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Recommended Reading

Seminar Readings:
   General Resources 
   Topic 1 | Topic 2 | Topic 3 
   Topic 4 | Topic 5 | Topic 6

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John Lavas
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Biological Sciences

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Recommended Reading 

Course readings may only be used for the University's educational purposes. You may print a copy for your own use, but you may not make a further copy for any other purpose. You may not copy or distribute any part of the reading to any other person. Failure to comply with these terms may expose you to legal action for copyright infringement and/or disciplinary action by the University.

General Resources  

• Baxevanis, A. D., & Ouellette, B. F. F. (2001). Bioinformatics : a practical guide to the analysis of genes and proteins (2nd ed.). New York: Wiley-Interscience. [print version]  

• Gibas, C., &  Jambeck, P. (2001). Developing Bioinformatics Computer Skills. Sebastopol, CA: O'Reilly. 

• Mount, D. W. (2001). Bioinformatics : sequence and genome analysis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. [alternate electronic version] [print version] [on-line publishers resources for the book]

 Topic 1. Introduction to Bioinformatics

• Koppel, M., Argamon, S. & Shimoni, A. R. (2002). Automatically Categorizing Written Texts by Author Gender. Literary and Linguistic Computing, 17(4), 401-412.
• Mount, D. W. (2001). Bioinformatics : sequence and genome analysis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. [alternate electronic version] Chapter 1. 

  Topic 2. Bioinformatics Information Resources

• NCBI Handbook - Index to individual chapters 
• Baxevanis, A. D., & Ouellette, B. F. F. (2001). Bioinformatics : a practical guide to the analysis of genes and proteins (2nd ed.). New York: Wiley-Interscience.[Platform: Wiley-Interscience] [print version], Chapters 2, 3, 7, 12.

 Topic 3. Inferring Homology from Sequence Comparison

• Baxevanis, A. D., & Ouellette, B. F. F. (2001). Bioinformatics : a practical guide to the analysis of genes and proteins (2nd ed.). New York: Wiley-Interscience.[Platform: Wiley-Interscience] [print version], Chapter 8.
• Feng, D.F. and Doolittle, R. F., (1987). Progressive Sequence Alignment as a Prerequisite. Journal of Molecular Evolution, 25(4), 351-360.
• Henikoff, S., & Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences of the United States of America, 89(22), 10915-10919. (Click "Download" on the screen to access a pdf of the article - recommended).
• Mount, D. W. (2001). Bioinformatics : sequence and genome analysis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. [Platform: ebrary] [alternate Ebsco version] [print version] [on-line resources for the book] chapters 3, 4, 7.
• Notredame, C., & Higgins, D.G. (1996). SAGA: sequence alignment by genetic algorithm. Nucleic Acids Research, 24(8),1515-1524.
• Thompson, J. D., Higgins, D. G., and Gibson, T. J., (1994). Improved Sensitivity of profile searches through the use of sequence weights and gap excision. Cabios, 10(1), 19-29. 

Topic 4. Phylogenetic Reconstruction 

READING RESOURCES

• Baldauf, S. L. (2003). Phylogeny for the faint hearted: a tutorial. Trends in Genetics, 19, 345-351.
• Baxevanis, A. D., & Ouellette, B. F. F. (2001). Bioinformatics : a practical guide to the analysis of genes and proteins (2nd ed.). New York: Wiley-Interscience. Chapter 14. 
• Mount, D. W. (2001). Bioinformatics : sequence and genome analysis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.  Chapter 6. 

READING FOR DISCUSSION

• Nickle, D. C., M. A. Jensen, D. Shriner, S. J. Brodie, L. M. Frenkel, J. E. Mittler, and J. I. Mullins. (2003). Evolutionary indicators of Human Immunodeficiency Virus type 1 reservoirs and compartments. Journal of Virology, 77, 5540-5546.
• Selje, N., M. Simon, and T. Brinkhoff. (2004). A newly discovered Roseobacter cluster in temperate and polar oceans. Nature, 427, 445-448.
• Yeh, S. H., Wang, H. Y., Tsai, C. Y., Kao, J. Y., Yang, H. W., Liu, I. J., Su, S. F., Tsai, D. S., Chen, P. J., and The National Taiwan University SARS Research Team. (2004). Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan: Molecular epidemiology and genome evolution, Proceedings of the National Academy of Sciences of the United States of America. 101(8), 2542-2547.

 Topic 5. Protein Sequence, Structure & Function

• Mount, D. W. (2001). Bioinformatics : sequence and genome analysis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. Chapter 9.

• Attwood, T. K. (2000). The Babel of Bioinformatics. Science, 290, 471-473.

• Berg, J. M., Tymoczko, J. L., & Stryer, L. (2002). Biochemistry (5th ed.). New York : W. H. Freeman.
  

ADDITIONAL RESOURCES

PSI-BLAST

Altschul, T.L. et al (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389.

Pfam

Bateman, A. et al (2002). The Pfam Protein Families Database. Nucleic Acids Research, 30(1), 276-280.

InterPro

Mulder, N. J. et al (2003). The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Research, 31(1), 315-318. 

Prosite

Sigrist et al (2002). PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioform, 3, 265-274.

Prints

Attwood, T. K. et al (2003). PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Research, 31(1), 400-402.

Topic 6. Genomes

• Gene neighbourhood:
  
  Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D. & Maltsev, N. (1999). The use of gene clusters to infer functional coupling. Proceedings of the National Academy of Sciences of the United States of America, 96, 2896-2901.
   
• Phylogenetic profiling:
  
  Pellegrini et al., (1999). Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proceedings of the National Academy of Sciences of the United States of America, 96, 4285-4288.
  
  
• Rosetta Stone Method:
  
  Marcotte, E. M., Pellegrini, M., Ng, H.-L., Rice, D. W., Yeates, T. O. & Eisenberg, D. (1999). Detecting Protein Function and Protein-Protein Interactions from Genome Sequences. Science, 285, 751-753.
  
  Enright et al., Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86-89 (1999)
  
  
• Review of the field:
  
  Special Supplement, Nature Structural Biology 7:927-994 (2000)
  
  

• Unifolds and mesofolds:

  Coulson, A. F. W. and Moult, J. A unifold, mesofold, and superfold model of protein fold use. PROTEINS: Structure, Function, and Bioinformatics 46:61-71 (2002)

• How many structures do we need?

  Vitkup et al., Completeness in structural genomics. Nature Structural Biology 8:559-566 (2001)

• Function from structure:

  Shapiro, L. & Harris, T. Finding function through structural genomics. Current Opinion in Biotechnology 11:31-35 (2000)
  
  Jones, S. & Thornton, J. M. Searching for functional sites in protein structures. Current Opinion in Chemical Biology 8:3-7 (2004)