2024
Uriu, K.,Hernandez-Sanchez, J.P., Kojima, S. (2024) Impacts on the negative feedback loop between sense-antisense RNA pair in regulating circadian rhythms. NPJ Systems Biology and Applications. https://doi.org/10.1038/s41540-024-00451-4.
Mao, L., Ngo, K., Weidemann, D.E., Unruh, B.A., Kojima S. (2024) A comparative study of algorithms detecting differential rhythmicity from transcriptomic data. Bioinformatics and Biology Insights. https://doi.org/10.1177/1177932224128118.
Unruh, B.A., Weidemann, D.E., Miao, L., Kojima, S. (2024) Coordination of rhythmic RNA synthesis and degradation orchestrates 24- and 12-h RNA expression patterns in mouse fibroblasts. Proceedings of the National Academy of Sciences of the United States of America. https://www.pnas.org/doi/10.1073/pnas.2314690121
2023
Gutman, R., Pendergast, J.S., Nakamura, W., Kojima, S. (2023) Editorial: Circadian desynchrony: Consequences, mechanisms, and Open Issues. Frontiers in Physiology. 10.3389/fphys.2023.1177643
2022
Mao, L., Batty, K.R., Jackson, A.N., Heather, A.P., Rhoades, M.W., Kojima, S. (2022) Genetic and environmental perturbations alter the rhythmic expression pattern of a circadian long non-coding RNA, Per2AS, in mouse liver. F1000Research https://doi.org/10.12688/f1000research.125628.1
Hildreth, S.B., Littleton, E.S., Clark, L.C., Puller, G.C., Kojima, S., Winkel, B.S.J. (2022) Mutations that alter Arabidopsis flavonoid metabolism affect the circadian clock. Plant Journal. 1140 (4): 932-945
https://doi.org/10.1111/tpj.15718
Mosig, R.A., and Kojima, S. (2022) Timing without coding: How do long non-coding RNAs regulate circadian rhythms? Seminars in Cell and Developmental Biology S1084-9521(21)00093-8
https://pubmed.ncbi.nlm.nih.gov/34116930/
2021
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. (2021) Natural antisense transcript of Period2, Per2AS, regulates the amplitude of the murine circadian clock. Genes and Development. 35: 899-913
https://pubmed.ncbi.nlm.nih.gov/34016691/
Attal, K., Wickman, J.A., Kojima, S., Blythe, S.N., Toporikova, S.N. (2021) Time-restricted feeding drives periods of rapid food consumption in rats fed a high-fat diet with liquid sucrose. Obesity Medicine. 24: 100347
https://doi.org/10.1016/j.obmed.2021.100347
Benjamin Unruh and Evan Littleton: 2021 Virginia Tech Science Festival “Rock around the Clock”
Youtube Video
2020
Littleton, E.S., Childress, M.L., Gosting, M.L., Jackson, A.N., Kojima, S. Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output. Scientific Reports,10:21839
https://pubmed.ncbi.nlm.nih.gov/33318596/
Unruh BA, and Kojima S. (2020) The Making and Breaking of RNAs: Dynamics of Rhythmic RNA Expression in mammals. Journal of Biological Rhythms. 35 (6): 519-529
https://pubmed.ncbi.nlm.nih.gov/32965157/
Yao, X, Kojima, S., and Chen, J. (2020) Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression. PLoS Computational Biology 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
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
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