Books and references for bioinformatics:

• N.C., Jones & P.A. Pevzner, "An introduction to Bioinformatics Algorithms", MIT Press.
  Algorithmic intro; strong on algorithms
• D. Mount, "Bioinformatics; Sequence and Genome Analysis", 2nd edition, Cold Spring Harbor Lab Press.
  Comprehensive reference book
• I. Eidhammer et al, "Protein Bioinformatics", J. Wiley.
  Comprehensive, concise reference book
• R. Durbin et al, "Biological Sequence Analysis", Cambridge University Press.
  Strong on probabilistic sequence analysis
• A.M., Campbell, L.J. Heyer, "Discovering Genomics, Proteomics and Bioinformatics", Benjamin Cummings.
  A gem; lots of application examples & hands-on discovery
• U. Alon, "An Introduction To Systems Biology; Design Principles of Biological Circuits", Chapman & Hall, 2007.
  Superb analysis of regulatory networks.
• B. O., Palsson, "Systems Biology; Properties of Reconstructed Networks", Cambridge University Press, 2006.
  Excellent analysis of metabolic networks.

Lecture notes

• Courses by Seraphim Batzoglou: (A) Computational Genomics and (B) (with Jean Claude Latombe) Algorithms for Structure & Motion in Biology
• Course notes by Piotr Indyk and Manolis Kellis: Computational Biology: Genomes, Networks, Evolution..
• Course notes by Ron Shamir; Algorithms in Molecular Biology.
• Course notes by Chris Burge, Amy Keating, Michael Yaffe and Peter Woolf: Foundations of Computational and Systems Biology.

Books and references for Biology:

• B. Alberts et al, "Molecular Biology of The Cell", 4th edition, Garland Science.
• R. Horton et al, "Principles of Biochemistry", 3rd Edition, Prentice Hall.
• J.D. Watson et al, "Molecular Biology of The Gene", 5th edition, Pearson Benjamin Cummings.
• M. Ptashne, A. Gann, "Genes & Signals", Cold Spring Harbor Lab Press, 2002.
  Superb description of regulatory mechanisms with in depth experimental insights.
• NCBI Introductory overview: http://www.ncbi.nih.gov/About/primer/index.html
• Animation sites:
  • http://www.johnkyrk.com
  • http://vcell.ndsu.nodak.edu/~christjo/vcell/animationSite