Iida, T and Kobayashi, T. (2019) RNA polymerase I activators count and adjust ribosomal RNA gene copy number. Mol. Cell

Hizume, K., Endo, S., Muramatsu, S., Kobayashi, T. and Araki, H. (2018) DNA polymerase ε-dependent modulation of the pausing property of the CMG helicase at the barrier. Genes Dev. 32 1315-1320

Mostofa, G., Rahman, M. A., Koike, N., Yeasmin, A.MST., Islam, N., Waliullah, T.M., Hosoyamada, S., Shimobayashi, M., Kobayashi, T., Hall, M. N., and Ushimaru, T. (2018) CLIP and cohibin separate rDNA from nucleolar proteins destined for degradation by nucleophagy. J. Cell Biol. 217: 2675-2690.

Sasaki, M., and Kobayashi, T. (2017)Ctf4 Prevents Genome Rearrangements by Suppressing DNA Double-Strand Break Formation and Its End Resection at Arrested Replication Forks. Mol. Cell 66:533-545

Kobayashi, T., and Sasaki, M. (2017) rDNA stability is supported by many "Buffer genes" -Introduction to the Yeast rDNA Stability Database. FEMS yeast res. doi: 10.1093/femsyr/fox001

Saka, K., Takahashi, A., Sasaki ,M, and Kobayashi, T. (2016) More than 10% of yeast genes are related to genome stability and influence cellular senescence via rDNA maintenance. Nucleic Acids Res. 44:4211-4221.

Kobayashi, T. (2016) Genome Instability of Repetitive Sequence: Lesson from the Ribosomal RNA Gene Repeat. “DNA Replication, Recombination, and Repair” Hanaoka, F and Sugasawa K. ed. Part IV, Chapter 10: 235-247.

Akamatsu, Y., and Kobayashi, T. (2015) The Human PolI Transcription Terminator Complex Acts as a Replication Fork Barrier that Coordinates the Progress of Replication with rRNA Transcription Activity. Mol Cell Biol. 35, 1871-1881

Kobayashi , T (2014) Ribosomal RNA gene repeats, their stability and cellular senescence. Proc Japan Acad, Ser B, 90, 119-129.

Fawcett, J.A., et al. (2014) Population Genomics of the Fission Yeast Schizosaccharomyces pombe. PLoS One. 9(8):e104241

Saka, K., Ide, S., Ganley, A.R., and Kobayashi, T.  (2013) Cellular Senescence in Yeast Is Regulated by rDNA Noncoding Transcription.  Curr Biol. 23, 1794-1798

Ide, S., Saka, K., and Kobayashi, T.  (2013). Rtt109 prevents hyper-amplification of ribosomal RNA genes through histone modification in budding yeast.  PLoS Genet. 9: e1003410.

Iida, T., Iida, N,. Tsutsui, Y., Yamao, F., and Kobayashi, T.  (2012). RNA interference regulates the cell cycle checkpoint through the RNA export factor, Ptr1, in fission yeast.   BBRC. 427: 143-147.

Poole, A.M., Kobayashi, T., and Ganley, A.R.  (2012). A positive role for yeast extrachromosomal rDNA circles?   Bioessays. 34: 725-729.

Ganley, A.R., Breitenbach, M., Kennedy, B.K., and Kobayashi, T.  (2012). Yeast hypertrophy: cause or consequence of aging? Reply to Bilinski et al . FEMS Yeast Res. 12: 267-268.

Kobayashi, T .  (2011)   . How does genome instability affect lifespan?: roles of rDNA and telomeres.  Genes Cells. 16: 617-624.

Ganley, A.R., and Kobayashi, T. (2011). Monitoring the Rate and Dynamics of Concerted Evolution in the Ribosomal DNA Repeats of Saccharomyces cerevisiae Using Experimental Evolution.   Mol Biol Evol. 28: 2883-2891.  

Miyazaki, T., and Kobayashi, T.  (2011). Visualization of the dynamic behavior of ribosomal RNA gene repeats in living yeast cells.   Genes Cells. 16: 491-502.

Kobayashi, T. (2011). Regulation of ribosomal RNA gene copy number and its role in modulating genome integrity and evolutionary adaptability in yeast. Cell Mol Life Sci. 68: 1395-1403.

Ide, S., and Kobayashi, T. (2010). Analysis of DNA Replication in S. cerevisiae by Two-Dimensional and Pulsed-Field Gel Electrophoresis. Curr. Prot. Sup49 UNIT22.14.1-12.

Ide, S., Miyazaki, T., Maki, H., and Kobayashi, T. (2010). Abundance of ribosomal RNA gene copies maintains genome integrity. Science 327, 693-696.

Ganley, A.R.D., Ide, S., Saka, K., and Kobayashi, T. (2009). The effect of replication initiation on gene amplification in the rDNA and its relationship to aging. Molecular Cell , 35, 683-693.

Iida, T., Nakayama, J. and Moazed, D. (2008). siRNA-mediated heterochromatin establishment requires HP1 and is associated with antisense transcription. Molecular Cell. 31, 178-189.

Kobayashi, T. (2008). A new role of the rDNA and nucleolus in the nucleus- rDNA instability maintains genome integrity-. BioEssays 30, 267-272.

Ganley, A.R.D. and Kobayashi, T. (2007). Phylogenetic footprinting to find functional DNA elements. Methods in Molecular Biology, Comparative Genomics v.1, Humana press, 367-379

Ganley, A.R.D. and Kobayashi, T. (2007). Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Res. 17, 184-191

Ide, S., Watanabe, K., Watanabe, H., Shirahige, K., Kobayashi, T., and Maki, H. (2007). Abnormality in initiation program of DNA replication is monitored by the highly repetitive rRNA gene array on chromosome XII in budding yeast. Mol Cell Biol. 27, 568-578.

Kobayashi, T. (2006). Strategies to maintain the stability of the ribosomal RNA gene repeats. Genes Genet. Syst. 81, 155-161.

Kobayashi. T. and Ganley, A. R. D. (2005). Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science, 309, 1581-1584.

Ganley, A. R. D., Hayashi, K., Horiuchi, T. and Kobayashi, T. (2005). Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc. Natl. Acad. Sci. USA, 102, 11787-11792.

Kobayashi, T., Horiuchi, T., Tongaonkar, P., Vu, L., and Nomura, M. (2004). SIR2 regulates recombination between different rDNA repeats, but not recombination within individual rRNA genes in yeast.Cell, 117, 441-453.

Serizawa, N., Horiuchi, T., and Kobayashi, T. (2004). Transcription-mediated hyper-recombination in HOT1. Genes Cells, 9, 305-315.

Kobayashi, T. (2003). The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication fork. Mol. Cell. Biol. 23, 9178-9188.

Takeuchi, Y., Horiuch, T. and Kobayashi, T. (2003). Transcription-dependent recombination and the role of fork collision in yeast rDNA. Genes Dev. 17, 1497-1506.

Morehouse, E., James, T.Y., Ganley, A.R.D., Vilgalys, R., Berger, L., Murphy, P.J., and Longcore, J.E. (2003). Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone. Molecular Ecology, 12, 395-403.

Kodama, K.-i., Kobayashi, T., Niki, H., Hiraga, S., Oshima, T., Mori, H., and Horiuchi, T. (2002). Amplification of Hot DNA segments in Escherichia coli. Mol. Microbiol. 45, 1575-1588.

Ganley, A.R.D., and Scott, B. (2002). Concerted evolution in the ribosomal RNA genes of an Epichloe endophyte hybrid. Comparison between tandemly-arranged rDNA and dispersed 5S rrn genes. Fungal Genetics and Biology, 35, 39-51.

Wai, H., Johzuka, K., Vu, L., Eliason, K., Kobayashi, T., Horiuchi, T., and Nomura, M.(2001). Yeast RNA polymerase I enhancer is dispensable for transcription of the chromosomal rRNA gene and cell growth, and its apparent transcription enhancement from ectopic promoters required Fob1 protein. Mol. Cell. Biol. 21, 5541-5553.

Kobayashi, T., Nomura, M., and Horiuch, T. (2001). Identification of DNA cis-elements essential for expansion of ribosomal DNA repeats in Saccharomyces cerevisiae: Mol. Cell. Biol 21, 136-147.

Rein, T., Kobayashi, T., Malott, M., Leffak, M., and DePamphilis. M. L. (1999). DNA methylation at mammalian replication origins. J. Biol. Chem. 274, 25792-25800.

Kobayashi, T., Heck, D.J., Nomura, M., and Horiuch, T. (1998). Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. Genes Dev. 12, 3821-3830.

Ganley, A.R.D. and Scott, B. (1998). Extraordinary ribosomal spacer length heterogeneity in a Neotyphodium endophyte hybrid: Implications for concerted evolution. Genetics, 150, 1625-1637.

Kobayashi, T., Rein, T., and DePamphilis, M. L. (1998). Identification of primary initiation sites for DNA replication in the hamster dihydrofolate reductase gene intiation zone. Mol. Cell. Biol. 18, 3266-3277.