Publications:

( Pubmed link for all publications)

2025

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.

RNA Pol I activity maintains chromatin condensation and the H3K4me3 gradient essential for oogenesis, independent of ribosome production. Mejia-Trujillo R, Zhao Q, Rahman A, Cenik ES. bioRxiv, 2025.05.07.652530; Link

Cycloheximide resistant ribosomes reveal adaptive translation dynamics in C. elegans. Zhao, Q, Bolton BM, Rothe R, Tachibana R, Cenik C, Cenik, ES. bioRxiv, 2025.05.07.652686; 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

2024

Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes. 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. bioRxiv [Nature Biotechnology, in press]. 2024 Aug 11:2024.08.11.607360. PMC preprint 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

2023

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

2022

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

2021

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

2019

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

2016 and earlier

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