Publications

 Niederer, R.O., Rojas-Duran, M.F., Zinshteyn, B., Gilbert, W.V. Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation. Cell Systems. Jan 11, 2022;S2405-4712(21)00485-3. doi: 10.1016/j.cels.2021.12.002.

Koubek, J., Niederer, R.O., Aitkin, C., Gilbert, W.V., Cellular translational enhancer elements that recruit eukaryotic initiation factor 3 (in revision)

Sullivan, M.C., Vock, I.W., Niederer, R.O., Kiefer, L., Gilbert, W.V., Simon, M.D., An internally normalized approach to comparing RNA levels between samples using nucleoside recoding chemistry (in revision)

Sun Y, Abriola L, Niederer RO, Pedersen SF, Alfajaro MM, Silva Monteiro V, Wilen CB, Ho YC, Gilbert WV, Surovtseva YV, Lindenbach BD, Guo JU, Restriction of SARS-CoV-2 Replication by Targeting Programmed −1 Ribosomal Frameshifting. PNAS. June 29, 2021 118 (26) e2023051118, doi: 10.1073/pnas.2023051118

Niederer, R.O., Hass, E.P., Zappulla, D.C. (2016) Long Noncoding RNAs in the Yeast S. cerevisiae. Adv Exp Med Biol. 2017;1008:119-132. doi: 10.1007/978-981-10-5203-3_4. PMID: 28815538

Niederer, R.O., Papadopoulos, N., Zappulla, D.C. (2016) Identification of novel lncRNAs in telomerase-negative yeast by RNA-seq. Sci Rep. Jan 20;6:19376. doi: 10.1038/srep19376. PMID: 26786024

Niederer R.O., Zappulla D.C. (2015) Refined secondary structure models of the core of yeast and human telomerase RNAs directed by SHAPE. RNA. 21(2):254-61. PMID: 25512567

Lebo, K.J., Niederer, R.O., Zappulla, D.C. (2015) A second essential function of the Est1-binding arm of yeast telomerase. RNA. 2015 May;21(5):862-76. doi: 10.1261/rna.049379.114. Epub 2015 Mar 3. PMID: 25737580

Jack K, Bellodi C, Landry D.M., Niederer R.O., Meskauskas A, Musalgaonkar S, Kopmar N, Krasnykh O, Dean A.M., Thompson S.R., Ruggero D, Dinman J.D. (2011). rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells. Mol Cell. 44(4):660-6. PMID: 22099312 

Hontz, R.D., Niederer, R.O., Johnson, J.M., Smith, J.S. (2009). Genetic Identification of Factors that Modulate Ribosomal DNA Transcription in Saccharomyces cerevisiae. Genetics. 182(1):105-19. PMID: 19270272

Manuscripts in preparation

Niederer, R.O., Gelsinger, D.R., Papadopoulos, N., Zappulla, D.C. Defining the distinct transcriptional response to short telomere-induced senescence

Niederer, R.O., and Gilbert, W.V., Determinants of translational efficiency in cellular RNAs. Critical Reviews in Biochemistry and Molecular Biology. Invited review. Publication date: December 2022