Extraction of Correlated Gene Clusters by Multiple Graph Comparison课件.ppt

Tue Sep 18 Intro 1: Computing, statistics, Perl, Mathematica Tue Sep 25 Intro 2: Biology, comparative genomics, models evidence, applications Tue Oct 02 DNA 1: Polymorphisms, populations, statistics, pharmacogenomics, databases Tue Oct 09 DNA 2: Dynamic programming, Blast, multi-alignment, HiddenMarkovModels Tue Oct 16 RNA 1: 3D-structure, microarrays, library sequencing quantitation concepts Tue Oct 23 RNA 2: Clustering by gene or condition, DNA/RNA motifs. Tue Oct 30 Protein 1: 3D structural genomics, homology, dynamics, function drug design Tue Nov 06 Protein 2: Mass spectrometry, modifications, quantitation of interactions Tue Nov 13 Network 1: Metabolic kinetic flux balance optimization methods Tue Nov 20 Network 2: Molecular computing, self-assembly, genetic algorithms, neural-nets Tue Nov 27 Network 3: Cellular, developmental, social, ecological commercial models Tue Dec 04 Project presentations Tue Dec 11 Project Presentations Tue Jan 08 Project Presentations Tue Jan 15 Project Presentations;Protein2: Last weeks take home lessons;Net1: Todays story goals;Networks Why model?;Types of interaction models;In vivo (classical) in vitro;Human Red Blood CellODE model;Factors Constraining Metabolic Function;Dynamic mass balances on each metabolite;RBC model integration;Scopes Assumptions;Glycolysis Dynamic Mass Balances;Enzyme Kinetic Expressions;Kinetic Expressions;Kinetic parameter assumptions;Additional constraints:Physicochemical constrains;RBC steady-state in vivo vs calculated;K;Red 0 hours Green 0.1 Blue 1.0 Yellow 10 End 300 ; 0 to 300 hour dynamics 34 metabolites calculated ;RBC Metabolic “Machinery”;Cell DivisionCycleG2 arrestto M arrest switch;Hill coefficients;Progesterone AA Mos Mos-P Mek Mek-P Mapk Mapk-P ;Net1: Todays story goals;Arkin A, Ross J, McAdams HH Genetics 1998 149(4):1633. ;Efficient exact