Mike Duff

Michael Duff


Department of Genetics and Genome Sciences

UConn Health Center
Institute for Systems Genomics
University of Connecticut
400 Farmington Ave
Farmington CT 06030
moduff@gmail.com

Graveley Lab

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.

  • NGS data analysis

    • DNA/RNA/ChIP/CLIP/iCLIP/RIP-seq data analysis(ENCODE)

    • alternative splicing and recursive splicing in D.melanogaster (modENCODE, DSCAM)

    • RNA interactions and functional intronic domains

    • lincRNA data analysis in hES differentiation

    • Human genetic variation, GWAS, and psychogenetics

    • analysis of RNAi off-target effects

    • transplicing

    • Polyomavirus editing, transcript expression profiling for the virus and its host

    • alternative-splicing changes during Human embryonic stem cell differentiation

    • Archaeal CRISPR-Cas systems

  • machine learning methods

    • probabilistic graphical models, model-structure induction, deep learning

    • causal inference and experimental design

    • reinforcement learning theory

    • sequential decision-making under uncertainty




How can Next-Generation-Sequencing be used to infer causal relationships between transcribed elements? How can ambiguity and bias be modeled and resolved?


Papers

Garren, 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.




Older things


My Erdos number is 3.