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== Memoranda Directory ==

=== Organized by Date ===

 * Adrian Dobra - Biostats Seminars - Lebovic Building - Thur 13 Nov 2007 <<BR>>
 ~-''Since I did not take part to the previous formal seminar, but just to the open discussion, I was almost clueless about the statistical model proposed. However, it was interesting to discuss the problem of searching genetic markers, and how to use prior information (e.g. known physical interaction) to enhance the search effectivity. Here follows a more general discussion on why the search of genetic markers is not such a straightforward process, because of context-dependence.''-~<<BR>>
 [[DanieleMerico/MemorandaDirectory/MarkersAndContext| The search for Genetic Markers and the Context-dependence problem]] 

 * Wed 14 Nov 2007 <<BR>>
 Lehar J & al., Nature Systems Biology, Feb 2007<<BR>>
 [[http://www.nature.com/msb/journal/v3/n1/full/msb4100116.html|Chemical combination effects predict connectivity in biological systems]]
   * issue: relations between the curve-shape of drug binary-combination effects and connectivity in metabolic pathawys
   * understanding of the general message: 90%
   * understanding of details: 40%  
   * [[DanieleMerico/MemorandaDirectory/ChemCombConnectPath| more detailed review]]

 * Fri 16 Nov 2007 <<BR>>
 T. Ideker's group & coll., Nature Systems Biology, Oct 2007<<BR>>
 [[http://www.nature.com/msb/journal/v3/n1/full/msb4100180.html;jsessionid=48FC8CABE6062769ACFD30A5256B8E6F|Network-based classification of breast cancer metastasis]]
   * issue: identifying subnetworks globally differential between metastasis-positive breast cancers and control patients, and exploting them for a better prediction (compared to flat markers lists)
   * understanding of the general message: 100%
   * understanding of details: 90%  
   * [[DanieleMerico/MemorandaDirectory/NetwClassBreastMet| more detailed review]]   

 * Mon 14 Jan 2008<<BR>>
 [[DanieleMerico/GOALIErevisited| a survey of transcriptional regulation of GO terms during yest cell cycle]]

 * Mon 21 Jan 2008<<BR>>
 [[DanieleMerico/MemorandaDirectory/MarkersAndContext/PCAexperiments_Experiments_to_better_understand_how_PCA_works]]

=== Organized by Issue ===
 
''(listed under this category only if not appearing in the Work Logs)''

 * Problems in the search for Disease Markers
   * [[DanieleMerico/MemorandaDirectory/MarkersAndContext| The search for Genetic Markers and the Context-dependence problem]]
 * Dimensionality Reduction
   * [[DanieleMerico/MemorandaDirectory/MarkersAndContext/PCAexperiments_Experiments_to_better_understand_how_PCA_works]]
 * critically revisiting the GOALIE approach: <<BR>>
   * [[DanieleMerico/GOALIErevisited| a survey of transcriptional regulation of GO terms during yest cell cycle]]