Mori and Ichizo Kobayashi. A reaction-diffusion model for interference in meiotic crossing-over. Genetics, 161: 365-372 (2002). [PubMed] [Journal]
  67. Ichizo Kobayashi. DNA double-strand break repair in bacteria.　In the Encyclopedia of Life Sciences, (Nature Publishing Group, Macmillan Reference Limited, London), (on-line publication) (2002).
  68. Keiichirou Nakao, Akito Chinen, Ayaka Nobusato, Youhei Fujitani, Ikuo Uchiyama and Ichizo Kobayashi. Relation between restriction modification genes and genome rearrangements suggested from genome sequence comparison within Genus Neisseria. In Genome Informatics 2001. H. Matsuda, L. Wong, S. Miyano, T. Takagi, Eds. (Universal Academy Press, Tokyo, Japan), pp. 398-399 (2001). [PDF]
  69. Ichizo Kobayashi. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Research, 29: 3742-3756 (2001). [PubMed] [Journal]
  70. Makoto Kuroda, Toshiko Ohta, Ikuo Uchiyama, Tadashi Baba, Harumi Yuzawa, Ichizo Kobayashi, Longzhu Cui, Akio Oguchi, Ken-ichi Aoki, Yoshimi Nagai, JianQi Lian, Teruyo Ito, Mutsumi Kanamori, Hiroyuki Matsumaru, Atsushi Maruyama, Hiroyuki Murakami, Akira Hosoyama, Yoko Mizutani-Ui, Noriko K Takahashi, Toshihiko Sawano, Ryu-ichi Inoue, Chikara Kaito, Kazuhisa Sekimizu, Hideki Hirakawa, Satoru Kuhara, Susumu Goto, Junko Yabuzaki, Minoru Kanehisa, Atsushi Yamashita, Kenshiro Oshima, Keiko Furuya, Chie Yoshino, Tadayoshi Shiba, Masahira Hattori, Naotake Ogasawara, Hideo Hayashi and Keiichi Hiramatsu. Whole genome sequencing of methicillin-resistant Staphylococcus aureus. The Lancet. 357, 1225-1240 (2001). [PubMed] [Journal]
  71. N. Handa, Y. Nakayama, M. Sadykov and I. Kobayashi. Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex. Mol. Microbiol. 40, 932-940 (2001). [PubMed] [Journal]
  72. Akito Chinen, Ikuo Uchiyama and Ichizo Kobayashi. Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms. Gene. 259, 109-121 (2000). [PubMed] [Journal]
  73. Ayaka Nobusato, Ikuo Uchiyama, Seishi Ohashi and Ichizo Kobayashi. Insertion with long target duplication: A mechanism for gene mobility suggested from comparison of two complete bacterial genomes. Gene. 259, 99-108 (2000). [PubMed] [Journal]
  74. Ayaka Nobusato, Ikuo Uchiyama and Ichizo Kobayashi. Diversity of restriction modification gene homologues in Helicobacter pylori. Gene. 259, 89-98 (2000). [PubMed] ? [Journal]
  75. Ikuo Uchiyama, Toshio Higuchi and Ichizo Kobayashi. CGAT: Comparative Genome Analysis Tool for Closely Related Microbial Genomes. In Genome Informatics 2000. A.K. Dunker, A. Konagaya, S. Miyano, T. Takagi, Eds. (Universal Academy Press, Tokyo, Japan, 2000) pp 341-343. [PDF]
  76. Akito Chinen, Yasuhiro Naito, Naofumi Handa and Ichizo Kobayashi. Evolution of sequence recognition by restriction-modification enzymes: selective pressure for specificity decrease. Mol. Biol. Evol. 17, 1610-1619(2000). [PubMed] [Journal]
  77. Deana A. Arnold, Naofumi Handa, Ichizo Kobayashi and Stephen C. Kowalczykowski. A novel, 11 nucleotide variant of chi, chi*: one of a class of sequences defining the Escherichia coli recombination hotspot chi. J. Mol. Biol.　300, 469-479 (2000). [PubMed] [Journal]
  78. K. Gerdes, S. Ayora, I. Canosa, P. Ceglowski, R. Diaz, T. Franch, A.P. Gultyaev, R.B. Jens?en, I. Kobayashi, C. Macpherson, D. Summers, C. Thomas, and U. Zielenkiewicz. Plasmid maintenance systems, in The Horizontal Gene Pool, Chap.2. M. Couturier and K. Gerdes, C.M. Thomas, Eds. (Harwood academic publishers gmbh, Amsterdam, 2000) pp. 49-86.
  79. Naofumi Handa, Asao Ichige, Kohji Kusano and Ichizo Kobayashi. Cellular responses to post-segregational killing by restriction-modification genes. J. Bacteriol. 182, 2218-2229 (2000). [PubMed] [Journal]
  80. Y. Fujitani, S. Mori, I. Kobayashi. A Reaction-Diffusion Model for Genetic Interference, in Currents in Computational Molecular Biology. S. Miyano, R. Shamir, T. Takagi, Eds. (Universal Academy Press Inc., Tokyo, 2000) pp. 230-231.
  81. Ichizo Kobayashi, Ayaka Nobusato, Noriko Kobayashi-Takahashi and Ikuo Uchiyama. Shaping the genome -- restriction-modification systems as mobile genetic elements. Current Opinion in Genetics and Development, 9, 649-656 (1999). [PubMed] [Journal]
  82. Naofumi Handa and Ichizo Kobayashi. Post-segregational killing by restriction modification gene complexes: observations of individual cell. Biochimie, 81, 931-938 (1999). [PubMed] [Journal]
  83. Youhei Fujitani and Ichizo Kobayashi. Effect of sequence divergence on homologous recombination as analyzed by the random walk model. Genetics, 153, 1973-1988 (1999). [PubMed] [Journal]
  84. Ichizo Kobayashi. Homologous recombination and sex as a strategy against selfish genes attacking genome. Ann. New York Acad. Sci. 870, 354-356 (1999). [PubMed]
  85. Ichizo Kobayashi. Selfishness and death: raison d'etre of restriction, recombination and mitochondria. Trends in Genetics 14, 368-374 (1998). [PubMed] [Journal]
  86. Y. Naito, T. Naito, I. Kobayashi. Selfish restriction modification genes: Resistance of a resident R/M plasmid to displacement by an incompatible plasmid mediated by host killing. Biol. Chem. 379, 429-436 (1998). [PubMed]
  87. Y. Nakayama and I. Kobayashi. Restriction-modification gene complexes as selfish gene entities: Roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion. Proc. Nat. Acad. Sci. USA 95, 6442-6447 (1998). [PubMed] [Journal]
  88. Y. Fujitani and I. Kobayashi. Mismatch-stimulated destruction of intermediates as an explanation for map expansion in genetic recombination. J. Theor. Biol. 189, 443-447 (1997). [PubMed] [Journal]
  89. N. Handa, S. Ohashi, I. Kobayashi. Clustering of chi sequence in Escherichia coli genome. Microb. Comp. Genomics 2, 287-298 (1997). [PubMed]
  90. N. Handa, S. Ohashi, K. Kusano, I. Kobayashi. c*, a chi-related 11-mer sequence partially active in an E. coli recC* strain. Genes to Cells 2, 525-536 (1997). [PubMed] [Journal]
    91. ?
  91. K. Kusano, K. Sakagami, T. Yokochi, T. Naito, Y. Tokinaga, E. Ueda, I. Kobayashi. A new type of illegitimate recombination is dependent on restriction and homologous interaction. J. Bacteriol. 179, 5380-5390 (1997). [PubMed] [Journal]
  92. N. K. Takahashi, K. Sakagami, K. Kusano, K. Yamamoto, H. Yoshikura, I. Kobayashi. Genetic Recombination through Double-strand Break Repair: Shift from Two-progeny Mode to One-progeny Mode by Heterologous Inserts. Genetics 146, 9-26 (1997). [PubMed] [Journal]
  93. I. Kobayashi. DNA modification and restriction: Selfish behavior of an epigenetic system, in Epigenetic mechanisms of gene regulation. V. Russo, R. Martienssen, A. Riggs, Eds. (Cold Spring Harbor Laboratory Press, New York, 1996) pp. 155-172.
  94. K. Yamamoto, N. Takahashi, Y. Fujitani, H. Yoshikura, I. Kobayashi. Orientation dependence in homologous recombination. Genetics 143, 27-36 (1996). [PubMed] [Journal]
  95. Youhei Fujitani and Ichizo Kobayashi. Random walk model of homologous recombination. Phys. Rev. E 52, 6607-6622 (1995). [PubMed] [Journal]
  96. A. Fujita, K. Sakagami, Y. Kanegae, I. Saito, I. Kobayashi. Gene targeting with a replication-defective adenovirus vector. J. Virol. 69, 6180-6190 (1995). [PubMed] [Journal]
  97. K. Kusano, T. Naito, N. Handa, I. Kobayashi. Restriction-modification systems as genomic parasites in competition for specific sequences. Proc. Natl. Acad. Sci. USA 92, 11095-11099 (1995). [PubMed] [Journal]
  98. Y. Fujitani, K. Yamamoto, I. Kobayashi. Dependence of Frequency of Homologous Recombination on the Homology Length. Genetics 140, 797-809 (1995). [PubMed] [Journal]
  99. T. Naito, K. Kusano, I. Kobayashi. Selfish Behavior of Restriction-Modification Systems. Science 267, 897-899 (1995). [PubMed] [Journal]
  100. T. Yokochi, K. Kusano, I. Kobayashi. Evidence for conservative (two-progeny) DNA double-strand break repair. Genetics 139, 5-17 (1995). [PubMed] [Journal]
  101. K. Kusano, N. Takahashi, H. Yoshikura, I. Kobayashi. Involvement of RecE exonuclease and RecT annealing protein in DNA double-strand break repair by homologous recombination. Gene 138, 17-25 (1994). [PubMed]
  102. Ichizo Kobayashi, Keiko Sakagami, Kohji Kusano, Fujitani Youhei, Noriko Takahashi-Kobayashi and Hiroshi Yoshikura. Homologous interaction as a gene destruction process: Homology-driven non-homologous recombination and double-strand break repair. In Modification of Gene Expression and Non-Mendelian Inheritance, Edited by Oono and Takaiwa, National Institute of Agrobiological Resources, 55-76 (1995).
  103. K. Kusano, N. Takahashi, H. Yoshikura, I. Kobayashi. Involvement of RecE exonuclease and RecT annealing protein in DNA double-strand break repair by homologous recombination. Gene 138, 17-25 (1994). [PubMed] [Journal]
  104. K. Sakagami, Y. Tokinaga, H. Yoshikura, I. Kobayashi. Homology-associated non-homologous recombination in mammalian gene targeting. Proc. Natl. Acad. Sci. USA 91, 8527-8531 (1994). [PubMed] [Journal]
  105. K. Kusano, Y. Sunohara, N. Takahashi, H. Yoshikura, I. Kobayashi. DNA double-strand break repair: Genetic determinants of flanking crossing-over. Proc. Natl. Acad. Sci. USA 91, 1173-1177 (1994). [PubMed] [Journal]
  106. N. Takahashi, K. Kusano, T. Yokochi, Y. Kitamura, H. Yoshikura, I. Kobayashi. Genetic analysis of double-strand break repair in Escherichia coli. J. Bacteriol. 175, 5176-5185 (1993). [PubMed] [Journal]
  107. Kenji Yamamoto, Kohji Kusano, Noriko Takahashi, Hiroshi Yoshikura and Ichizo Kobayashi. Gene conversion in the Escherichia coli RecF pathway: a successive half crossing-over model. Mol. Gen. Genet. 234, 1-13 (1992). [PubMed] [Journal]
  108. N. K. Takahashi, K. Yamamoto, Y. Kitamura, Si-Qin. Luo, H. Yoshikura, I. Kobayashi. Nonconservative recombination in Escherichia coli. Proc. Natl. Acad. Sci. USA 89, 5912-5916 (1992). [PubMed] [Journal]
  109. Ichizo Kobayashi. Mechanisms for gene conversion and homologous recombination: The double-strand break repair model and the successive half crossing-over model. Adv. Biophys. 28, 81-133 (1992). [PubMed] [Journal]
  110. Yoshihiro Kitamura, Hiroshi Yoshikura and Ichizo Kobayashi. Homologous recombination in a mammalian plasmid. Mol. Gen. Genet. 222, 185-191 (1990). [PubMed] [Journal]
  111. N. Takahashi and I. Kobayashi. Evidence for the double-strand break repair model of bacteriophage lambda recombination. Proc. Natl. Acad. Sci. USA 87, 2790-2794 (1990). [PubMed] [Journal]
  112. Kenji Yamamoto, Hiroshi Yoshikura, Noriko Takahashi and Ichizo Kobayashi. Apparent gene conversion in an Escherichia coli rec+ strain is explained by multiple rounds of reciprocal crossing-over. Mol. Gen. Genet. 212, 393-404 (1988). [PubMed] [Journal]
  113. K. Yamamoto, N. Takahashi, H. Yoshikura, I. Kobayashi. Homologous recombination involving a large heterology in Escherichia coli. Genetics 119, 759-769 (1988). [PubMed] [Journal]
  114. I. Kobayashi and N. Takahashi. Double-stranded gap repair of DNA by gene conversion in Escherichia coli. Genetics 119, 751-757 (1988). [PubMed] [Journal]
  115. F. W. Stahl, I. Kobayashi, D. Thaler, M. M. Stahl. Direction of travel of RecBC recombinase through bacteriophage lambda DNA. Genetics 113, 215-227 (1986). [PubMed] [Journal]
  116. Susan M. Rosenberg, Mary M. Stahl, Ichizo Kobayashi and Franklin W. Stahl. Improved in vitro packaging of coliphage lambda DNA: A one strain system free from endogenous phage. Gene 38, 165-175 (1985). [PubMed] [Journal]
  117. Franklin W. Stahl, Ichizo Kobayashi and Mary M. Stahl. In phage lambda, cos is a recombinator in the Red pathway. J. Mol. Biol. 181, 199-209 (1985). [PubMed] [Journal]
  118. I. Kobayashi, M. M. Stahl, F. W. Stahl. The mechanism of the Chi-cos interaction in RecA-RecBC-mediated recombination in phage lambda. Cold Spring Harbor Symp. Quant. Biol. 49, 497-506 (1984). [PubMed]
  119. Ichizo Kobayashi, Mary M. Stahl, Frederic R. Fairfield and Franklin W. Stahl. Coupling with Packaging Explains Appar?ent Nonreciprocality of Chi-Stimulated Recombination of Bacteriophage Lambda by RecA and RecBC Functions. Genetics 108, 773-794 (1984). [PubMed] [Journal]
  120. F. W. Stahl, I. Kobayashi, M. M. Stahl. Chi is activated by a variety of routes, in Mechanisms of DNA replication and recombination, N. R. Cozzarelli, Ed. (Alan R. Liss, New York, 1983) pp. 773-783. [Journal]
  121. M. M. Stahl, I. Kobayashi, F. W. Stahl, S. K. Huntington. Activation of Chi, a recombinator, by the action of an endonuclease at a distant site. Proc. Natl. Acad. Sci. USA 80, 2310-2313 (1983). [PubMed] [Journal]
  122. Ichizo Kobayashi, Mary M. Stahl, David Leach and Franklin W. Stahl. The interaction of cos with Chi is separable from DNA packaging in recA-recBC-mediated recombination of bacteriophage lambda. Genetics 104, 549-570 (1983). [PubMed] [Journal]
  123. Ichizo Kobayashi and Hideo Ikeda. Double Holliday Structure: A possible in vivo intermediate form of general recombination in Escherichia coli. Mol. Gen. Genet. 191, 213-220 (1983). [PubMed] [Journal]
  124. M. Feiss, I. Kobayashi, W. Widner. Separate sites for binding and nicking of bacteriophage lambda DNA by terminase. Proc. Natl. Acad. Sci. USA 80, 955-959 (1983). [PubMed] [Journal]
  125. Franklin W. Stahl, Mary M. Stahl, Lisa Young and Ichizo Kobayashi. Chi-stimulated recombination between phage lambda and the plasmid lambdadv. Genetics 102, 599-613 (1982). [PubMed] [Journal]
  126. F. W. Stahl, I. Kobayashi, M. M. Stahl. Distance from cohesive end site cos determines the replication requirement for recombination in phage lambda. Proc. Natl. Acad. Sci. USA 79, 6318-6321 (1982). [PubMed] [Journal]
  127. I. Kobayashi, H. Murialdo, J. M. Crasemann, M. M. Stahl, F. W. Stahl. Orientation of cohesive end site cos determines the active orientation of chi sequence in stimulating recA, recBC-mediated recombination in phage lambda lytic infections. Proc. Natl. Acad. Sci. USA 79, 5981-5985 (1982). [PubMed] [Journal]
  128. Hideo Ikeda and Ichizo Kobayashi. recA--mediated recombination of bacteriophage lambda: Structure of recombinant and intermediate DNA molecules and their packaging in vitro. Cold Spring Harbor Symp. Quant. Biol. 43, 1009-1021 (1979). [PubMed]
  129. Ichizo Kobayashi and Hideo Ikeda. On the role of recA gene product in genetic recombination: An analysis by in vitro packaging of recombinant DNA molecules formed in the absence of protein synthesis. Mol. Gen. Genet. 166, 25-29 (1978). [PubMed] [Journal]
  130. Ichizo Kobayashi and Hideo Ikeda. Formation of recombinant DNA of bacteriophage lambda by recA function of Escherichia coli without duplication, transcription, translation, and maturation. Mol. Gen. Genet. 153, 237-245 (1977). [PubMed] [Journal]
  131. Hideo Ikeda and Ichizo Kobayashi. Involvement of DNA-dependent RNA polymerase in a recA-independent pathway of genetic recombination in Escherichia coli. Proc. Natl. Acad. Sci. USA, 74: 3932-3936 (1977).[PubMed] [Journal]
  132. I. Kobayashi and I. Kimura. Effects of chemical animalization and cell dissociation on RNA synthesis in sea urchin embryos. Exp. Cell Res, 97:413-417 (1976).[PubMed] [Journal]

Last modified on05/14/2012