[BT]
 C. Branden and J. Tooze. Introduction to Protein Structure (2nd edition), Garland Publishing Inc., 1999.
[CLR]
 T. Cormen, C. Leiserson, R. Rivest, and C. Stein. Introduction to Algorithms, Second Edition. MIT Press, 2001.
[DE]
 R. Durbin, S. Eddy, A. Krogh, G. Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998.
[EG]
 W. Evans and G. Grant. Statistical Methods in Bioinformatics. Springer-Verlag, 2002.
[GG*]
 A. Griffiths, W. Gelbart, J. Miller, and R. Lewontin. Modern Genetic Analysis. Freeman, 1999.
[L]
 A. R. Leach. Molecular Modelling. Principles and Applications. Addison Wesley, 1996.
[M]
 D. W. Mount. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Lab Press, 2000.
[P]
 P. Pevzner. Computational Molecular Biology. The MIT Press, 2000.
[S]
 T. Schlick. Molecular Modeling and Simulation. Springer-Verlag, 2002.
[St]
 M. Sternberg. Protein Structure Prediction, IRL Press, 1996.
[W]
 M. Waterman. Introduction to Computational Biology. Chapman & Hall, 1995.
I.
 Introduction
A.
 A. Griffiths, W. Gelbart, J. H. Miller, and R. Lewontin. Modern Genetic Analysis, W. H. Freeman, 1999.
B.
 Molecular Biology for Computer Scientists, by Lawrence Hunter.
http://www.cs.duke.edu/education/courses/fall03/ cps260/
notes/hunter.pdf
C.
 The NCBI Science Primer
http://www.ncbi.nlm.nih.gov/About/primer/index.html
D.
 The DOE Science Primer
http://www.ornl.gov/TechResources/Human_Genome/ publicat/
primer/index.html
E.
 The DOE Human Genome Project Site
http://www.ornl.gov/TechResources/Human_Genome/
F.
 Double helix: 50 years of DNA
http://www.nature.com/nature/dna50/index.html.
II.
 Algorithmic Techniques
A.
 D. Gusfield. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge University Press; 1st edition (January 15, 1997)
III.
 Sequence Alignment
A.
 W. R. Pearson Protein sequence comparison and Protein evolution, Tutorial ISMB2000
B.
 S. F.Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. Review.
C.
 S. Henikoff and J. G. Henikoff. Amino Acid Substitution Matrices from Protein Blocks, PNAS 1992 89: 10915-10919.
D.
 W. R. Pearson and D. J. Lipman. Improved tools for biological sequence comparison, PNAS 1988 Apr; 85(8):2444-8.
IV.
 Genome Assembly
A.
 J. C. Venter et. al. The sequence of the Human Genome, Science 2001 Feb; Vol 291
B.
 E. W. Myers et. al. The genome sequence of Drosophila melanogaster, Science 2000 Mar; Vol 287
C.
 W. J. Kent and D. Haussler. Assembly of the working draft of the human genome with GigAssembler, Genome Res. 2001 Sep; 11(9)
D.
 R. H. Waterston, E. S. Lander, J. E. Sulston. More on the sequencing of the human genome, PNAS 2003 Mar; 100(6):3022-4.
E.
 Analysis of Human Genome Project, Nature 2001 Feb; Vol 509:814-958.
F.
 J. L. Weber and E. W. Myers. Human whole-genome shotgun sequencing, Genome Res. 1997 May;7(5):401-9.
F.
 E. W. Myers. Whole-Genome DNA sequencing, IEEE 1999 May-June.
V.
 Hidden Markov Models
A.
 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.
B.
 A. Krogh, M. Brown, I. S. Mian, K. Sjolander, and D. Haussler. Hidden Markov models in computational biology: Applications to protein modeling, Journal of Molecular Biology, 235:1501-1531, Feb. 1994.
C.
 L. Rabiner and B. Juang.An introduction to hidden Markov models, IEEE ASSP Magazine, January 1986, 4-16.
D.
 HMM Toolbox for Matlab
http://www.ai.mit.edu/~murphyk/Software/HMM/hmm.html
VI.
 Gene Prediction
A.
 D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, and D. L. Wheeler. GenBank, Nucleic Acids Research 31 (2003), 23-27.
B.
 C. Burge and S. Karlin. Prediction of complete gene structure in human genomic DNA, J. Mol. Biology 268 (1997), 78-94.
C.
 J. W. Fickette. Finding genes by computer: the state of art, Trends Genet. 12 (1996) 316-320.
D.
 D. Haussler. Computational genefinding., Trends Biochemical Science 1998, 215-222.
E.
 C. Mathe, M.-F. Sagot, T. Schiex, and P. Rouze. Current methods of gene prediction, their strengths and weaknesses, Nucleic Acids Research 30 (2002) 4103-4117.
F.
 J. Ohler and H. Niemann. Identification and analysis of eukaryotic promoters: recent computational approaches, Trends Genet. 17 (2001) 223-234.
VII.
 Gene Expression
A.
 Asa Ben-Hur, David Horn, Hava T. Siegelmann, and Vladimir Vapnik. Support vector clustering, Journal of Machine Learning Research, 2:125-137, 2001.
B.
 T. Hastie, R. Tibshirani, and J. Friedman. The Elements of Statistical Learning, Springer-Verlag, Berlin, Germany, 2001.
C.
 D. J. Lockhart and E. A. Winzeler. Genomics, gene expression and DNA arrays, Nature, 405(6788):827-836, 2000.
D.
 R. Shamir and R. Sharan. Algorithmic approaches to clustering gene expression data, In T. Jiang, T. Smith, Y. Xu, and M. Q. Zhang, editors, Current Topics in Computational Biology. MIT press, 2001.
E.
 R. Tibshirani, T. Hastie, M. Eisen, D. Ross, D. Botstein, and P. Brown. Clustering methods for the analysis of dna microarray data, Technical report, Department of Health Research and Policy, Stanford University, 1999.
VIII.
 Protein Structure
A.
 S. Presnell, B. Cohen, F. Cohen. A segment-based approach to protein secondary structure prediction, Biochemistry 31 (1992) 983--993.
B.
 R. Bonneau and D. Baker. Ab initio protein structure prediction: Progress and Prospects, Annu. Rev Biophys. Biomol. Struct 30 (2001), 73-89.
C.
 P. Koehl. Protein Structure Similarities, Curr. Opin. Struct. Biol. 11 (2001), 348-353.
D.
 P. Koehl and M. Levitt. A brighter future for protein structure prediction, Nature Struct. Biol. 6 (1999), 108-111.
E.
 Thomas E. Creighton. Protein Structure and Protein Function: A Practical Approach (The Practical Approach Series , No 174&175), Irl Pr; 2nd edition (August 1997).
IX.
 Protein Dynamics
A.
 D. Frenkel and B. Smit. Understanding Molecular Simulation, Acdemic Press, San Diego, 1996.
B.
 A. Fersht.Structure and Mechanism in Protein Science, W H Freeman & Co.; (January 1999).
C.
 J. E. Shea and C. L. Brooks.From Folding theories to folding proteins: A Review and Assessment of Simulation Studies of Protein Folding and Unfolding, Annu Rev Biophys Biomol Struct, 30 (2001), 173-89.
D.
 R. Bonneau and D. Baker.Mechanisms of protein folding, Annu Rev Biophys Biomol Struct, 30 (2001), 173-89.
E.
 Proteins: Structure, Function, and Genetics 53:6 (2003), [Special issue on CASP5].
F.
 S. Wodak and J. Janin.Structural basis of macromolecular recognition, in Advances in Protein Chemistry vol. 61 (J. Janin and S. Wodak, eds.), 9-73, Academic Press, 2003.
G.
 I. Halperin, B. Mao, H. Wolfson, and R. Nussinov.Principles of docking: An overview of search algorithms and a guide to scoring functions, Proteins 47 (2002), 409-443.
H.
 Proteins: Structure, Function, and Genetics 52:1 (2003), [Special issue on CAPRI].
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