Education
Ph.D. 2015 Johns Hopkins University,
Program in Cell, Molecular, Developmental Biology, and Biophysics
B.S. 2009 University of Maryland, College Park, Cell biology and molecular genetics (with high honors)
B.S. 2009 University of Maryland, College Park, Biochemistry
Research experience
2022 - present University of Michigan Medical School, Biological Chemistry
Assistant Professor
RNA Faculty Scholar of the Center for RNA Biomedicine, Member Rogel Cancer Center
2017 – 2022 Yale University, Molecular Biophysics and Biochemistry
Postdoctoral Fellow
Research focus: Mechanisms of translational control
Faculty Mentor: Dr. Wendy Gilbert
2016 University of Massachusetts Medical School, RNA Therapeutics Institute
Postdoctoral Associate
Research focus: RNA conformational changes within the spliceosome active site
The relationship between the DNA damage response and alternative splicing
Faculty mentor: Dr. Melissa Moore (Position ended due to Dr. Moore becoming CSO at Moderna Therapeutics)
2009 – 2015 Johns Hopkins University, Department of biology
Ph.D. research
Research focus: Structure-function relationships in telomerase RNA
Transcriptional response to telomerase deletion in yeast
Faculty mentor: Dr. David Zappulla
2007 – 2009 University of Maryland, Department of cell biology and molecular genetics
Undergraduate honors research
Research focus: Protein and rRNA modification in ribosome assembly and function
Faculty Mentor: Dr. Jonathan Dinman
2006 – 2007 University of Virginia, Department of biochemistry and molecular genetics
Research focus: Regulatory mechanisms of RNA polymerase I
Faculty Mentor: Dr. Jeffrey Smith
Awards and honors
2021 ISFS Fellow
2021 NextGen Symposium Honorable Mention
2020 NIH Pathway to Independence award (K99)
2019 American Cancer Society Postdoctoral Fellowship
2018 Rudolph J. Anderson Endowed Postdoctoral Fellowship
2016 T32 Institutional training grant
2013 RNA society travel fellowship
2008 – 2009 HHMI Undergraduate Research Fellow
2008 Tau Sigma Honor Society
2008 Primmanum Honor Society
2007 – 2009 Cell Biology and Molecular Genetics Honors Program
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 Syst. 2022 Jan 11: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 NAR
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., and Gilbert, W.V., Determinants of translational efficiency in cellular RNAs. Critical Reviews in Biochemistry and Molecular Biology. Invited review. Publication date: December 2022
Niederer, R.O., Gelsinger, D.R., Papadopoulos, N., Zappulla, D.C. Defining the distinct transcriptional response to short telomere-induced senescence (in preparation)
Teaching experience
2015 Intersession instructor, RNA in disease
Johns Hopkins University
Proposed and developed the course covering:
Molecular mechanisms underlying RNA-based diseases
Practical, hands on experience processing gene expression datasets using Tuxedo suite tools and R
2014 Teaching assistant, lecture
Cell biology, Johns Hopkins University
Duties: grading problem sets & exams, led 4 recitation sessions
2013 Teaching assistant, lab
Genetics, Johns Hopkins University
Duties: Introduced weekly lab concepts and techniques, supervised experimental procedures, graded lab reports, held office hours
2011 Teaching assistant, lab
Cell biology, Johns Hopkins University
Duties: Introduced weekly concepts and techniques, supervised experimental procedures, graded weekly lab reports, held optional review for final exam
2010 Teaching assistant, lab
Biochemistry, Johns Hopkins University
Duties: Introduced weekly concepts and techniques, supervised experimental procedures, graded weekly lab reports
2005 Teaching assistant, lab and lecture
General biology, Cabrillo College, Aptos, CA
Duties: Held weekly office hours, graded lab reports, problem sets and weekly quizzes, supervised experimental procedures
Mentoring experience
2017 – present Yale University
Graduate students: Austin Draycott, Allison Butt, Shivali Patel, Tianshu Liu
Undergraduate students: Caitlin Chun, Afia Kuragu
2009 – 2015 Johns Hopkins University
Graduate students: Michael Bemben, Josh Spurrier, Justin Brodie-Kommit, Jessica Winger, Diego Gelsinger
Undergraduate students: Jeffrey Nelson, Praneeth Sadda, Michael Setteducato, Eduardo Urias (BioREU participant)
Presentations and posters
2021 Rust Belt RNA 2021
Niederer, R.O., Rojas-Duran, M.F., Zinshteyn, B., Gilbert, W.V. Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation (Talk) Award for Outstanding Oral Presentation
2021 RNA 2021
Niederer, R.O., Rojas-Duran, M.F., Zinshteyn, B., Gilbert, W.V. Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation (Talk)
2020 Translational Control, Cold Spring Harbor, NY
Niederer, R.O., Rojas-Duran, M.F., Zinshteyn, B., Gilbert, W.V. Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation (Talk)
2020 7th Annual RNA Symposium, University at Albany, New York (Cancelled due to pandemic)
Niederer, R.O., Rojas-Duran, M.F., Zinshteyn, B., Gilbert, W.V. Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation (Talk)
2019 Protein Synthesis and Translational Control, EMBO Heidelberg
Niederer, R.O., Rojas-Duran, M.F., Zinshteyn, B., Gilbert, W.V. Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation (Poster)
2018 Translational Control, Cold Spring Harbor, NY
Niederer, R.O., Rojas-Duran, M.F., Zinshteyn, B., Gilbert, W.V. Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation (Talk)
2017 Protein Synthesis and Translational Control, EMBO Heidelberg
Niederer, R.O., Rojas-Duran, M.F., Zinshteyn, B., Gilbert, W.V. Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation (Poster)
2015 Telomeres and Telomerase, Cold Spring Harbor, NY
Niederer, R.O., Wang, Y., Papadopoulos, N., Zappulla, D.C. Defining the distinct transcriptional response to short telomere-induced senescence (Poster)
2015 RNA Biology, NIH, Frederick, MD
Niederer, R.O., Wang, Y., Papadopoulos, N., Zappulla, D.C. Global changes in transcription and rna processing during short telomere-induced senescence in yeast identified by RNA-seq (Poster)
2013 RNA Society meeting, Davos, Switzerland
Niederer, R.O., Zappulla, D.C. Investigating the structures of the yeast and human telomerase RNAs by SHAPE (Poster)
2008 Bioscience Day, University of Maryland, College Park
Niederer, R.O., Dinman J.D. Genetic Characterization of CBF5 mutants: implications with regard to Dyskeratosis congenita
2007 Summer Research Symposium, University of Virginia
Niederer R.O., Smith, J.S. A Role for DNA replication in the inheritance of rDNA silencing (Talk)
2006 Summer Research Symposium, University of Virginia
Niederer, R.O., Smith, J.S. Regulatory mechanisms of RNA Polymerase I (Talk)