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Items: 1 to 20 of 21

1.

Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast.

Wang H, McManus J, Kingsford C.

J Comput Biol. 2016 Oct 11. [Epub ahead of print]

PMID:
27726445
2.

Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.

Wang H, McManus J, Kingsford C.

Bioinformatics. 2016 Jun 15;32(12):1880-2. doi: 10.1093/bioinformatics/btw085.

3.

Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling.

Spealman P, Wang H, May G, Kingsford C, McManus CJ.

Methods Mol Biol. 2016;1358:71-97. doi: 10.1007/978-1-4939-3067-8_5.

PMID:
26463378
4.

Next-generation analysis of gene expression regulation--comparing the roles of synthesis and degradation.

McManus J, Cheng Z, Vogel C.

Mol Biosyst. 2015 Oct;11(10):2680-9. doi: 10.1039/c5mb00310e. Review.

5.

Mod-seq: A High-Throughput Method for Probing RNA Secondary Structure.

Lin Y, May GE, Joel McManus C.

Methods Enzymol. 2015;558:125-52. doi: 10.1016/bs.mie.2015.01.012.

PMID:
26068740
6.

Molecular Mechanisms and Evolutionary Processes Contributing to Accelerated Divergence of Gene Expression on the Drosophila X Chromosome.

Coolon JD, Stevenson KR, McManus CJ, Yang B, Graveley BR, Wittkopp PJ.

Mol Biol Evol. 2015 Oct;32(10):2605-15. doi: 10.1093/molbev/msv135.

7.

DNA copy number evolution in Drosophila cell lines.

Lee H, McManus CJ, Cho DY, Eaton M, Renda F, Somma MP, Cherbas L, May G, Powell S, Zhang D, Zhan L, Resch A, Andrews J, Celniker SE, Cherbas P, Przytycka TM, Gatti M, Oliver B, Graveley B, MacAlpine D.

Genome Biol. 2014 Aug 28;15(8):R70. doi: 10.1186/gb-2014-15-8-r70.

8.

Mod-seq: high-throughput sequencing for chemical probing of RNA structure.

Talkish J, May G, Lin Y, Woolford JL Jr, McManus CJ.

RNA. 2014 May;20(5):713-20. doi: 10.1261/rna.042218.113.

9.

Tempo and mode of regulatory evolution in Drosophila.

Coolon JD, McManus CJ, Stevenson KR, Graveley BR, Wittkopp PJ.

Genome Res. 2014 May;24(5):797-808. doi: 10.1101/gr.163014.113.

10.

Evolution of splicing regulatory networks in Drosophila.

McManus CJ, Coolon JD, Eipper-Mains J, Wittkopp PJ, Graveley BR.

Genome Res. 2014 May;24(5):786-96. doi: 10.1101/gr.161521.113.

11.

Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins.

Rafiq K, Shashikant T, McManus CJ, Ettensohn CA.

Development. 2014 Feb;141(4):950-61. doi: 10.1242/dev.105585. Erratum in: Development. 2014 Jun;141(12):2542.

12.

Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast.

McManus CJ, May GE, Spealman P, Shteyman A.

Genome Res. 2014 Mar;24(3):422-30. doi: 10.1101/gr.164996.113.

13.

Identification of the binding site of Rlp7 on assembling 60S ribosomal subunits in Saccharomyces cerevisiae.

Dembowski JA, Ramesh M, McManus CJ, Woolford JL Jr.

RNA. 2013 Dec;19(12):1639-47. doi: 10.1261/rna.041194.113.

14.

Genomic imprinting absent in Drosophila melanogaster adult females.

Coolon JD, Stevenson KR, McManus CJ, Graveley BR, Wittkopp PJ.

Cell Rep. 2012 Jul 26;2(1):69-75. doi: 10.1016/j.celrep.2012.06.013.

15.

RNA structure and the mechanisms of alternative splicing.

McManus CJ, Graveley BR.

Curr Opin Genet Dev. 2011 Aug;21(4):373-9. doi: 10.1016/j.gde.2011.04.001. Review.

16.

Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster.

May GE, Olson S, McManus CJ, Graveley BR.

RNA. 2011 Feb;17(2):222-9. doi: 10.1261/rna.2521311.

17.

Global analysis of trans-splicing in Drosophila.

McManus CJ, Duff MO, Eipper-Mains J, Graveley BR.

Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12975-9. doi: 10.1073/pnas.1007586107. Erratum in: Proc Natl Acad Sci U S A. 2013 May 7;110(19):7958.

18.

Regulatory divergence in Drosophila revealed by mRNA-seq.

McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ.

Genome Res. 2010 Jun;20(6):816-25. doi: 10.1101/gr.102491.109. Erratum in: Genome Res. 2014 Jun;24(6):1051.

19.

Getting the message out.

McManus CJ, Graveley BR.

Mol Cell. 2008 Jul 11;31(1):4-6. doi: 10.1016/j.molcel.2008.06.010.

20.

A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation.

McManus CJ, Schwartz ML, Butcher SE, Brow DA.

RNA. 2007 Dec;13(12):2252-65.

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