PUBLICATIONS

2025

Telomerase RNA structural heterogeneity in living human cells detected by DMS-MaPseq. Forino NM, Woo JZ, Zaug AJ, Jimenez AG, Edelson E, Cech TR, Rouskin S, Stone MD. Nat Commun. 2025 Jan 22; 16(1):925. PMID: 39843442; PMCID: PMC11754830.

2024

The Folding of Germ Granule mRNAs Controls Intermolecular Base Pairing in Germ Granules and Maintains Normal Fly Development. Tian, S., Nguyen, H., Ye, Z., Rouskin, S., Thirumalai, D., Trcek, T. (2024) bioRxiv. doi: 10.1101/2024.05.31. PMID: 38853845; PMCID: PMC11160705.

The human mitochondrial mRNA structurome reveals mechanisms of gene expression. Moran, J. C., Brivanlou, A., Brischigliaro, M., Fontanesi, F., Rouskin, S., Barrientos, A. (2024) Science 385(6706): eadm9238. doi: 10.1126/science.adm9238. PMID: 39024447; PMCID: PMC11510358.

Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA. Allan, M. F., Aruda, J., Plung, J. S., Grote, S. L., Martin des Taillades, Y. J., de Lajarte, A. A., Bathe, M., Rouskin, S. (2024) bioRxiv. doi: 10.1101/2024.07.28. PMID: 38746332; PMCID: PMC11092567.

Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA. Allan, M. F., Aruda, J., Plung, J. S., Grote, S. L., des Taillades, Y. J. M., de Lajarte, A. A., Bathe, M., Rouskin, S. (2024) Research Square. doi: 10.21203/rs.3.rs-4066822/v1. PMID: 39149495; PMCID: PMC11326378.

Untangling the pseudoknots of SARS-CoV-2: Insights into structural heterogeneity and plasticity. Aruda, J., Grote, S. L., Rouskin, S. (2024) Current Opinion in Structural Biology 88: 102912. doi: 10.1016/j.sbi.2024.102912. PMID: 39168046.

Telomerase RNA structural heterogeneity in living human cells detected by DMS-MaPseq. Forino, N. M., Woo, J. Z., Zaug, A. J., Jimenez, A. G., Edelson, E., Cech, T. R., Rouskin, S., Stone, M. D. (2024) bioRxiv. doi: 10.1101/2024.08.29. PMID: 37873413; PMCID: PMC10592977.

SEISMICgraph: a web-based tool for RNA structure data visualization. Wightman, F. F., Yang, G., Martin des Taillades, Y. J., L'Esperance-Kerckhoff, C., Grote, S., Allan, M. F., Herschlag, D., Rouskin, S., Hagler, L. D. (2024) bioRxiv. doi: 10.1101/2024.09.26. PMID: 39386640; PMCID: PMC11463429.

KREH2 helicase represses ND7 mRNA editing in procyclic-stage Trypanosoma brucei by opposite modulation of canonical and 'moonlighting' gRNA utilization creating a proposed mRNA structure. Meehan, J., Ivens, A., Grote, S., Rodshagen, T., Chen, Z., Goode, C., Sharma, S. K., Kumar, V., Frese, A., Goodall, Z., McCleskey, L., Sechrist, R., Zeng, L., Savill, N. J., Rouskin, S., Schnaufer, A., McDermott, S. M., Cruz-Reyes, J. (2024) Nucleic Acids Research 52(19): 11940–11959. doi: 10.1093/nar/gkae821. PMID: 39149912; PMCID: PMC11514453.

Viral RNA Interactome: The Ultimate Researcher's Guide to RNA-Protein Interactions. Hanson, W. A., Romero Agosto, G. A., Rouskin, S. (2024) Viruses 16(11). doi: 10.3390/v16111485. PMID: 39599817; PMCID: PMC11599142.

DMS-MapSeq Analysis of Antisense Oligonucleotide Binding to lncRNA PANDA. Romero Agosto, G. A., Cox, E., Rouskin, S. (2024) Current Protocols 4(11): e70038. doi: 10.1002/cpz1.70038. PMID: 39589322.

Structure-informed mutagenesis identifies a conserved region critical for mouse insulin receptor 5'UTR IRES function. Dahl, W. B., Lan, T. C. T., Rouskin, S., Marr, M. T. (2024) bioRxiv. doi: 10.1101/2024.11.05. PMID: 39574669; PMCID: PMC11580878.

2023

Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts. Choquet, K., Koenigs, A., Dülk S. L. J., Smalec B. M., Rouskin, S. Churchman, L. S. (2023) Nature Structural and Molecular Biology doi: 10.1038/s41594-023-01035-2

RNA levers and switches controlling viral gene expression. Allan, M. F., Brivanlou, A., Rouskin, S. (2023) Trends in Biochemical Sciences doi: 10.1016/j.tibs.2022.12.002

3D RNA-scaffolded wireframe origami. Parsons, M.F., Allan, M.F., Li, S., Shepherd, T.R., Ratanalert, S., Zhang, K., Pullen, K.M., Chiu, W., Rouskin, S., Bathe, M. (2023) Nature Communications, 14(1) doi: 10.1038/s41467

Structure of pre-miR-31 reveals an active role in Dicer processing. Ma, S., Kotar, A., Grote, S., Rouskin, S., Keane, S. C. (2023) bioRxiv preprint

2022

Probing RNA structures with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells. Dülk, S.L.J., Rouskin, S. (2022) Journal of Visualized Experiments: Jove, (190). doi: 10.3791/64820

Recurrent emergence of Klebsiella penumoniae carbapenem resistance mediated by an inhibitory ompK36 mRNA secondary structure. Wong, J. L. C., David, S., Sanchez-Garrido, J., Woo, J. Z., Low, W. W., Morrechiato, F., Giani T., Rossolini, G. M., Beis, K., Brett S. J., Clements, A., Aanensen, D. M., Rouskin, S., Frankel, G. (2022) PNAS 119 (38) e2203593119. doi: 10.1073/pnas.220359311 bioRxiv preprint

Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts. Choquet, K., Koenigs, A., Dülk S. L. J., Smalec B. M., Rouskin, S. Churchman, L. S. (2022) bioRxiv preprint

An intranasal ASO therapeutic targeting SARS-CoV-2. Zhu, C., Lee J. Y., Woo, J. Z., Xu, L., Nguyenla, X., Yamashiro, L. H., Ji, F., Biering, S. B., Van Dis, E., Gonzalez, F., Fox, D., Wehri, E., Rustagi, A., Pinsky, B. A., Schaletzky, J., Blish, C. A., Chiu, C., Harris, E., Sadreyev, R. I., Stanley, S., Kauppinen, S., Rouskin, S, Näär, A.M. (2022) Nature Communications. 13 (4503.) doi: 10.1038/s41467-022-32216-0 bioRxiv preprint

Web-based platform for analysis of RNA folding from high throughput chemical probing data. Jurich, C. P., Brivanlou, A., Rouskin, S., Yesselman, J. D. (2022) Nucleic Acid Research, gkac435. doi: 10.1093/nar/gkac435

Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. Lan, T. C. T., Allan, M. F., Malsick, L. E., Woo, J. Z., Zhu, C., Zhang, F., Khandwala, S., Nyeo, S. Y. S., Sun, Y., Guo, J. U., Bathe, M., Näär, A. M., Griffiths, A., Rouskin, S. (2022) Nature Communications, 13, 1128. doi: 10.1038/s41467-022-28603-2 bioRxiv preprint.

2021

Sigma factor dependent translational activation in Bacillus subtilis. McCormick, D. M., Lalanne, J., Lan, T. C. T., Rouskin, S., Li, G. (2021) RNA doi: 10.1261/rna.078747.121

2020

Determination of RNA structural diversity and its role in HIV-1 RNA splicing regulation. Tomezsko, P., Corbin, V., Gupta, P., Swaminathan, H., Glasgow, M., Persad, S., Edwards, M., Mcintosh, L., Papenfuss, A., Emery, A., Swanstrom, R., Zang, Z., Lan, T., Bieniasz, P., Kuritzkes, D., Tsibris, A., Rouskin, S. (2020). Nature. 582(7812):438-442. doi:10.1038/s41586-020-2253-5

Viral RNA structure analysis using DMS-MaPseq. Tomezsko, P., Swaminathan, H., & Rouskin, S. (2020). Methods. doi:10.1016/j.ymeth.2020.04.001

2019

2018

A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation. Zhang, Y., Burkhardt, D. H., Rouskin, S., Li, G., Weissman, J. S., & Gross, C. A. (2018). Molecular Cell, 70(2). doi:10.1016/j.molcel.2018.02.035

2017

Operon mRNAs are organized into ORF-centric structures that predict translation efficiency. Burkhardt, D. H., Rouskin, S., Zhang, Y., Li, G., Weissman, J. S., & Gross, C. A. (2017). ELife, 6. doi:10.7554/elife.22037

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Zubradt M, Gupta P, Persad S, Lambowitz AM, Weissman JS, Rouskin S. Nat Methods. 2017 Jan;14(1):75-82. 

2014

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS. Nature. 2014 Jan 30;505(7485):701-5.

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, Weissman JS, Koller D. Mol Syst Biol. 2014 Dec 23;10:770. 

Past Publications

Genome-wide annotation and quantitation of translation by ribosome profiling. Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. Curr Protoc Mol Biol. 2013 Jul;Chapter 4:Unit 4.18.

A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, Li GW, Zhou S, King D, Shen PS, Weibezahn J, Dunn JG, Rouskin S, Inada T, Frost A, Weissman JS. Cell. 2012 Nov 21;151(5):1042-54. 

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. Nat Protoc. 2012 Jul 26;7(8):1534-50.

Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children. Chiu CY, Urisman A, Greenhow TL, Rouskin S, Yagi S, Schnurr D, Wright C, Drew WL, Wang D, Weintrub PS, Derisi JL, Ganem D. J Pediatr. 2008 Jul;153(1):76-83. 

Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity. Kistler A, Avila PC, Rouskin S, Wang D, Ward T, Yagi S, Schnurr D, Ganem D, DeRisi JL, Boushey HA. J Infect Dis. 2007 Sep 15;196(6):817-25. 

Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray. Chiu CY, Alizadeh AA, Rouskin S, Merker JD, Yeh E, Yagi S, Schnurr D, Patterson BK, Ganem D, DeRisi JL. J Clin Microbiol. 2007 Jul;45(7):2340-3. 

Genome-wide diversity and selective pressure in the human rhinovirus. Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL. Virol J. 2007 May 3;4:40. 

Microarray detection of human parainfluenzavirus 4 infection associated with respiratory failure in an immunocompetent adult. Chiu CY, Rouskin S, Koshy A, Urisman A, Fischer K, Yagi S, Schnurr D, Eckburg PB, Tompkins LS, Blackburn BG, Merker JD, Patterson BK, Ganem D, DeRisi JL. Clin Infect Dis. 2006 Oct 15;43(8):e71-6.