Lab Projects2006

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Lab Projects2006


Software engineering: Andrew Uzilov

Generic Genome Browser.

  • 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

xrate applications.


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.

TKF91 analysis

See Tkf Indel Model Path Summaries.

HIV quasispecies data analysis

Tentative - permission needed

  • Can the following be observed...
    • Covariation?
    • Consistent phylogeny?
    • Rate variation?
    • Indel polymorphism?
    • Inversions, duplications?


-- Ian Holmes - 08 Sep 2006