Study Materials

This page includes supplementary readings and a sample version of the final quiz.


Motif Discovery

These reference materials have been compiled with introductory notes by course TA Tim Danford.

Barash, Bejerano, and Friedman. "A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites." Lecture Notes in Computer Science 2149 (2001).

Bailey, and Elkan. "The value of prior knowledge in discovering motifs with MEME." Proc Int Conf Intell Syst Mol Biol 3 (1995). (PS)

Neuwald, A. F., J. S. Liu, and C. E. Lawrence. "Gibbs motif sampling: Detection of bacterial outer membrane protein repeats." Protein Science 4, no. 8 (1995).

Lawrence, Altschul, Boguski, Liu, Neuwald, and Wootton. "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment." Science 262, no. 5131 (1993).

Sinha, Saurabh, and Martin Tompa. "Discovery of novel transcription factor binding sites by statistical overrepresentation." Nucleic Acids Research 30, no. 24 (2002): 5549–5560.

Benos, Panayiotis V., Martha L. Bulyk, and Gary D. Stormo. "Additivity in protein-DNA interactions: how good an approximation is it?" Nucleic Acids Res. 30, no. 20 (2002): 4442–4451.

Bulyk, Martha L., Philip L. F. Johnson, and George M. Church. "Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors." Nucleic Acids Res. 30, no. 5 (2002): 1255-1261.

Roth, Frederick P., Jason D. Hughes, Preston W. Estep, and George M. Church. "Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation." Nature Biotechnology 16 (1998): 939-945.

Hughes, Jason D., Preston W. Estep, Saeed Tavazoie, and George 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 (2000): 1205-1214.

Liu, X. Shirley, Douglas L. Brutlag, and Jun S. Liu. "An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments." Nature Biotechnology 20, no. 8 (2002): 835-839.

Sequence Alignment

These reference materials have been compiled with introductory notes by course TA Tim Danford.

Zhu, Jun, Jun S. Liu, and Charles E. Lawrence. "Bayesian adaptive sequence alignment algorithms." Bioinformatics 14, no. 1 (1998): 25-39.

Thompson, J. D., D. G. Higgins, and T. J. Gibson. "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic Acids Research 22, no. 22 (1994): 4673–4680.

Henikoff, S., and J. G. Henikoff. "Amino acid substitution matrices from protein blocks." PNAS 89, no. 22 (1992): 10915–10919.

Lipman, D. J., S. F. Altschul, and J. D. Kececioglu. "A tool for multiple sequence alignment." PNAS 86, no. 12 (1989): 4412–4415.

Microarray Normalization and Expression

Newton, M. A., C. M. Kendziorski, C. S. Richmond, F. R. Blattner, and K. W. Tsui. "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.

Dror, Ron O., Jonathan G. Murnick, Nicola J. Rinaldi, Voichita D. Marinescu, Ryan M. Rifkin, and Richard A. Young. "Bayesian Methods for Transcript Level Estimation from Noisy Array Measurements."

Ideker, Trey, Vesteinn Thorsson, Andrew F. Siegel, and Leroy E. Hood. "Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data." Journal of Computational Biology 7, no. 6 (2000): 805-817.

Hartemink, Alexander J., David K. Gifford, Tommi S. Jaakkola, and Richard A. Young. "Maximum likelihood estimation of optimal scaling factors for expression array normalization." (PDF - 1.7 MB)

Baldi, Pierre, and Anthony D. Long. "A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes." Bioinformatics 17, no. 6 (2001): 509-519.

Yang, Yee Hwa, Sandrine Dudoit, Percy Luu, David M. Lin, Vivian Peng, John Ngai, and Terence P. Speed. "Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation." Nucleic Acids Research 30, no. 4 (2002): e15.

Sample Quiz

Potential version of Final Quiz (PDF)