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Benchmarking parameter estimation and reverse engineering strategies
Published on Apr 04, 20077548 Views
Parameter estimation has become a central problem in systems biology, both in the form of calibration of bottom-up models or as a component of reverse engineering algorithms. With a proliferation of a
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Benchmarking parameter estimation and reverse engineering strategies00:00
pasi01:31
Original paper02:18
Parameter estimation02:43
Optimization methods04:43
3-step pathway with gene expression06:30
3-step model07:54
3-step model – results09:42
3-step model – results12:08
Results, 2nd attempt…13:06
Issues with parameter estimation15:28
Top-down modeling Reverse engineering16:36
The DREAM projet17:44
In silico biochemical networks for algorithm comparison23:13
Biochemical networks24:48
Bioinformatics26:41
Kinetics of transcription29:08
Kinetics for AGN29:19
Adding noise to simulated data30:17
Evaluation of Statistical Methods in Microarray Differential Expression Analysis31:11
Comparison: false positives32:00
Comparison: false negatives32:16
Effect of kinetics33:20
CoopSF4133:33
CoopSF41:33:42
Metrics34:22
How about the rest of biochemistry ?35:57
The Claytor Network36:11
Protein synthesis and signaling37:02
Protein synthesis and signaling37:12
Genetic regulation37:54
Gene knock-out experiments38:06
Gene knock-out experiments38:38
Gene knock-out experiments38:46
Gene knock-out experiments38:51
Comparison of four reverse engineering methods38:53
Increasing noise levels38:54
ROC curve for effect of noise39:11
Heterozygous mutant experiments39:41
Acknowledgements39:49