Publications:

( Pubmed link for all publications)

RNA Pol I shapes meiotic chromatin, germline H3K4me3 dynamics, and oogenesis independent of ribosome assembly. Mejia-Trujillo R*, Zhao Q*, Abraham F, Rahman A, Cenik ES. * equal contribution. Cell Reports, 2026, 45(2), 116866. Link

Original pipeline used for germ nuclei linearization and confocal intensity quantification is hosted on the GitHub repository: https://github.com/raqmejtru/germ-nuclei-linearization.

Surya A*, Zhao Q*, Voigt B, Rangan R, Cenik ES. Ribosomal biogenesis defects trigger subunit specific developmental checkpoints via TOR signaling and gap junction in C. elegans. Developmental Biology, 2026, 529, pg 46-55, *equal contribution. Link

Zhao Q, Cenik ES. Is the mitocondrial function at the heart of ribosome-related diseases? Trends in Cell Biology, 2025 Oct;35(10):815-818; Link

 

Kim J, Bolton B ,Moshksayan K, Khanna R, Swartz M , Ziemczonok M, Kamra M, Jorn KA Parekh P, Kujawińska N, Eberhart J , Sarinay Cenik E, Ben-Yakar A , Chowdhury S. Inverse-scattering in biological samples via beam-propagation. bioRxiv 2025.08.17.670744. Link

Cardona EA, Wu Z, Bolton BM, Cenik ES, Pierce-Shimomura J. APOE4-induced patterned behavioral decline and neurodegeneration requires endogenous tau in a C. elegans model of Alzheimer's disease. bioRxiv, 2025.05.06.652574. Link.

Cycloheximide resistant ribosomes reveal adaptive translation dynamics in C. elegans. Zhao, Q, Bolton BM, Rothe R, Tachibana R, Cenik C, Cenik, ES. Genetics, 2025; Volume 232, Issue 1, iyaf189,Article link

Original Python-supported script to predict codons based on Ribo-seq data is hosted on the GitHub repository: https://github.com/reikostachibana/ribopy_analysis.

Translation efficiency covariation identifies conserved coordination patterns across cell types. Liu Y, Hoskins I, Geng M, Zhao Q, Chacko J, Qi K, Persyn L, Wang J, Zheng D, Zhong Y, Rao S, Park D, Cenik ES, Agarwal V, Ozadam H, Cenik C. Nature Biotechnology. 2025. Jul 25:10.1038/s41587-025-02718-5. Article link

Differential impacts of ribosomal protein haploinsufficiency on mitochondrial function. Surya A, Bolton BM, Rothe R, Mejia-Trujillo R, Leonita A, Zhao Q, Arya A, Liu Y, Rangan R, Gorusu Y, Nguyen P, Cenik C, Sarinay Cenik E. Journal of Cell Biology, 2025 Mar 3;224(3):e202404084. Article link, BioRxiv link

Note: You can find the raw datasets for this manuscript in the following Texas Data Repository link

Ribosomal proteins' unforeseen impact on mitochondrial integrity. Zhao Q, Sarinay Cenik E. Biomedical Research, 2024. Vol 35, Issue 3. Review Article link

 

Fasting shapes chromatin architecture through an mTOR/RNA Pol I axis. Al-Refaie, N, Padovani, F, Hornung, J , Pudelko L, Binando F, del Carmen Fabregat A, Zhao Q, Towbin B, Sarinay Cenik E, Stroustrup N, Padeken J, Schmoller K, Cabianca D. Nature Cell Biology, 2024. Article link

Inhibition of ribosome biogenesis in the epidermis is sufficient to trigger organism-wide growth quiescence independently of nutritional status in C. elegans Zhao, Q, Rangan, R, Weng, S, Ozdemir, C , Cenik, ES. PLOS Biology, 2023. Article link

Ribosome biogenesis disruption mediated chromatin structure changes revealed by SRAtac, a customizable end to end analysis pipeline for ATAC-seq. Freeman, TF, Zhao, Q, Surya A, Rothe R, Cenik ES. BMC Genomics, 2023.10.1186/s12864-023-09576-y. Article link

NOTE: You can find the SRAtac tool, an end-to-end customizable analysis pipeline for alignment and ATAC-seq analysis across different model organisms, at the following GitHub repositories: https://github.com/trev-f/SRAlign, https://github.com/trev-f/SRAtac

Cell autonomous and non-autonomous consequences of deviations in translation machinery on organism growth and the connecting signalling pathways Surya, A & Cenik, ES. Open Biology, 2022. April 27; 12: 210308. Review article link

Loss of coordinated expression between ribosomal and mitochondrial genes revealed by comprehensive characterization of a large family with a rare Mendelian disorder. Panici, B, Nakajima, H, Carlston, C M, Ozadam, H, Cenik, C, Cenik, ES. Genomics, 2021. July; 113(4):1895-1905. Article link

Genes with 5’terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 NSP1 protein. Rao, S, Hoskins, I, Garcia, D, Tonn, T, Ozadam, H, Cenik, ES, Cenik, C. RNA, 2021. Jun 14. 2021 Recipient of the RNA Journal Prize. Article link

Functional and structural basis of extreme non-coding conservation in vertebrate mRNAs. Byeon, GW, Cenik, ES, Jiang, L, Tang, H, Das, R, & Barna, M. Nature Genetics, 2021. highlighted in the same issue with News & Views by Gupta & Beaudoin. Article link

Maternal ribosomes are sufficient for tissue diversification during embryonic development in C. elegans. Cenik ES, Meng X, Tang NH ,Hall RN, Arribere JA, Cenik C, Jin Y, Fire AZ. Developmental Cell, 2019. Mar25;48(6), 811-826.e6. Featured in Faculty of 1000. Article link

Highlighted in the same issue with a preview by Haag & Dinman, 2019, Link

Translation Readthrough Mitigation. Arribere, JA, Cenik ES, Jain N, Hess G, Lee C, Bassik MC, Fire AF. Nature, 2016. Jun 1;534(7609):719-723. Article link

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. Cenik C, Cenik ES, Byeon GW, Grubert F, Candille S, Spacek D, Alsallakh B, Tilgner H, Araya CL, Tang H, Ricci E, Snyder MP. Genome Research, 2015. Nov;25(11):1610-21. Article link

Argonaute proteins. Cenik, ES, & Zamore, PD. Current Biology, 2011. 21(12), R446-9. Review Article link

Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease. Cenik, ES, Fukunaga, R, Lu, G, Dutcher, R, Wang, Y, Tanaka Hall, TM, Zamore, PD. Molecular Cell, 2011. 42(2), 172-184. Featured in Faculty of 1000. Article link