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. PNAS.


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


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

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

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


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

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

Benjamin Unruh and Evan Littleton: 2021 Virginia Tech Science Festival “Rock around the Clock”
Youtube Video


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

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

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.

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.


Kojima, S. and Cimini D. (2019) Aneuploidy and gene expression: Is there dosage compensation? Epigenomics. 11(16): 1827-1837.


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.

Kojima, S. (2018) “徒然独立日記〜黎明編〜” Japanese Society for Chronobiology Magazine 24 (1), 59-65. (Japanese)

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


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.


​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

Kojima, S., and Green, C.B. (2015) Analysis of Circadian Regulation of Poly(A)-Tail Length. Methods in Enzymology 551:387-403

Kojima, S., and Green, C.B. (2015) Circadian genomics reveals a role for post-transcriptional regulation in mammals. Biochemistry 54(2):124-133.