Readings:

Background

Human Genome Project

• DOE What's the Human Genome Project, 2004

• DOE Genomics and Its Impact on Science and Society The Human Genome Project and Beyond, 2003

• Jasny & Kennedy, The Human Genome, Science, Vol 291, Issue 5507, 1153 , 16 February 2001

Molecular genetics

• DOE Genomics A Primer: From DNA to Life

• NCBI Basic Intro to Molecular genetics

• DOE Primer on Molecular Genetics

• Roche CD-ROM Interactive Roche Genetics Education Program

• Krane&Raymer Chapter 1 -- Molecular Biology and Biological Chemistry

• Jasny & Kennedy, The Human Genome, Science, Vol 291, Issue 5507, 1153 , 16 February 2001

Computer Science

• Krane&Raymer Appendix 1 -- A Gentle Introduction to Computer Programming and Data Structures

Biological databases

• The Molecular Biology Database Collection: 2006 update Nucleic Acids Research. You could browse the list itself.
• NCBI Entrez tutorial

Sequence alignments

• Per Kraulis' Lecture Notes on Dynamic Programming alignments

BLAST

• The NCBI BLAST education pages

• Altschul, et al on PSI-BLAST and on improving PSI-BLAST

FASTA

• Pearson & Lipman, Improved tools for biological sequence comparison, Proc Natl Acad Sci U S A 1988, 85 (8):2444-8

Hidden Markov Models

• Sean Eddy's Review article on HMMs, Bioinformatics 14:755-763 (1998).
• Rachel Karchin's ISMB '99 HMM tutorial Hidden Markov Models and Protein Sequence Analysis

Phylogenetic inference

• Kim & Warnow's Tutorial on Phylogenetic Tree Estimation

Protein structure and its prediction

• Rising accuracy of protein secondary structure prediction. Burkhard Rost, CUBIC, Columbia University
• Local structure prediction using a library of sequence-structure motifs. Journal of Molecular Biology. 281, 565-77. (1998)
• HMMSTR: a Hidden Markov Model for Local Sequence-Structure Correlations in Proteins. Journal of Molecular Biology, Vol. 301, No. 1, Aug 2000, pp. 173-190.

• The HP model: Dill, et al Principles of protein folding - A perspective from simple exact models, Protein Science, Vol 4, Issue 4 561-602 (1995).

• Karplus & McCammon's Molecular dynamics simulations of biomolecules Nature: Structural Biology 2002 Sep;9(9):646-52.
• The Olympic Games of Protein Structure Prediction 2002

Gene expression arrays

• Atul Butte, The Use and Analysis of Microarray Data, Nature Reviews Drug Discovery 1, 951 -960 (2002)