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Computational Functional Genomics >> Content Detail



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Part 1: Using DNA Sequence to Explain Mechanism
1Course Introduction
2Pairwise AlignmentAmazon logo Durbin, Richard, Sean R. Eddy, Anders Krogh, and Graeme Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge, UK: Cambridge University Press, 1999. ISBN: 9780521629713.
3Finding Regulatory Sequences in DNA: Motif DiscoveryHughes, J. D., P. W. Estep, S. Tavazoie, and G. M. Church. "Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae." Journal of Molecular Biology 296, no. 5 (March 10, 2000): 1205-14.
4Finding Regulatory Sequences in DNA: Motif Discovery (cont.)
Part 2: Observing the Mechanism of Transcriptional Regulation
5Microarray TechnologyMicroarray Core Facility - Laboratory Services

Pan, Qun, et al. "Revealing Global Regulatory Features of Mammalian Alternative Splicing Using a Quantitative Microarray Platform." Molecular Cell 16, no. 6 (December 22, 2004): 929-941.

Zhang, Wen, et al. "The Functional Landscape of Mouse Gene Expression." Journal of Biology 3, no. 5 (2004): 21.

Lee, Tong Ihn, et al. "Transcriptional Regulatory Networks in Saccharomyces cerevisiae." Science 298, no. 5594 (October 25, 2002): 799-804.
6Expression Arrays, Normalization, and Error ModelsYang, Yee Hwa, et al. "Normalization for cDNA Microarray Data: A Robust Composite Method for Addressing Single and Multiple Slide Systematic Variation." Nucleic Acid Research 30, no. 4 (2002).

Newton, M. A., et al. "On Differential Variability of Expression Ratios: Improving Statistical Inference about Gene Expression Changes from Microarray Data." Journal of Computational Biology 8, no. 1 (2001): 37-52.
7Expression Profiles, Clustering, and Latent ProcessesEisen, M. B., et al. "Cluster Analysis and Display of Genome-wide Expression Patterns." PNAS 95, no. 25 (December 8, 1998): 14863-8.

Liao, J. C., et al. "Network Component Analysis: Reconstruction of Regulatory Signals in Biological Systems." PNAS 100, no. 26 (December 23, 2003): 15522-7.

Dueck, and Frey. "Probabilistic Sparse Matrix Factorization." Technical Report, University of Toronto, 2004. (PDF)
8Computational Functional GenomicsIntroduction to SVD
9Stem Cells and Transcriptional RegulationDor, Y., J. Brown, O. Martinez, and D. A. Melton. "Adult pancreatic beta-cells are formed by self-duplication rather than stem-cell differentiation." Nature 429, no. 6987 (2004): 41-6.
10Part One: An Example of Clustering Expression Data

Part Two: Computational Functional Genomics (cont.)
Alizadeh, A. A., et al. "Distinct Types of Diffuse Large B-cell Lymphoma Identified by Gene Expression Profiling." Nature 403, no. 6769 (February 3, 2000): 503-11.

Ramalho-Santos, M., et al. ""Stemness": Transcriptional Profiling of Embryonic and Adult Stem Cells." Science 298, no. 5593 (October 18, 2002): 597-600.

Ivanova, N. B., et al. "A Stem Cell Molecular Signature." Science 298, 5593 (October 18, 2002): 601-4.

Fortunel, et al. "Comment on "'Stemness': transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature"." Science 302, no. 5644 (2003): 393.

Evsikov, et al. "Comment on "'Stemness': transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature"." Science 302, no. 5644 (2003): 393.

Ivanova, N. B., et al. "Response to comments on "'Stemness': transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature"." Science 302 no. 5644 (2003): 393.

Vogel, G. "'Stemness' Genes Still Elusive." Science 302, no. 5644 (October 17, 2003): 371.
11Project Group Meetings
12Project Group Initial Presentations
13Computational Discovery of Regulatory Networks
14RNA Silencing
Part 3: Building Predictive Network Models of Transcriptional Regulation
15Computational Functional Genomics (cont.)Heckerman, David. "A Tutorial on Learning with Bayesian Networks." Microsoft Technical Report MSR-TR-95-06, 1996.

Hartemink, Alex. "Principled Computational Methods for the Validation and Discovery of Genetic Regulatory Networks." MIT Ph.D. Thesis (2001). (PDF - 9.0 MB)
16Human Regulatory NetworksCooper, G. F., and E. Herskovits. "A Bayesian Method for the Induction of Probabilistic Networks from Data." KSL-91-02 (Knowledge Systems Laboratory, Stanford University), November 1993.
17Protein NetworksLi, S., et al. "A Map of the Interactome Network of the Metazoan C. elegans." Science 303, no. 5657 (January 23, 2004): 540-3.

Giot, L., et al. "A Protein Interaction Map of Drosophila melanogaster." Science 302, no. 5651 (December 5, 2003): 1727-36.

Gavin, A. C., et al. "Functional organization of the yeast proteome by systematic analysis of protein complexes." Nature 415, no. 6868 (2002): 141-7.

Ho, Y., et al. "Systematic Identification of Protein Complexes in Sacchormyces cerevisiae by Mass Spectrometry." Nature 415, no. 6868 (January 10, 2002): 180-3.

Tong, A. H., et al. "Global mapping of the yeast genetic interaction network." Science 303, no. 5659 (2004): 808-13.

Phizicky, E., P. I. Bastiaens, H. Zhu, M. Snyder, and S. Fields. "Protein Analysis on a Proteomic Scale." Nature 422, no. 6928 (March 13, 2003): 208-15.

von Mering, C., et al. "Comparative Assessment of Large-scale Data Sets of Protein-protein Interactions." Nature 417, no. 6887 (May 23, 2002): 399-403.
18Causal ModelsHeckerman, David. "A Tutorial on Learning with Bayesian Networks." Microsoft Technical Report MSR-TR-95-06, 1996.

Yeang, C. H., et al. "Physical Network Models." Journal of Computational Biology 11, no. 2-3 (2004): 243-263.
19Causal Bayesian Networks, Active LearningSegal, E., et al. "Module Networks: Identifying Regulatory Modules and their Condition Specific Regulators from Gene Expression Data." Nature Genetics 34, no. 2 (2003): 166-76.

McCuine S., C. Workman, T. Jaakkola, T. Ideker, C-H. Yeang, H. Mak. "Validation and refinement of gene-regulatory pathways on a network of physical interactions." Genome Biology 6, no. 7 (2005): R62.

Oliver, S. G., et al. "Functional genomic hypothesis generation and experimentation by a robot scientist." Nature 427 (2004): 247 - 252.
20From Biological Data to Biological Insight
21Modeling Transcriptional RegulationSegal, E., et al. "Module Networks: Identifying Regulatory Modules and their Condition Specific Regulators from Gene Expression Data." Nature Genetics 34, no. 2 (2003): 166-76.

Said, M., A. Oppenheim, and D. Lauffenburger. "Modeling Cellular Signal Processing Using Interacting Markov Chains." In Proceedings of the International Conference on Acoustics, Speech, Signal Processing, 2003.
22DynamicsArkin, Ross, and McAdams. "Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage Lambda-Infected Escherichia coli Cells." Genetics 149 (August 1998): 1633-1648.

Gilman, Arkin. "Genetic 'Code': Representations and Dynamic Models of Genetic Components and Networks." Annu. Rev. Genomics Hum. Genet. 3 (2002): 341-69.

McAdams, Arkin. "It's A Noisy Business!: Gene Regulation at the Nanomolar Scale." Trends in Genetics 15 (1999): 65-69.

———. "Simulation of Genetic Circuits." Annu. Rev. Biophys. Biomol. Struct. 27 (1998): 199-224.

Gillespie. "Exact Stochastic Simulation of Coupled Chemical Reactions." Journal of Physical Chemistry 81, no. 25 (1977): 2340-2361.

 








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