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  1. Read/skim Haussler papers
    1. Ultraconserved Elements in the Human Genome
    2. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
  2. Read/skim Kelly thesis proposal
    1. Entire proposal here, relevant sections are 3.5 and 4.3.
    2. Also, in wiki format and slightly updated here.
  3. Read/skim Alon paper
    1. Optimality and evolutionary tuning of the expression level of a protein