BCB 444/544 Introduction to Bioinformatics Bioinformatics and Computational Biology

Required Reading Assignment 1

Altschul SF, Gish W. Local Alignment Statistics Methods Enzymology, 1996; 266:460-80

Prakash A, Tompa M. Statistics of Local Multiple Alignments Bioinformatics, 2005; 21 Suppl 1:i344-50

Reading Assignment 2

Mount Chapter 9 pp 361-385 "Gene Prediction and Regulation"

online: Overview for Chapter 7: "Understanding a Genome Sequence" from Genomes, 2nd Edition, TA Brown

online: Section 7.1: "Locating Genes in a Genome Sequence" from Genomes, 2nd Edition, TA Brown

READINGS FOR EXAM 2:

A. Krogh.
An introduction to hidden Markov models for biological sequences.
In S. L. Salzberg, D. B. Searls, and S. Kasif, editors, Computational Methods in Molecular Biology, chapter 4, pages 45-63. Elsevier, Amsterdam, 1998.

Altschul SF, Madden TL, Schaffer, AA, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17): 3389-3402.

Required Reading Assignment

Burge, C, Karlin, S. Prediction of Complete Gene Structures in Human Genomic DNA JMB, 1997; 268:78-94.

Optional Reading Assignment

Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., Baker, D. Progress in Modeling of Protein Structures and Interactions Science, 2005; 310:638-642.

Required Reading Assignment

Gibbs, R. Deeper Into the Genome Nature, 2005; 437:1233-1234

Goldstein, D.B., Cavalleri, G.L. Genomics: Understanding Human Diversity Nature, 2005; 437:1241-1242

Optional Reading Assignment

The International HapMap Consortium A Haplotype Map of the Human Genome Nature, 2005; 437:1299-1320