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My research interests involve the use of computational biology to answer fundamental evolution questions. Specifically, I am investigating large scale genomic evolution and developing a pathway that can be followed throughout evolution of the genome sequence. The biological processes involved may be polyploidization, smaller scale duplication events, rearrangements, transposable element movement and proliferation, and small scale localized indel mutation rates, all resulting in the generation of novel gene functions. Each research project below focuses on aspects of this overall research goal.
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Comparative genome analysis can elucidate the sequence of common ancestral organisms, which in turn, gives insight to the step-by-step evolution process. I have developed evolution simulations to model the genome sequence changes seen from evolution timepoints. This computational simulation calculates the ancestral organism sequence based on transposable element insertions, point mutations, and small insertions and deletions, with rates observed from the final genome. Further develop will add large scale genomic evolution events such as genome rearrangements and polyploidization events.
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| Transposable Element Annotation |
| Many plant genomes are highly repetitive and due to the density of repeats transposable elements insert within one another causing nested repeats. I have developed the TE nest software package, to correctly annotate nested transposable elements. With TE nest, clustered transposable elements can be reconstructed to their original structure to evalulate their phylogenetic relationships, preferences of insertion locations, and chronological history of the genome sequence.
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| Cytoplasmic Male Sterility |
| CMS plants, coupled with a restorer gene, give a genetic method to produce hybrid maize without the need for detasseling. Cms-T maize produces a mitochondrial protein URF13, necessary for male sterility, but causes susceptibility to the fungus C. heterostrophus. Restoration of fertility is achieved by the combination of two genes, Rf2 and Rf1. We have mapped and sequenced a 1.5 Mb region surrounding the rf1 locus on maize ch 3. We are completing microarray, hybridization, PCR, rtPCR, Mu insertion, and transformation experiments to identify the Rf1 gene in B73 (non-functional) and Wf9-B (functional) genomes. |
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Current sequence assembly and finishing techniques focus on the individual section of the genome under analysis, the insert within the sequenced BAC. I have developed two novel methods aimed to use biological sequence information of the organism to assist assembly closure, extremely useful for the difficult regions of repetitive sequence. Using structures such as transposable elements, gaps can be spanned and repetitive assembly collapses can be repaired. Software tools for automation of these processes are under development.
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TE nest: Automated annotation and visualization of maize
nested transposable elements.
49th Annual Maize Genetic Conference, March 23, 2007
Click here for abstract: Abstract
TE nest: Automated annotation and visualization of maize
nested transposable elements.
Plant and Animal Genome XV Conference, January 16, 2007
Click here for abstract: Abstract
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TE nest: Automated annotation and visualization of maize
nested transposable elements.
Kronmiller B.A., et al. 2007. Submitted
Click here for abstract: Abstract
Finishing a whole-genome shotgun: release 3 of the Drosophila
melanogaster euchromatic genome sequence.
Celniker S.E., et al. Genome Biol. 2002;3(12)
Click here: Abstract, Full Manuscript
The transposable elements of the Drosophila melanogaster
euchromatin: a genomics perspective.
Kaminker, et al. Genome Biol. 2002;3(12)
Click here: Abstract, Full Manuscript
Click here for full list: Publications
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TE nest: Automated annotation and visualization of maize
nested transposable elements.
48th Maize Genetics Conference, 2006
Click here for abstract: Abstract
Sequencing a 1.3 Mb contig spanning the rf1 fertility restorer
locus as a prototype to assess complex-genome coverage
strategies.
47th Maize Genetics Conference, 2005
Click here for abstract: Abstract
Click here for full list: Publications
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