- 1 Lab Projects2006
- 1.1 Ongoing
- 1.2 Possible
Software engineering: Andrew Uzilov
- Search facility
- Community annotation upload facility
- Drag-and-drop track sorting
- Tiles-on-demand: faster rendering
- Mashups, richer data views, crosslinks to Amigo
Position(s) open for Fall '06, Spring '07...
Graduate research project: Robert Bradley
Algorithms to compose multi-sequence Tree Transducers. Reconstruction of ancestral RNA.
Possible extensions: Telegraph-style grammar compiler
Graduate research project: Yuri Bendana
Drosophila ncRNA gene prediction pipeline using xrate
- Feature-rich modeling approach (varying G+C, protein/RNA/miRNA...)
Possible extension: Use of phylo-EM counts as log-likelihood log-derivatives in conditional log-linear evolutionary SCFG
- BFGS nonlinear optimization
- C++ extensions to DART
Research: Ian Holmes
Evaluation of String Transducers for alignment, phylogeny and profiling.
Development of xrate.
Development of stemloc.
Intern: Gabriel Wu
Rate profiling using xrate
- application to Acidothermus cellulolyticus
Visitor: Andreas Heger
Suitable as final projects for Teaching.BioE241 in Fall '06. Successful projects to be candidates for continuation, Spring '07.
Genome pair HMM
Find highest-scoring (in a minimum-message-length sense) string transducer for pairwise alignment of Drosophila genomes.
Graphical modeling in systems biology
Use MCMC to find informative interaction terms in Gibbs random field potential for co-representation of
- Pfam and Rfam domains;
- Biological function ontologies (e.g. EcoCyc, GO...)
- Microbial genomes
- Environmental sequencing reads
Applications to automated genome annotation.
Sequence database compression
Use of Arithmetic Coding, together with pair HMMs, etc. Corpus: Genbank.
Probabilistic modeling for RNA design
Software for forward RNA engineering, using SCFGs and CLLMs.
HIV quasispecies data analysis
Tentative - permission needed
- Can the following be observed...
- Consistent phylogeny?
- Rate variation?
- Indel polymorphism?
- Inversions, duplications?
-- Ian Holmes - 08 Sep 2006