COT 6936/CAP 6990 Bioinformatics: Fall 02
Suggested Reading

• Molecular Biology: made simple and fun, Cache River Press.
• Human Genome Program, U.S. Department of Energy, Primer on Molecular Genetics, Washington, D.C., 1992. Prepared by Denise Casey, Human Genome Management Information System, Oak Ridge National Laboratory, for the 1991-92 DOE Human Genome Program Report.
• An animated primer on the basics of DNA, genes, and heredity., 2002 Merlot Classics.
• Dolan DNA Learning Center Multimedia Guides to Molecular Biology.
• About the Human Genome Project
• DNA seen through the eyes of a coder
• Chapter 13, Pevzner's text.

Human Genome Project & Sequencing

• (Publicly Funded) Human Genome Draft and Nature Website 
• Multimedia Presentations and descriptions of many Molecular Biology techniques and concepts: The Human Genome Project

• Sequence Alignment in Molecular Biology, by A. Apostolico and R. Giancarlo, Journal of Computational Biology 5,2 (1998).
• CLUSTALW Paper, by Thompson, Higgins & Gibson.
• Chapter 6-7, Pevzner's text.
• Chapter 7-8, Gibas/Jambeck text.

• The famous BLAST paper by Altschul, et al., J Mol Biol, 1990.
• Read about BLAST (Go through the BLAST Tutorial; For more information, read the BLAST Manual and/or BLAST References) and FASTA (Look at the FASTA Help Document).
• Chapters 1-6, Gibas/Jambeck text.

• Review of HMMs , by Lawrence Rabiner, Proc IEEE, 1989.
• Review of Profile HMMs , by Sean Eddy, Bioinformatics, 1998.
• Review of CpGs.
• See chapters 7-8 from Bioinformatics, by Baldi & Brunak.
• See chapters 1-5, from Biological Sequence Analysis , by Durbin, Eddy, Krogh, Mitchison.

• Review of Gene Detection , by David Haussler.
• Review of Gene Detection , by Jean-Michel Claverie, Bioinformatics 1997.
• See chapter 9, from Pevzner text.

• Read chapters 1,2,7,8 from Introduction to Protein Structure , by Branden and Tooze.
• Read about the GYM program in Mining Protein Sequences for Motifs [pdf Version] , by Narasimhan, Bu, Gao, Wang, Xu, and Mathee, Journal of Computational Biology, 2002.

Protein Structure Classification

• Paper on Pfam Database, by Bateman et al., from Nucleic Acids Research, 2002.
• SCOP: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures, by Murzin et al., J Mol. Biol. 1995.
• Identification of homology in protein structure classification, by Holm & Sander, Nature, 2001.
• Dictionary of recurrent domains in protein structures, by Holm & Sander, Proteins, 1998.

Machine Learning

• Look at the wonderful notes/slides by Andrew Moore and Tom Mitchell.
• Read the book Machine Learning, Tom Mitchell, McGraw Hill, 1997.
• General introduction to SVMs, by Hearst, Scholkopf, Platt, Dumais, Osuma, IEEE Intelligent Systems, 1998.
• Tutorials on SVMs: Burges (1998), and Smola & Scholkopf (1998).
• Read the book Support Vector Machines, by Cristianini & Shawe-Taylor, 2000.
• You can ask hard questions about SVMs by posting messages to the messageboard at: www.kernel-machines.org/blackboard

Gene Expression (Microarrays)

• Nature article on Microarray technology.
• CAMDA: Critical Assessment of Microarray Data Analysis.
• MAIME: towards standards for microarray data.
• Microarray data analysis using SAM: paper by Tusher, Tibshirani, & Chu (PNAS, 2001).

• Molecular Classification of Human Carcinomas by Use of Gene Expression Signatures, by Su et al., Cancer Research, 2001.

Phylogenetic Trees

• Read the superb book titled Fundamentals of Molecular Evolution, by Graur & Li (2000).

Genetic & Physical Mapping

• Read chapters 1-3 from Pevzner's text.