Bibliography for my talk “Why Do Restriction Enzymes Prefer 4 and 6 Base DNA Sequences?”
Background papers: [1] [2] [3] [4] [5] [6] [7] [8] [9] [10]
[1] T. D. Schneider. Information theory primer. Published on the web at https://alum.mit.edu/www/toms/papers/primer/, 2010.
[2] T. D. Schneider, G. D. Stormo, L. Gold, and A. Ehrenfeucht. Information content of binding sites on nucleotide sequences. J. Mol. Biol., 188:415–431, 1986. https://alum.mit.edu/www/toms/papers/schneider1986/.
[3] T. D. Schneider and R. M. Stephens. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res., 18:6097–6100, 1990. https://alum.mit.edu/www/toms/papers/logopaper/.
[4] T. D. Schneider. Evolution of biological information. Nucleic Acids Res., 28:2794–2799, 2000. https://alum.mit.edu/www/toms/papers/ev/.
[5] I. Lyakhov, K. Annangarachari, and T. D. Schneider. Discovery of Novel Tumor Suppressor p53 Response Elements Using Information Theory. Nucleic Acids Res., 36:3828–3833, 2008. https://alum.mit.edu/www/toms/papers/p53/.
[6] T. D. Schneider. Theory of molecular machines. I. Channel capacity of molecular machines. J. Theor. Biol., 148:83–123, 1991. https://alum.mit.edu/www/toms/papers/ccmm/.
[7] T. D. Schneider. Theory of molecular machines. II. Energy dissipation from molecular machines. J. Theor. Biol., 148:125–137, 1991. https://alum.mit.edu/www/toms/papers/edmm/.
[8] T. D. Schneider. Sequence logos, machine/channel capacity, Maxwell’s demon, and molecular computers: a review of the theory of molecular machines. Nanotechnology, 5:1–18, 1994. https://alum.mit.edu/www/toms/papers/nano2/.
[9] T. D. Schneider. 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence. Nucleic Acids Res., 38:5995–6006, 2010. doi:10.1093/nar/gkq389, https://alum.mit.edu/www/toms/papers/emmgeo/.
[10] T. D. Schneider. A brief review of molecular information theory. Nano Communication Networks, 1:173–180, 2010. http://dx.doi.org/10.1016/j.nancom.2010.09.002, https://alum.mit.edu/www/toms/papers/brmit/.