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Progress report Sandro Andreotti fall 2010

Work performed last 6 months

  • Several programming tasks were performed for the major revision of the ANTILOPE paper.
  • Writing the major revision of the ANTILOPE paper.
  • Together with Stefan Canzar and Gunnar we continued on the RNA transcript inference problem. The imlementation is almost complete. Two major problems remaining are how to set the parameters balancing errors vs. number of predicted isoforms. Incorporate paired end reads directly into the column generation approach. We plan to solve at least the first open problem in January during my visit to Amsterdam.
  • Implementation of some MS/MS simulation software based on machine learning. Still requires some evaluation and comparison to other approaches. If it is competitive possibly a short application note. Otherwise replace by some other model like Zhang's kinetic model (implementation might be a Bachelor thesis).
  • Some small programming tasks in OpenMS, mostly small fixes and preparation for the release.

Plan for the next 6 months (Bring in the harvest)

  • Isoform prediction: Complete the implementation of our isoform prediction software, test on our simulated data and compare to available algorithms and write the paper as soon as possible.
  • MSE: After we could evaluate the performance of the EtiSeq programm, we are very confident that it will not be a problem to beat them:
    • Reimplement the EtiSeq approach, but with a clearer algorithmic strategy. Use mass traces instead of scan wise selection, identify charge variants and adducts beforehand (Paper?).
    • Implement identification based strategy to disentangle overlapping signals in the MSE spectrum. This problem is similar to identification of peptides with chimeric spectra. Therefore a promising approach for the MSE disentanglement might also solve (or improve) another interesting problem. (Paper!)
    • Possibly some interesting project in colaboration with the Schlüter group who are very interested in MSE.

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