CS 838 (Spring 2003): Learning and Modeling Biological Networks

General Course Information

Course Overview and Requirements

This will be a special topics course that focusing on recent work that involves modeling metabolic, signaling, and gene regulation networks in cells, with a particular focus on using machine learning methods to induce models from data.

There are three parts to this course's requirements:

  1. Students will be expected to present 2-3 papers.
  2. Students will be expected to read each week's papers and participate in the discussions.
  3. Students will do substantial class projects of their choice. Project proposals will be due early in the semester, and a progress report will be due mid-semester. Team projects are acceptable.
Students who are auditing the course will be expected to present one paper and attend regularly.

Possible Readings

Background Reading

Learning and Modeling Genetic Networks

Learning and Modeling Metabolic Networks

Learning and Modeling Signaling Networks

Schedule of Presentations

date required readings recommended readings presenter
1/24 Genomic Biology
Modelling Cellular Behavior
Molecular Biology for Computer Scientists --
1/27 From Promoter Sequence to Expression: A Probabilistic Framework -- Joe Bockhorst
1/31 Minreg: Inferring an Active Regulator Set. -- Irene Ong
2/5 (Wednesday) continue From Promoter Sequence to Expression: A Probabilistic Framework -- Joe Bockhorst
2/7 Combining Inductive Logic Programming, Active Learning, and Robotics to Discover the Function of Genes Developing a logical model of yeast metabolism. Mark Rich
2/10 Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network -- Elenita Ilieva Kanin
2/14 Revising Regulatory Networks: From Expression Data to Linear Causal Models -- Wei Luo
2/17 Discovery of Regulatory Interactions through Perturbation: Inference and Experimental Design -- Cheryl Barkauskas
2/21 Transcriptional Regulation in Constraints-based Metabolic Models of Escherichia coli -- Yue Pan
2/24 topic: High-throughput Methods for Gathering Data about Cells (no readings) -- Chris Warren
2/28 NO CLASS -- --
3/3 Prediction of Mutant Expression Patterns using Gene Circuits -- Aaron Darling
3/7 Computational Expansion of Genetic Networks -- Burr Settles
3/10 NO CLASS -- Uri Keich talk at 2:25pm in B135 Van Vleck -- --
3/14 Computational Modeling of the EGF Receptor System: A Paradigm for Systems Biology -- Michael Molla
3/24 project discussion -- --
3/28 Discovery of Causal Relationships in a Gene Regulation Pathway from a Mixture of Experimental and Observational DNA Microarray Data -- Keith Noto
3/31 tutorial on enzyme kinetics Energy and Enzymes
Michaelis-Menten Kinetics
Michaelis-Menten Kinetics Applet
Symbolism and Terminology in Enzyme Kinetics
Dan McFarlin
4/4 Automatic Model Generation for Signal Transduction with Applications to MAP-Kinase Pathways -- Beverly Seavey
4/7 Inferring Subnetworks from Perturbed Expression Profiles -- Cheryl Barkauskas
4/11 Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes -- Aaron Darling
4/14 Extreme Pathway Lengths and Reaction Participation in Genome-Scale Metabolic Networks -- Yue Pan
4/18 NO CLASS -- --
4/21 Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks -- Wei Luo
4/25 -- -- --
4/28 Effects of Escherichia coli Physiology on Growth of Phage T7 In Vivo and In Siloco -- guest lecturer: Prof. John Yin
5/5 -- -- --
5/9 -- -- --

Research Groups and other Relevant Links

Mark Craven
Last modified: Mon Apr 14 09:06:57 CDT 2003