May GE, Akirtava C, Agar-Johnson M, Micic J, Woolford J, McManus J. (2023) Unraveling the influences of sequence and position on yeast uORF activity using massively parallel reporter systems and machine learning. eLife

Cravener MV, Do E, May G, Zarnowski R, Andes DR, McManus CJ, Mitchell AP. (2023) Reinforcement amid genetic diversity in the Candida albicans biofilm regulatory network. PLoS Pathogens

Akirtava C, May GE, McManus J. (2022) False-positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5′ UTR annotations. PNAS. See the ISCB journal club video here. Barna lab commentary and response available here

Do E, Cravener MV, Huang MY, May G, McManus CJ, Mitchell AP. (2022) Collaboration between Antagonistic Cell Type Regulators Governs Natural Variation in the Candida albicans Biofilm and Hyphal Gene Expression Network. mBio

May G, McManus J. (2022) Multiplexed Analysis of Human uORF Regulatory Functions During the ISR Using PoLib-Seq. Methods Mol Biol.

May G, McManus J. (2022)  High-Throughput Quantitation of Yeast uORF Regulatory Impacts Using FACS-uORF. Methods Mol Biol.

Konikkat S, Scribner MR, Eutsey R, Hiller NL, Cooper VS, McManus J. (2021) Quantitative mapping of mRNA 3′ ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3′ end formation in response to azithromycin. PLoS Genetics

Spealman P, Naik A, McManus J. (2021) uORF-seqr: A Machine Learning-Based Approach to the Identification of Upstream Open Reading Frames in Yeast. Methods in Mol. Biol

Lagree K, Woolford CA, Huang MY, May G, McManus CJ, Solis NV, Filler SG, Mitchell AP. (2020) Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality. PLoS Genetics

Lin Y, May G, Kready H, Nazzaro L, Mao M, Spealman P, Creeger Y, McManus CJ. (2019) Impacts of uORF codon identity and position on translation regulation. Nucleic Acids Research

Huang MY, Woolford CA, May G, McManus CJ, Mitchell AP. (2019) Circuit diversification in a biofilm regulatory network. PLoS Pathogens

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.

Wang H, Kingsford C, McManus CJ. (2018) Using the Ribodeblur pipeline to recover A-sites from yeast ribosome profiling data. Methods

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.