Kusano, K., Naito, T., Handa, N., and  Ichizo Kobayashi. (1995).
Restriction-Modification Systems as Genomic Parasites in Competition for Specific Sequences.
Proc. Natl. Acad. Sci. (USA) 92, 11095-11099. PMID: 7479944. PMCID: PMC40578.

Handa, N., Ohashi, S., Kusano, K., and Kobayashi, I. (1997).
Chi-star, a chi-related 11-mer sequence partially active in an E. coli recC1004 strain.
Genes Cells. 2, 525-536. PMID: 9348042.

Handa, N., Ohashi, S., and Kobayashi, I. (1997).
Clustering of chi sequence in Escherichia coli genome.
Microb. Comp. Genomics 2, 287-298. PMID: 9689227.

Handa, N., and Kobayashi, I. (1999).
Post-segregational killing by restriction modification gene complexes: Observations of individual cell deaths.
Biochimie 81, 931-938. PMID: 10572308.

Handa, N., Ichige, A., Kusano, K., and Kobayashi, I. (2000).
Cellular Responses to Postsegregational Killing by Restriction-Modification Genes.
J. Bacteriol. 182, 2218-2229. PMID: 10735865. PMCID: PMC111271.

Arnold, D.A., Handa, N., Kobayashi, I., and Kowalczykowski, S.C. (2000)
A novel, 11 nucleotide variant of χ, χ∗: one of a class of sequences defining the Escherichia coli recombination hotspot χ.
J. Mol. Biol., 300, 469-479. PMID: 10884344. [Abstract] [Full Text] [PDF]

Handa, N., Noguchi, Y., Sakuraba, Y., Ballario, P., Macino, G., Fujimoto, N., Ishii, C., and Inoue, H. (2000).
Characterization of the Neurospora crassa mus-25 mutant: the gene encodes a protein which is homologous to the Saccharomyces cerevisiae Rad54 protein.
Mol. Gen. Genet. 264, 154-163. PMID: 11016845.

Chinen, A., Naito, Y., Handa, N., and Kobayashi, I. (2001).
Evolution of Sequence Recognition by Restriction-Modification Enzymes: Selective Pressure for Specificity Decrease.
Mol. Biol. Evol. 18, 276. PMID: 11070049.

Handa, N., Nakayama, Y., Sadykov, M., and Kobayashi, I. (2001).
Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction–modification gene complex.
Mol. Microbiol. 40, 932-940. PMID: 11401700.

Takahashi, N., Naito, Y., Handa, N., and Kobayashi, I. (2002).
A DNA Methyltransferase Can Protect the Genome from Postdisturbance Attack by a Restriction-Modification Gene Complex.
J. Bacteriol. 184, 6100-6108. PMID: 12399478. PMCID: PMC151934.

Sadykov, M., Asami, Y., Niki, H., Handa, N., Itaya, M., Tanokura, M., and Kobayashi, I. (2003).
Multiplication of a Restriction–Modification Gene Complex.
Mol. Microbiol. 48, 417-427 (2003). PMID: 12675801.

Handa, N. and Kobayashi, I. (2003).
Accumulation of Large Non-Circular Forms of the Chromosome in Recombination-Defective Mutants of Escherichia coli.
BMC Mol. Biol. Apr 28;4:5 Epub 2003 Apr 28. PMID: 12718760. PMCID: PMC156651.

Handa, N., Bianco, P.R., Baskin, R.J., and Kowalczykowski, S.C. (2005)
Direct visualization of RecBCD movement reveals co-translocation of the RecD motor after c-recognition.
Mol. Cell, 17, 745-750. PMID: 15749023. [Abstract] [Full Text] [PDF] [Supplemental Data] [Movie 1 - Chi⁰] [Movie 2 - Chi⁺]

Ino, A., Naito, Y., Mizuguchi, H., Handa, N., Hayakawa, T., and Kobayashi, I. (2005).
A Trial of Somatic Gene Targeting in vivo with an Adenovirus Vector.
Genet. Vaccines Ther. Oct 12;3:8. PMID: 16219108. PMCID: PMC1277836.

Handa, N. and Kobayashi, I. (2005).
Type III Restriction Is Alleviated by Bacteriophage (RecE) Homologous Recombination Function but Enhanced by Bacterial (RecBCD) Function.
J. Bacteriol. 187, 7362-7373. PMID: 16237019. PMCID: PMC1272966.

Chédin, F., Handa, N., Dillingham, M.S., and Kowalczykowski, S.C. (2006).
The AddAB helicase/nuclease forms a stable complex with its cognate chi sequence during translocation.
J. Biol. Chem., 281, 18610-18617. PMID: 16632468. (published online April 21, 2006 as doi:10.1074/jbc.M600882200).  [Abstract] [Full Text] [PDF]

Watanabe, M., Yuzawa, H., Handa, N., and Ichizo Kobayashi, I. (2006).
Hyperthermophilic DNA Methyltransferase M.PabI from the Archaeon Pyrococcus abyssi.
Appl. Environ. Microbiol. 72, 5367-5375. PMID: 16885288. PMCID: PMC1538712.

Handa, N. and Kowalczykowski, S.C. (2007)
A RecA mutant, RecA^730, suppresses the recombination deficiency of the RecBC1004D–χ* interaction in vitro and in vivo.
J. Mol. Biol., 365, 1314-1325. (published online November 1, 2006 as doi:10.1016/j.jmb.2006.10.090). PMID: 17141804; PMCID: PMC1847798. [Abstract] [Full Text] [PDF]

Ohno, S., Handa, N., Watanabe-Matsui, M., Takahashi, N., and Kobayashi, I. (2008).
Maintenance Forced by a Restriction-Modification System Can Be Modulated by a Region in Its Modification Enzyme Not Essential for Methyltransferase Activity.
J. Bacteriol. 190, 2039-2049. PMID: 18192396. PMCID: PMC2258900.

Ishikawa, K., Handa, N., and Kobayashi, I. (2009).
Cleavage of a model DNA replication fork by a Type I restriction endonuclease.
Nucleic Acids Res. 37, 3531-3544. PMID: 19357093. PMCID: PMC2699502.

Handa, N., Ichige, A., and Kobayashi, I. (2009).
Contribution of RecFOR machinery of homologous recombination to cell survival after loss of a restriction–modification gene complex.
Microbiology 155, 2320-2332. PMID: 19389761.

Handa, N., Amitani, I., Gumlaw, N., Sandler, S.J., and Kowalczykowski, S.C. (2009).
Single molecule analysis of a red fluorescent RecA Protein reveals a defect in nucleoprotein filament nucleation that relates to its reduced biological functions.
J. Biol. Chem., 284, 18664-73 (published online May 5, 2009, doi:10.1074/jbc.M109.004895). PMID: 19419960; PMCID: PMC2707236  [Abstract]  [Full Text]  [PDF]

Handa, N., Morimatsu, K., Lovett, S.T., and Kowalczykowski, S.C. (2009)
Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli.
Genes & Dev., 23, 1234-1245. PMID: 19451222; PMCID: PMC2685532  [Abstract] [Full Text] [PDF] [Supplemental Material]
(see Current Biology Dispatch: DNA Repair: Common Approaches to Fixing Double-Strand Breaks [PDF])

Kobayashi, I. and Handa, N. (2009)
DNA double-strand breaks and their consequences in bacteria. In Encylopedia of Life Sciences, (Nature Publishing Group, Macmillan Reference Limited, London), A21652, John Wiley & Sons, Chichester, http://www.els.net.

Furuta, Y., Kawai, M., Yahara, K., Takahashi, N., Handa, N., Tsuru, T., Oshima, K., Yoshida, M., Takeshi Azuma, Hattori, M., Uchiyama, I., and Kobayashi, I.(2011)
Birth and death of genes linked to chromosomal inversion.
Proc. Natl. Acad. Sci. (USA) 108, 1501-1506 . PMID: 21212362. PMCID: PMC3029772.

Ishikawa, K., Handa, N., Sears, L., Raleigh, E.A., and Kobayashi, I. (2011).
Cleavage of a model DNA replication fork by a methyl-specific endonuclease.
Nucleic Acids Res. 39, 5489-5498. PMID: 21441537. PMCID: PMC3141261.

Kawai, M., Furuta, Y., Yahara, K., Tsuru, T., Oshima, K., Handa, N., Takahashi, N., Yoshida, M., Azuma, T., Hattori, M., Uchiyama, I., and Kobayashi, I. (2011).
Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes.
BMC Microbiol. 11, 104. PMID: 21575176. PMCID: PMC3120642.

Yahara, K., Kawai, M., Furuta, Y., Takahashi, N., Handa, N., Tsuru, T., Oshima, K., Yoshida, M., Azuma, T., Hattori, M., Uchiyama, U., and Kobayashi, I. (2012).
Genome-Wide Survey of Mutual Homologous Recombination in a Highly Sexual Bacterial Species.
Genome Biol. Evol. 4, 628-640. PMID: 22534164. PMCID: PMC3381677.

Handa, N., Yang, L., Dillingham, M. S., Kobayashi, I., Wigley, D.B., and Kowalczykowski, S.C. (2012)
Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, χ, by RecBCD enzyme.
Proc. Natl. Acad. Sci. (USA), 109, 8901-8906 (published online 17 May 2012, 10.1073/pnas.1206076109). PMID: 22603794; PMCID: PMC3384139 [Abstract] [Full Text] [PDF] [Supporting Information]

Yang, L., Handa, N., Liu, B., Dillingham, M. S., Wigley, D.B., and Kowalczykowski, S.C. (2012)
Alteration of χ recognition by RecBCD reveals a regulated molecular latch and suggests a channel-bypass mechanism for biological control.
Proc. Natl. Acad. Sci. (USA), 109, 8907-8912 (published online 17 May 2012, 10.1073/pnas.1206081109). PMID: 22603793; PMCID: PMC3384165  [Abstract] [Full Text] [PDF] [Supporting Information]

Chan, Y.L., Brown, M.S., Qin, D., Handa, N., and Bishop, D.K. (2014)
The third exon of the budding yeast meiotic recombination gene HOP2 is required for calcium-dependent and recombinase Dmc1-specific stimulation of homologous strand assimilation.
J. Biol. Chem. 289, 18076-18086 (published online 5 May 2014, 10.1074/jbc.M114.558601). PMID: 24798326; PMCID: PMC4140259. [Abstract] [Full Text] [PDF]

Chen, H., Donnianni, R.A., Handa, N., Deng, S.K., Oh, J., Timashev, L.A., Kowalczykowski, S.C., and Symington, L.S. (2015)
Sae2 promotes DNA damage resistance by removing the Mre11-Rad50-Xrs2 complex from DNA and attenuating Rad53 signaling.
Proc. Natl. Acad. Sci. (USA), 112, E1880-1887 (published online March 23, 2015 as pii:201503331). PMID: 25831494; PMCID: PMC4403154. [Abstract] [Full Text] [PDF]

Lee, K.Y., Im, J.S., Shibata, E., Park, J., Handa, N., Kowalczykowski, S.C., and Dutta, A. (2015)
MCM8-9 complex promotes resection of double-strand break ends by MRE11-RAD50-NBS1 complex.
Nat. Commun. (published online July 28, 2015, 10.1038/ncomms8744). PMID: 26215093; PMCID: PMC4525285. [Abstract] [Full Text] [PDF] [Supplementary Information]

Gong, Y., Handa, N., Kowalczykowski, S.C., and de Lange, T. (2017)
PHF11 promotes DSB resection, ATR signaling, and HR.
Genes Dev. 31, 46-58. PMID: 28115467; PMCID: PMC5287112. [Abstract] [Full Text] [PDF] [Supplemental Information]