Lin Y, Schmidt B, Bruchez M, McManus CJ. (2018) Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture. Nucleic Acids Research.

Spealman P, Naik A, May G, Kuersten S, Freebert L, Murphy R, McManus J. (2017) Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data. Genome Research.

Wang H, McManus J, Kingsford C. (2017) Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast. Journal of Computational Biology.

Wang H, McManus J, Kingsford C. (2016)  Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap. Bioinformatics

Spealman P, Wang H, May G, Kingsford C, McManus CJ. (2016) Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling. Methods in Molecular Biology

McManus J, Cheng Z, Vogel C (2015) Next-generation analysis of gene expression regulation – comparing the roles of synthesis and degradation. Molecular Biosystems

Lin Y, May GE, McManus CJ. (2015) Mod-seq: A High-Throughput Method for Probing RNA Secondary Structure. Methods in Enzymology

Coolon, J. D., Stevenson, K. R., McManus, C. J., Yang, B., Graveley, B. R., & Wittkopp, P. J. (2015) Molecular mechanisms and evolutionary processes contributing to accelerated divergence of gene expression on the Drosophila X chromosome. Molecular Biology and Evolution

Talkish J, May GE, Lin Y, Woolford JL. Jr, McManus CJ. (2014) Mod-seq: High-throughput sequencing for chemical probing of RNA structure. RNA

Coolon JD, McManus CJ, Stevenson KR, Graveley BR, and Wittkopp PJ. (2014) Tempo and Mode of Regulatory Evolution in Drosophila Genome Research

McManus CJ, Coolon JD, Eipper-Mains J., Wittkopp PJ, and Graveley BR. (2014) Evolution of Splicing Regulatory Networks in Drosophila. Genome Research

Rafiq K, Shashikant T, McManus CJ, Ettensohn CA. (2014) Genome-Wide Analysis of the Skeletogenic Gene Regulatory Network of Sea Urchins. Development

Lee H, McManus CJ, Cho D-Y, Eaton M, Renda F, Somma MP, Cherbas L, May G, Powell S, Zhang D, Zhan L, Resch A, Andrews J, Celniker SE, Cherbas P, Przytzcka TM, Gatti M, Oliver B, Graveley BR, MacAlpine D. (2014) The Genome structures and effect of DNA copy number variation in Drosophila modENCODE cell lines. Genome Biology

McManus CJ, May G, Spealman P, Shteyman A. (2013) Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast. Genome Research

Dembowski JA, Ramesh M, McManus CJ, Woolford JL Jr. Identification of the binding site of Rlp7 on assembling 60S ribosomal subunits in Saccharomyces cerevisiae. RNA 19(12):1639-47, 2012

Coolon JD, Stevenson KR, McManus CJ, Graveley BR, Wittkopp PJ. Genomic imprinting absent in Drosophila melanogaster adult females. Cell Reports. Jul 26;2(1):69-75, 2012.

McManus CJ, Graveley BR. RNA Structure and the mechanisms of alternative splicing. Curr Opin Genet Dev 21(4):373-9,2011.

May GE, Olson S, McManus CJ, and Graveley BR. Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster. RNA 17(2):222-229,2011.

McManus CJ, Duff MO, Eipper-Mains J, and Graveley BR. Global analysis of trans-splicing in DrosophilaProc Natl Acad Sci USA 107(29):12975-12979, 2010.

McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, and Wittkopp PJ. Regulatory Divergence in Drosophila revealed by mRNA-seq. Genome Res 20(6):816-825, 2010.

McManus CJ, Graveley BR. Getting the message out. Mol Cell. 31(1):4-6, 2008.

McManus CJ, Schwartz ML, Butcher SE, Brow DA. A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation. RNA 13(12):2252-65, 2007

Sashital DG, Cornilescu G, McManus CJ, Brow DA, Butcher SE. U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction. Nat Struc Mol Biol. 11(12):1237-42, 2004.