1. MEM2 - merging of different datasets for expression analysis, - tools development for parallel processing for MEM analysis for multiple genes, network construction using co-expressed data link
  2. MEM - How simillar are the expression between duplicates of very Recent origin, - duplicates and their expression similarities, -bidirectional sequence hits vs bidirectional gene expression hits
  3. Sequence - probe set - expression, given any sequence is it possible to identify probe sets and show the expression in genome browsers along with the next gene sequence data
  4. Next generation sequencing software - pipeline for analysis of next gen data, - setting up parallel processing using cloud computing
  5. Protein sequence analysis (phylogeny) and domain parsing - given any protein alignment with conserved domains in this family, construct a phylogenetic tree displaying different conserved domains. This is a usefull tool for large scale comparative genomics. The tool should be command line and also web based. (in addition if possible to display the expression data) The output should be similar to this link
  6. Comparative evolutionary analysis of genomes - set up the pipelines and visualization of data
  7. Expression data visualization in genome browser. See - genome browser, circos
  8. Double mutant expression prediction - Predict the expression of double mutants based on the single mutants article
  9. 1000 human genomes - analysis
  10. Analysis of co-expressed genes, comparing different softwares and identifying the better model.
  11. proteins with unknown function, genes/mRNA/protein -> gene expression/co-expression -> unknown funcion, these expressed genes with unknown function can they be annotated using gene expression/co-expression, systems biology data.
  12. g:profiler - do a CCancer: a bird’s eye view on gene lists reported in cancer-related studies (different gene lists for differenbt diseases) -- biology students can do this (ignore this project)
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