Phone: (303) 492-8204
BioFrontiers 596 UCB - JSCBB B416
D.Sc., Washington University in St. Louis, 2004
Noncoding transcription, comparative genomics, transcriptional regulation, bioinformatics.
The cell utilizes transcription as a means of interpreting the genome. Large scale transcriptome profiling indicates a large fraction of the genome is transcribed. Most of the observed transcripts do not correspond with annotated features. One open question regarding these transcripts is whether they have a functional purpose within the cell or just represent the byproduct of transcriptional noise. Functional non-coding transcripts may be regulatory or they may produce, as of yet uncharacterized, structural non-coding RNAs. Understanding how transcription is regulated is key to understanding how new transcripts arise and potentially impact phenotype. Our comparative work with yeast strains indicates these transcripts vary even between closely related individuals and are a key component of individual phenotypic differences.
How much biologically meaningful information can we assert about an individual given their genome? Whole genome sequence has the potential to link variation to phenotype in an unbiased fashion. However, mechanistic models are needed to explain how specific variants impact the information processing capabilities of complex biomolecular networks and consequently translate into phenotypic differences.
Tissue-specific transcriptional regulation has diverged significantly between human and mouse.
Odom, DT, Dowell, RD, Jacobsen, ES, Gordon, W, Danford, TW, MacIsaac, KD, Rolfe, PA, Conboy, CM, Gifford, DK, and Fraenkel, E Nat Genet, 39(6):730-2. 2007
Genotype to Phenotype: A Complex Problem
Dowell, R, Ryan, O, Jansen, A, Cheung, D, Agarwala, S, Danford, T, Bernstein, D, Rolfe, PA, Heisler, L, Chin, B, Nislow, C, Giaever, G, Phillips, P, Fink, G, Gifford, D, and Boone, C Science, 328(5977):469. 2010
Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast.
Bumgarner, SL, Dowell, RD, Grisafi, P, Gifford, DK, and Fink, GR Proceedings of the National Academy of Sciences, 106(43):18321-18326. 2009
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.
Dowell, RD and Eddy, SR BMC Bioinformatics, 7:400. 2006
Discovering Regulatory Overlapping RNA Transcripts
Danford, T, Dowell, R, Agarwala, S, Grisafi, P, Fink, G, and Gifford, D Springer, Berlin Heidelberg, vol. LNBI (6044), 14th Annual International Conferece, RECOMB 2010 Lecture Notes in Computer Science. (ISBN: 3-642-12682-0). 2010