Full articles can be downloaded from my Researchgate page. Or click the PubMed links below.
2020
Mosig, R.A., Castaneda, A.N., Deslauriers, J.C., Frazier, L.P., He, K.L., Maghzian, N., Pokharel, A., Schrier, C.T., Zhu, L., Koike, N., Tyson, J.J., Green, C.B., Takahashi, J.S., Kojima, S. Natural antisense transcript of Period2, Per2AS, regulates the amplitude of the murine circadian clock.
https://www.biorxiv.org/content/10.1101/2020.07.27.222760v1
Littleton, E.S. and Kojima, S. Genome-wide correlation analysis reveals Rorc as potential amplitude regulator of circadian transcriptome output.
https://www.biorxiv.org/content/10.1101/2020.06.19.161307v1
Yao, X, Kojima, S., and Chen, J. (2020) Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression. PLoS Comput. Biol. 16(4):e1007842.
https://www.ncbi.nlm.nih.gov/pubmed/32339166
Mosig, R.A. and Kojima, S. To code or not to code? That is the question for RNA in timekeeping. Biochem (Lond) 42 (2): BIO04202005.
https://doi.org/10.1042/BIO04202005
https://www.biorxiv.org/content/10.1101/2020.07.27.222760v1
Littleton, E.S. and Kojima, S. Genome-wide correlation analysis reveals Rorc as potential amplitude regulator of circadian transcriptome output.
https://www.biorxiv.org/content/10.1101/2020.06.19.161307v1
Yao, X, Kojima, S., and Chen, J. (2020) Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression. PLoS Comput. Biol. 16(4):e1007842.
https://www.ncbi.nlm.nih.gov/pubmed/32339166
Mosig, R.A. and Kojima, S. To code or not to code? That is the question for RNA in timekeeping. Biochem (Lond) 42 (2): BIO04202005.
https://doi.org/10.1042/BIO04202005
2019
Kojima, S. and Cimini D. (2019) Aneuploidy and gene expression: Is there dosage compensation? Epigenomics. 11(16): 1827-1837.
https://www.ncbi.nlm.nih.gov/pubmed/31755744
https://www.ncbi.nlm.nih.gov/pubmed/31755744
2018
Gendreau K.L*., Unruh, B.A*., Zhou, C., and Kojima. S. (2018) Identification and Characterization of Transcripts Regulated by Circadian Alternative Polyadenylation in Mouse Liver. G3: Genes, Genomes, Genetics. 8 (11), 3539-3548.
www.ncbi.nlm.nih.gov/pubmed/30181259
Kojima, S. (2018) “徒然独立日記〜黎明編〜” Japanese Society for Chronobiology Magazine 24 (1), 59-65. (Japanese)
http://chronobiology.jp/journal/JSC2018-1-059.pdf
Battogtokh D., Kojima, S., Tyson, J.J., (2018) Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network. PLoS Comput. Biol., 14 (2), e1005967
www.ncbi.nlm.nih.gov/pubmed/29447160
2017
Yoo, S-H, Kojima, S., Shimomura, K., Koike, N., Buhr, E., Furukawa, T., Ko, C.H., Gloston, G., Ayoub, C., Nohara, K., Reyes, B.A., Tsuchiya, Y., Yoo, O-J., Yagita, K., Lee, C., Chen, Z., Yamazaki, S., Green, C.B., Takahashi, J.S. (2017) Period2 3'-UTR and microRNA-24 regulate circadian rhythms by repressing PERIOD2 protein accumulation. Proc. Natl. Acad. Sci. USA, 114 (42), E8855-E8864.
https://www.ncbi.nlm.nih.gov/pubmed/28973913
https://www.ncbi.nlm.nih.gov/pubmed/28973913
2015
Kojima, S., Gendreau, K.L., Sher-Chen, E.L., Gao, P., and Green, C.B. (2015) Changes in poly(A) tail length dynamics from the loss of the circadian deadenylase, Nocturnin. Sci. Rep., 5: 17059
https://www.ncbi.nlm.nih.gov/pubmed/26586468
Kojima, S., and Green, C.B. (2015) Analysis of Circadian Regulation of Poly(A)-Tail Length. Methods in Enzymology 551:387-403
www.ncbi.nlm.nih.gov/pubmed/25662466
Kojima, S., and Green, C.B. (2015) Circadian genomics reveals a role for post-transcriptional regulation in mammals. Biochemistry 54(2):124-133.
www.ncbi.nlm.nih.gov/pubmed/25303020
https://www.ncbi.nlm.nih.gov/pubmed/26586468
Kojima, S., and Green, C.B. (2015) Analysis of Circadian Regulation of Poly(A)-Tail Length. Methods in Enzymology 551:387-403
www.ncbi.nlm.nih.gov/pubmed/25662466
Kojima, S., and Green, C.B. (2015) Circadian genomics reveals a role for post-transcriptional regulation in mammals. Biochemistry 54(2):124-133.
www.ncbi.nlm.nih.gov/pubmed/25303020
Before 2015
Kojima, S. (2014) Circadian rhythms and post-transcriptional gene regulatory mechanisms. Japanese Society for Chronobiology Magazine 20: 3-7. (Japanese)
Godwin, A.R.* Kojima, S.*, Green, C.B. Wilusz, J. (2013) Kiss your tail goodbye: the role of PARN, Nocturnin, and Angel deadenylases in mRNA biology. Biochim. Biophys. Acta. -Gene Regulatory Mechanisms 1829(6-7):571-579.
Kojima, S. (2013) “The Green lab in the brown land” Japanese Society for Chronobiology Magazine 19(1):38-43. (Japanese)
Kojima, S., Sher-Chen, E.L. Green, C.B. (2012) Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression. Gene. Dev. 26(24):2724-2736.
Niu, S., Shingle, D.L., Garbarino-Pico, E., Kojima, S., Gilbert, M.R., Green, C.B. (2011) The Circadian Deadenylase Nocturnin is Necessary for Stabilization of the iNOS mRNA in Mice. PLoS ONE 6(11):e26954
Kojima, S., Shingle, D.L., Green, C.B. (2011) Post-transcriptional control of circadian rhythms. J.Cell Sci., 124(Pt 3):311-320.
Douris, N*, Kojima, S.*, Pan, X.*, Lerch-Gaggl, A.F., Duong, S.Q., Hussain, M.M., Green, C.B. (2011) Nocturnin Regulates Circadian Trafficking of Dietary Lipid in Intestinal Enterocytes. Curr. Biol. 21:1-9.
Kojima, S., Gatfield, D., Esau, C.C., Green, C.B. (2010) MicroRNA-122 Modulates the Rhythmic Expression Profile of the Circadian Deadenylase Nocturnin in Mouse Liver. PLoS ONE 5(6): e11264.
Kawai,M., Green, C.B., Lecka-Czernik, B., Douris, N., Gilbert, M.R. Kojima, S., Ackert-Bicknell, C., Garg, N., Horowitz, M.C., Adamo,M.L., Clemmons,D.R., Rosen,C.J. (2010) A circadian-regulated gene, Nocturnin, promotes adipogenesis by stimulating PPAR-gamma nuclear translocation. Proc. Natl. Acad. Sci. USA 107 (23) 10508-10513.
Green, C.B*., Douris, N*., Kojima, S., Strayer, C.A., Fogerty, J., Lourim, D., Keller, S.R. and Besharse, J.C. (2007) Loss of Nocturnin, a circadian deadenylase, confers resistance to hepatic steatosis and diet-induced obesity. Proc. Natl. Acad. Sci. USA 104 (23) 9888-9893.
Kojima, S., Matsumoto, K., Hirose, M., Shimada, M., Nagano, M., Shigeyoshi, Y., Hoshino, S., Ui-Tei, K., Saigo, K., Green, C.B. Sakaki, Y., Tei, H. (2007) LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1. Proc. Natl. Acad. Sci. USA, 104 (6), 1859-1864.
Kojima, S., Hirose, M., Tokunaga, K., Sakaki, Y., Tei, H. (2003) Structural and functional analysis of 3' untranslated region of mouse Period1 mRNA. Biochem Biophys Res Commun. 301 (1), 1-7.
Kojima, S., Sakaki, Y., Tei, H. (2002) “The significance of peripheral clocks on feeding behavior” Gendai Iryou. 34, 1367-1391. (Japanese)
Kojima, S., Yanagihara, I., Kono, G., Sugahara, T., Nasu, H., Kijima, M., Hattori, A., Kodama, T., Nagayama, K.I., Honda, T. (2000) mkp-1 encoding mitogen-activated protein kinase phosphatase 1, a verotoxin 1 responsive gene, detected by differential display reverse transcription-PCR in Caco-2 cells. Infect. Immun. 68 (5), 2791-2796.
Kojima, S., Honda, T. (2000) “Infectious Enteritis” Shoukaki no Rinsho. 3, 249-257. (Japanese)
Yanagihara, I., Kojima, S., Honda, T. (1999) “Considering food poisoning. Intestinal hemorrhagic Escherichia coli O 157.” Japan Medical Journal. 3919, 22-29. (Japanese)
* Equally contributed authors
Godwin, A.R.* Kojima, S.*, Green, C.B. Wilusz, J. (2013) Kiss your tail goodbye: the role of PARN, Nocturnin, and Angel deadenylases in mRNA biology. Biochim. Biophys. Acta. -Gene Regulatory Mechanisms 1829(6-7):571-579.
Kojima, S. (2013) “The Green lab in the brown land” Japanese Society for Chronobiology Magazine 19(1):38-43. (Japanese)
Kojima, S., Sher-Chen, E.L. Green, C.B. (2012) Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression. Gene. Dev. 26(24):2724-2736.
Niu, S., Shingle, D.L., Garbarino-Pico, E., Kojima, S., Gilbert, M.R., Green, C.B. (2011) The Circadian Deadenylase Nocturnin is Necessary for Stabilization of the iNOS mRNA in Mice. PLoS ONE 6(11):e26954
Kojima, S., Shingle, D.L., Green, C.B. (2011) Post-transcriptional control of circadian rhythms. J.Cell Sci., 124(Pt 3):311-320.
Douris, N*, Kojima, S.*, Pan, X.*, Lerch-Gaggl, A.F., Duong, S.Q., Hussain, M.M., Green, C.B. (2011) Nocturnin Regulates Circadian Trafficking of Dietary Lipid in Intestinal Enterocytes. Curr. Biol. 21:1-9.
Kojima, S., Gatfield, D., Esau, C.C., Green, C.B. (2010) MicroRNA-122 Modulates the Rhythmic Expression Profile of the Circadian Deadenylase Nocturnin in Mouse Liver. PLoS ONE 5(6): e11264.
Kawai,M., Green, C.B., Lecka-Czernik, B., Douris, N., Gilbert, M.R. Kojima, S., Ackert-Bicknell, C., Garg, N., Horowitz, M.C., Adamo,M.L., Clemmons,D.R., Rosen,C.J. (2010) A circadian-regulated gene, Nocturnin, promotes adipogenesis by stimulating PPAR-gamma nuclear translocation. Proc. Natl. Acad. Sci. USA 107 (23) 10508-10513.
Green, C.B*., Douris, N*., Kojima, S., Strayer, C.A., Fogerty, J., Lourim, D., Keller, S.R. and Besharse, J.C. (2007) Loss of Nocturnin, a circadian deadenylase, confers resistance to hepatic steatosis and diet-induced obesity. Proc. Natl. Acad. Sci. USA 104 (23) 9888-9893.
Kojima, S., Matsumoto, K., Hirose, M., Shimada, M., Nagano, M., Shigeyoshi, Y., Hoshino, S., Ui-Tei, K., Saigo, K., Green, C.B. Sakaki, Y., Tei, H. (2007) LARK activates posttranscriptional expression of an essential mammalian clock protein, PERIOD1. Proc. Natl. Acad. Sci. USA, 104 (6), 1859-1864.
Kojima, S., Hirose, M., Tokunaga, K., Sakaki, Y., Tei, H. (2003) Structural and functional analysis of 3' untranslated region of mouse Period1 mRNA. Biochem Biophys Res Commun. 301 (1), 1-7.
Kojima, S., Sakaki, Y., Tei, H. (2002) “The significance of peripheral clocks on feeding behavior” Gendai Iryou. 34, 1367-1391. (Japanese)
Kojima, S., Yanagihara, I., Kono, G., Sugahara, T., Nasu, H., Kijima, M., Hattori, A., Kodama, T., Nagayama, K.I., Honda, T. (2000) mkp-1 encoding mitogen-activated protein kinase phosphatase 1, a verotoxin 1 responsive gene, detected by differential display reverse transcription-PCR in Caco-2 cells. Infect. Immun. 68 (5), 2791-2796.
Kojima, S., Honda, T. (2000) “Infectious Enteritis” Shoukaki no Rinsho. 3, 249-257. (Japanese)
Yanagihara, I., Kojima, S., Honda, T. (1999) “Considering food poisoning. Intestinal hemorrhagic Escherichia coli O 157.” Japan Medical Journal. 3919, 22-29. (Japanese)
* Equally contributed authors
