Different views of bioinformatics

1
Different views of bioinformatics

• CS view what are the algorithms, data structures
  and other concepts needed to develop tools to
  solve biological problems
• Biologist view how to use tools to solve typical
  problems of interest in biology
• More theoretical view what new algorithms are
  suggested by biological applications

2
Too much for one quarter

• Genomics DNA, RNA
• Protein structure, function and interactions
• Drug design
• Algorithms for sequence alignment
• Tree representations of relationships
• Gene microarrays
• Proteomics/Mass spec
• Protein structure prediction

3
Our runner-up course book

• "Protein Bioinformatics An Algorithmic Approach
  to Sequence and Structure Analysis"Ingvar
  Eidhammer Hardcover 69.86
• Takes the CS point of view
• Limited to issues regarding proteins
• Too many errors for my comfort zone

4
Background reference

• "Protein Stucture and Function (Primers in
  Biology) Gregory A. Petsko and Dagmar Ringe
  Paperback 47.66
• Excellent material on basic biology (great
  pictures!) but not bioinformatics.
• Describes how proteins function
• Good reference for biochemistry of proteins and
  their function

5
Biologist-focused book

• "Bioinformatics and Functional Genomics"
• Jonathan Pevsner Paperback 72.16
• First class had 80 grad students and several
  hundred auditors at Johns Hopkins
• Presents how to use bioinfo tools from the
  perspective of a biomedical researcher
• Not so much on how the algorithms work but a good
  way to see how they are used

6
Comprehensive reference

• "Bioinformatics A Practical Guide to the
  Analysis of Genes and Proteins, Third
  Edition"Andreas D. Baxevanis and B. F. Francis
  Ouellette, eds Hardcover 60.00
• This is an edited collection of essays by experts
  on the use of different bioinfo tools in
  different areas.
• Intended as a reference (not a textbook)

7
Just the algorithms

• "An Introduction to Bioinformatics Algorithms
  (Computational Molecular Biology) Neil C. Jones
  Hardcover 42.67
• More of a focus on algorithms, with less coverage
  of applications
• The next step in the CS direction in
  bioinformatics (e.g., PhD level course)