CS590G: Analysis of Biochemical Networks
Tu, Th, 4:30 - 5:50 PM
Instructor: Ananth Grama, LWSN 3-154G, Office Hours: W: 1:30 - 3:00 and by
CS590G, Analysis of Biochemical Networks, deals with abstractions,
algorithms, and statistical models, for gathering information from
a broad class of rapidly emerging datasets, referred to as biochemical
networks. While domain experts see great value in such data and how
it can be used for phenotype characterization, knockout experiments,
drug design, and, in general, understanding the biochemical processes
in the cell, there is increasing realization that the computational
framework needed to answer the questions needs to be developed.
This course surveys developments in the past few years in techniques
for generating, validating, and analyzing network data -- contributing
directly to the broader systems view to biology.
The course is structured as a reading course. The first part of the
course deals with introductory material, setting the scene for
presentations of a variety of recent results. Students will be
expected to present 1-2 papers, and undertake a semester-long
project, culminating in a paper and a presentation. This will
determine their grade in the class.
List of Papers
Kinetics of Networks
Gene Regulatory Networks
P. A. Spiro, J. S. Parkinson, and H. G. Othmer,
A model of excitation
and adaptation in bacterial chemotaxis. PNAS 94, 7263-7268 (1997).
N. Barkai and S. Leibler. Robustness in simple biochemical networks. Nature 387, 913-917 (1997).
J. Hasty, J. Pradines, M. Dolnik, and J. Collins.
Noise-based Switches and Amplifiers for Gene Expression.
Proc. Natl. Acad. Sci. USA 97, no. 5 (Feb 29, 2000): 2075-80.
F. Isaacs, J. Hasty, C. Cantor, and J. Collins.
Prediction and Measurement of an Autoregulatory Genetic Module. PNAS 100, no. 13 (June 24, 2003): 7714-19.
T. Gardner, C. Cantor, and J. Collins.
Construction of a Genetic Toggle Switch in Escherichia coli. Nature 403, no. 6767 (January 20, 2000): 339-42.
Protein Interaction Networks
Domain Interaction Networks
- P. Legrain, J. Wojcik, and J. M. Gauthier, Protein-protein
interaction maps: A lead towards cellular functions,
TRENDS in Genetics, 2001.
- B. Titz, M. Schlesner, and P. Uetz, What
do we learn from high-throughput protein interaction data?,
Expert Rev. Proteomics, 2004.
- I. Lee, S. V. Date, A. T. Adai, and E. M. Marcotte,
probabilistic functional network of yeast genes,
Inferring domain-domain interactions from protein-protein interactions,
domain interaction databases.
Topology of Biological Networks
- H. Lee, M. Deng, F. Sun, and T. Chen,
An integrated approach
to the prediction of domain-domain interactions,
BMC Bioinformatics, 2006.
- K. S. Guimaraes, R. Jothi, E. Zotenko, and T. M. Przytycka,
interactions using a parsimony approach,
Genome Biology, 2006.
- A. L. Barabasi and Z. N. Oltvai, Network
biology: Understanding the cell's functional organization,
Nature Reviews Genetics, 2004.
- N. Przulj, D. A. Wigle, and I. Jurisica,
topology in a network of protein interactions, Bioinformatics, 2004.
- S. Wuchty, Z. N. Oltvai, and A. L. Barabasi, Evolutionary conservation of motif constituents in the yeast protein interaction network,
Nature Genetics, 2003.
- R. Sharan, I. Ulitsky, and R. Shamir.
based prediction of protein function,
Molecular Systems Biology, 2007.
- A. Vazquez, A. Flammini, A. Maritan, and A. Vespignani,
protein function prediction from protein-protein interaction networks,
Nature Biotechnology, 2003.
Schedule of Presentations
Derek Drake, 11/27, Network biology: Understanding the cell's
Sabrina Jedlicka, 11/13, TBD.
Sael Lee, 11/20, A Probabilistic Functional Network of Yeast Genes,
Lee et al., Science, 2004.
Bin Li, 11/29, TBD.