Department of Genetics and Genome Sciences
UConn Health Center
Institute for Systems Genomics
University of Connecticut
400 Farmington Ave
Farmington CT 06030
Efforts in the lab are directed toward bringing computational approaches, statistical modeling methods, and bioinformatics tools to bear upon problems posed by the analysis of Next-Generation-Sequencing (NGS) data, including the standard repertoire of techniques drawn from computational genomics: genome assembly, sequence alignment, gene-expression analysis, motif finding, SNP and structural-variant detection, phylogenetic analysis, and identification of regulatory sequences and networks---as well as the development of special-purpose ad-hoc computational tools for particular applications and novel techniques for data visualization.
PapersGarren, S., Duff, M.O., & Carmichael, G. (2015) Global analysis of mouse polyomavirus infection reveals dynamic regulation of viral and host gene expression and promiscuous viral RNA editing. PLOS Pathogens, 11(9), September 25.
Stoiber, M.H. et al (2015). Extensive cross-regulation of posttranscriptional regulatory networks in Drosophila, published onlinein Genome Research, Aug 20.
Brooks, A.N., Duff, M.O., May, G., Yang, L., Landolin, J., Wan, K., Sandler, J., Celniker, S.E., Graveley, B.R. and Brenner, S.E. (2015) Regulation of alternative splicing in Drosophila by 56 RNA binding proteins, published online in Genome Research, Aug 20.
Duff, M.O., Olson, S, Wei, X,, Osman, A., Plocik, A., Bolisetty, M. Celniker, S. & Graveley, B.R. (2015) Genome-wide Identification of Zero Nucleotide Recursive Splicing in Drosophila. Nature 521, May 21, 376-9.
Gerstein, M.B., et al (2014) Comparative analysis of the transcriptome across distant species. Nature 512, 445-448.
Chen, Z.X. et al (2014) Comparative validation of the D. melanogaster modENCODE Transcriptome Annotation. Genome Res. July;24(7):1209-23.
Brown, J.B. et al (many authors). 2014. Diversity and dynamics of the Drosophila transcriptome. Nature, published online March 16, 2014.
Eipper-Mains JE et al (2013) Effects of cocaine and withdrawal on the mouse nucleus accumbens transcriptome. Genes Brain Behav.12:21-33
Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman R C, Andrews J, Kaufman T, Cherbas P, Celniker SE, Graveley BR, Lai EC. (2012) Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Reports, Feb 23.
Yang L., Duff MO, Graveley BR, Carmichael GG and Chen L-L. 2011. Genomewide characterization of long nonpolyadenylated RNAs. Genome Biology, Feb 16.
Roy, S. et al (many authors). 2010. Identification of functional elements and regulatory circuits in Drosophila by large-scale data integration. Science, Dec 24.
Graveley, B. et al (many authors). 2010. The developmental transcriptome of Drosophila melanogaster. Nature, Dec 22.
Cherbas, L., et al (many authors). 2010. The transcriptional diversity of 25 Drosophila cell lines. Genome Research, Dec 22.
Brooks, A.N., Yang. L., Duff, M.O., Hansen, K.D., Dudoit, S., Brenner, S.E., Graveley, B.R. 2010. Conservation of an RNA Regulatory Map between Drosophila and Mammals. Genome Research, Oct 4.
McManus, C.J., Duff, M.O., Eipper-Mains, J., Graveley, B.R. 2010. Global Analysis of Transplicing in Drosophila. Proc Natl Acad Sci, July 1.
McManus, C.J., Coolon, J.D., Duff, M.O., Eipper-Mains, J., Graveley, B.R. and Wittkopp, P.J. 2010. Regulatory Divergence in Drosophila Revealed by mRNA-Seq . Genome Research, 20(6):816-25.
Hale, C.R., Zhao, P., Olsen, S., Duff, M.O., Graveley, B.R., Wells, L., Terns, R.M., and Terns, M.P. 2009 . RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell, 139(5):945-56. Nov 25.