Computational Functional Genomics

LEC #: 1 · TOPICS: Course Introduction; Overview · READINGS: No readings for this lecture.

LEC #: 3 · TOPICS: Global Alignment of Protein Statistics · READINGS: No readings for this lecture.

LEC #: 16 · TOPICS: Protein Interaction Networks · READINGS: No readings for this lecture.

Leach, Andrew. Molecular Modelling: Principles and Applications . Prentice Hall, 2001. ISBN: 9780582382107.

Durbin, Richard, Sean R. Eddy, et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids . Cambridge University Press, 1998. ISBN: 9780521629713.

Gonick, Larry, and Woollcott Smith. The Cartoon Guide to Statistics . Paw Prints, 2008. ISBN: 9781435242715.

LEC #: 2 · TOPICS: Pairwise Alignment · READINGS: Durbin, R., S. R. Eddy, A. Krogh, and G. Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge, UK: Cambridge University Press, 1999. ISBN: 9780521629713.

LEC #: 3 · TOPICS: Finding Regulatory Sequences in DNA: Motif Discovery · READINGS: Hughes, et al. Journal of Molecular Biology 296, no. 5 (2000): 1205-14.

Qun Pan, et al. “Revealing Global Regulatory Features of Mammalian Alternative Splicing Using a Quantitative Microarray Platform.” Molecular Cell 16 (December 22, 2004): 929–941.

Wen Zhang, et al. “The Functional Landscape of Mouse Gene Expression.” Journal of Biology (2004): 3:21.

Tong Ihn Lee, et al. “Transcriptional Regulatory Networks in Saccharomyces Cerevisiae .” Science (2002).

Hwa Yang, Yee, 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, 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).

Eisen, et al. “Cluster Analysis and Display of Genome-wide Expression Patterns.” PNAS 95, no. 25 (1998).

Liao, et al. “Network Component Analysis: Reconstruction of Regulatory Signals in Biological Systems.” PNAS 100, no. 26 (2003).

LEC #: 9 · TOPICS: Stem Cells and Transcriptional Regulation · READINGS: Dor, 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.

Alizadeh, et. al. “Distinct Types of Diffuse Large B-cell Lymphoma Identified by Gene Expression Profiling.” Nature 403 (February 2000).

Ramalho-Santos, et. al. “Stemness: Transcriptional Profiling of Embryonic and Adult Stem Cells.” Science 298 (October 2002).

Ivanova, et. al. “A Stem Cell Molecular Signature.” Science 298 (October 2002).

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. “‘Stemness’ Genes Still Elusive.” Science 302 (October 2003).

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 PhD Thesis (2001).

Li, et al., “A Map of the Interactome Network of the Metazoan C. elegans .” Science 303 (January 2004).

Giot, et al. “A Protein Interaction Map of Drosophila melanogaster .” Science 302 (December 2003).

Gavin, et al. “Functional Organization of the Yeast Proteome by Systematic Analysis of Protein Complexes.” Nature 415 (January 2002).

Ho, et al. “Systematic Identification of Protein Complexes in Sacchormyces Cerevisiae by Mass Spectrometry.” Nature 415 (January 2002).

Tong, Lesage, et al. “Global Mapping of the Yeast Genetic Interaction Network.” Science 303 (February 2004).

Phizicky, Bastiaens, Zhu, Snyder, and Fields. “Protein Analysis on a Proteomic Scale.” Nature 422 (March 2003).

von Mering, et al. “Comparative Assessment of Large-scale Data Sets of Protein-protein Interactions.” Nature 417 (May 2002).

Heckerman. “A Tutorial on Learning with Bayesian Networks.” Microsoft Technical Report MSR-TR-95-06, 1996.

Yeang, et al. “Physical Network Models.” Journal of Computational Biology 11, nos. 2-3 (2004): 243-263.

Gavin, A. C., et al. “Functional Organization of the Yeast Proteome by Systematic Analysis of Protein Complexes.” Nature 415, no. 6868 (2002): 141-7.

Tong, A. H., et al. “Global Mapping of the Yeast Genetic Interaction Network.” Science 303, no. 5659 (2004): 808-13.

Arkin, 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.