Systems Biology

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[edit] Contents

• Introduction
• Terminology
• Part One: Biological Systems and Process
  1. Biological Systems and Control
  2. Biological Process-Replication, Transcription and Translation
  3. Dynamic Nature of Biological System
  4. Structural features determine interactions between biological molecules
  5. Intermolecular interactions confer function on biological molecules
  6. The central dogma of molecular biology: DNA -> RNA -> Protein
  7. Structures of nucleic acids provide a continuum of expression
  8. Structures of proteins provide a continuum of function
  9. Prediction using single sequences

• Part Two: Treatment of sequences and structures
  1. Biostatistics overview
  2. Evolution of sequences
  3. Sequence trees
  4. Sequence alignments
  5. Structure alignments
  6. Gene transfer
  7. Prediction using alignments

• Part Three: Biological sequences and biological diversity
  1. Chemical diversity, arising from sequence diversity, allows biological diversity
  2. How biological complexity is expressed in genomic differences
  3. Biological sequence data indicate a common ancestor for all living things
  4. Unique features of biological sequences derived from extremophiles
  5. The genetic origins of oxygen adapted life, mitochondria and chloroplasts
  6. The genetic origins of multi-cellularity
  7. A living species is defined as much by genetic diversity as by the genome of any particular individual
  8. How genetic variability within a species allows for speciation

• Part Four: Other types of biological data
  1. Medical informatics
  2. Environmental or population data
  3. Morphological data
  4. Relational databases and biological data

Part Four needs to be fleshed out, probably split into pieces.

Alternative, fancier titles for chapters in part 2:

       An Alignment Serves to Equate Positions Between Two or More Sequences
       An Alignment of Sequences Represents Similar Chemistry Translated Through Time and Circumstance
       Bayesian Inference from Maximum Likelihood is at the Root of Most Bioinformatics Applications
       How Biological Sequences Evolve Over Time
       How Different Circumstances Effect Sequence Evolution
       Protein Domains – Different Units with Conserved Chemistry Recombine to Form Novel Proteins
       Quantitative Measures of Properties of Sequence Alignments
       Etz'Choyim (The Tree of Life)
       The Role of Viruses - Interspecies Gene Exchange