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Bibliography

Atkins, 1984
Atkins, P. W. (1984).
The Second Law.
W. H. Freeman and Co., N. Y.

Berg & von Hippel, 1987
Berg, O. G. & von Hippel, P. H. (1987).
Selection of DNA binding sites by regulatory proteins, statistical-mechanical theory and application to operators and promoters.
J. Mol. Biol. 193, 723-750.

Berg & von Hippel, 1988
Berg, O. G. & von Hippel, P. H. (1988).
Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites.
J. Mol. Biol. 200, 709-723.

Bradley, 1993
Bradley, D. (1993).
Will future computers be all wet?
Science, 259, 890-893.

Brillouin, 1951
Brillouin, L. (1951).
Maxwell's daemon cannot operate: information and entropy. I.
J. of Applied Physics, 22, 334-337.

Day, 1992
Day, I. N. M. (1992).
Analysis of the 5'-AAUAAA motif and its flanking sequence in human RNA: relevance to cDNA library sorting.
Gene, 110, 245-249.

Delvin et al., 1990
Delvin, J. J., Panganiban, L. C. & Delvin, P. E. (1990).
Random peptide libraries: a source of specific protein binding molecules.
Science, 249, 404-406.

Drexler, 1981
Drexler, K. E. (1981).
Molecular engineering: an approach to the development of general capabilities for molecular manipulation.
Proc. Natl Acad. Sci. USA, 78, 5275-5278.

Drexler, 1986
Drexler, K. E. (1986).
Engines of Creation.
Anchor Press, Garden City, New York.

Eiglmeier et al., 1989
Eiglmeier, K., Honoré, N., Iuchi, S., Lin, E. C. C. & Cole, S. T. (1989).
Molecular genetic analysis of FNR-dependent promoters.
Mol. Microb. 3, 869-878.

Fermi, 1936
Fermi, E. (1936).
Thermodynamics.
Dover Publications, Inc., New York.

Feynman, 1961
Feynman, R. P. (1961).
There's plenty of room at the bottom.
In Miniaturization, (Gilbert, H. D., ed.), pp. 282-296, Reinhold Publishing Corporation, New York.

Feynman, 1987
Feynman, R. P. (1987).
Tiny computers obeying quantum mechanical laws.
In New Directions in Physics: The Los Alamos 40th Anniversary Volume, (Metropolis, N., Kerr, D. M. & Rota, G., eds), pp. 7-25, Academic Press, Inc., Boston.

Fields, 1990
Fields, C. (1990).
Information content of Caenorhabditis elegans splice site sequences varies with intron length.
Nucleic Acids Res. 18, 1509-1512.

Gersting, 1986
Gersting, J. L. (1986).
Mathematical structures for computer science.
second edition, W. H. Freeman and Co., New York.

Gilbert & Greenberg, 1984
Gilbert, S. F. & Greenberg, J. P. (1984).
Intellectual traditions in the life sciences. II. Stereocomplementarity.
Perspect. Biol. Med. 28, 18-34.

Gold et al., 1981
Gold, L., Pribnow, D., Schneider, T., Shinedling, S., Singer, B. S. & Stormo, G. (1981).
Translational initiation in prokaryotes.
Annu. Rev. Microbiol. 35, 365-403.

Gonick, 1991a
Gonick, L. (1991a).
The Cartoon Guide to Computers.
second edition, HarperCollins, New York, NY.

Gonick, 1991b
Gonick, L. (1991b).
The Cartoon Guide to Genetics.
updated edition, Barnes & Nobel, New York, NY.

Herman & Schneider, 1992
Herman, N. D. & Schneider, T. D. (1992).
High information conservation implies that at least three proteins bind independently to F plasmid incD repeats.
J. Bacteriol. 174, 3558-3560.

Jaynes, 1988
Jaynes, E. T. (1988).
The evolution of Carnot's principle.
In Maximum-Entropy and Bayesian Methods in Science and Engineering, (Erickson, G. J. & Smith, C. R., eds), vol. 1, pp. 267-281, Kluwer Academic Publishers, Dordrecht, The Netherlands.
http://bayes.wustl.edu/etj/articles/ccarnot.ps.gz http://bayes.wustl.edu/etj/articles/ccarnot.pdf.

Keyes, 1988
Keyes, R. W. (1988).
Miniaturization of electronics and its limits.
IBM J. Res. Dev. 32 (1), 24-28.

Kohara et al., 1987
Kohara, Y., Akiyama, K. & Isono, K. (1987).
The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library.
Cell, 50, 495-508.

Landauer, 1991
Landauer, R. (1991).
Information is physical.
Physics Today, 44 (5), 23-29.

Leff & Rex, 1990
Leff, H. S. & Rex, A. F. (1990).
Maxwell's Demon: Entropy, Information, Computing.
Princeton University Press, Princeton, N. J.

Lewis & Priore, 1988
Lewis, A. & Priore, L. V. D. (1988).
The biophysics of visual photoreception.
Physics Today, 41, 38-46.

Macaulay, 1988
Macaulay, D. (1988).
The Way Things Work.
Houghton Mifflin Company, Boston.

Mars & Beaud, 1987
Mars, M. & Beaud, G. (1987).
Characterization of vaccinia virus early promoters and evaluation of their informational content.
J. Mol. Biol. 198, 619-631.

Maxwell, 1904
Maxwell, J. C. (1904).
Theory of Heat.
Longmans, Green and Co., London.

McClare, 1971
McClare, C. W. F. (1971).
Chemical machines, Maxwell's demon and living organisms.
J. Theor. Biol. 30, 1-34.

Mead & Conway, 1980
Mead, C. & Conway, L. (1980).
Introduction to VLSI Systems.
Addison-Wesley Publishing Company, Reading, Mass.

Nyquist, 1928
Nyquist, H. (1928).
Thermal agitation of electric charge in conductors.
Physical Review, 32, 110-113.

Papp et al., 1993
Papp, P. P., Chattoraj, D. K. & Schneider, T. D. (1993).
Information analysis of sequences that bind the replication initiator RepA.
J. Mol. Biol. 233, 219-230.

Penotti, 1990
Penotti, F. E. (1990).
Human DNA TATA boxes and transcription initiation sites: a statistical study.
J. Mol. Biol. 213, 37-52.

Penotti, 1991
Penotti, F. E. (1991).
Human pre-mRNA splicing signals.
J. Theor. Biol. 150, 385-420.

Pierce, 1980
Pierce, J. R. (1980).
An Introduction to Information Theory: Symbols, Signals and Noise.
second edition, Dover Publications, Inc., New York.

Pingoud, 1985
Pingoud, A. (1985).
Spermidine increases the accuracy of type II restriction endonucleases. Suppression of cleavage at degenerate, non-symmetrical sites.
Eur. J. Biochem, 147, 105-109.

Polisky et al., 1975
Polisky, B., Greene, P., Garfin, D. E., McCarthy, B. J., Goodman, H. M. & Boyer, H. W. (1975).
Specificity of substrate recognition by the EcoRI restriction endonuclease.
Proc. Natl Acad. Sci. USA, 72, 3310-3314.

Rosenberg et al., 1987
Rosenberg, J. M., McClarin, J. A., Frederick, C. A., Wang, B. C., Boyer, H. W., Grable, J. & Greene, P. (1987).
The structure and function of EcoRI endonuclease.
In Biological Organization: Macromolecular Interactions at High Resolution, (Burnett, R. M. & Vogel, H. J., eds), pp. 11-43, Academic Press, Inc., Orlando.

Rudd & Schneider, 1992
Rudd, K. E. & Schneider, T. D. (1992).
Compilation of E. coli ribosome binding sites.
In A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria, (Miller, J. H., ed.), pp. 17.19-17.45, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Schilling et al., 1989
Schilling, D. L., Belove, C., Apelewicz, T. & Saccardi, R. J. (1989).
Electronic circuits, discrete and integrated.
third edition, McGraw-Hill, New York.

Schneider, 1988
Schneider, T. D. (1988).
Information and entropy of patterns in genetic switches.
In Maximum-Entropy and Bayesian Methods in Science and Engineering, (Erickson, G. J. & Smith, C. R., eds), vol. 2, pp. 147-154, Kluwer Academic Publishers, Dordrecht, The Netherlands.

Schneider, 1991a
Schneider, T. D. (1991a).
Theory of molecular machines. I. Channel capacity of molecular machines.
J. Theor. Biol. 148, 83-123.
http://www.lecb.ncifcrf.gov//paper/ccmm/.

Schneider, 1991b
Schneider, T. D. (1991b).
Theory of molecular machines. II. Energy dissipation from molecular machines.
J. Theor. Biol. 148, 125-137.
http://www.lecb.ncifcrf.gov//paper/edmm/.

Schneider & Stephens, 1990
Schneider, T. D. & Stephens, R. M. (1990).
Sequence logos: a new way to display consensus sequences.
Nucleic Acids Res. 18, 6097-6100.
http://www.lecb.ncifcrf.gov//paper/logopaper/.

Schneider & Stormo, 1989
Schneider, T. D. & Stormo, G. D. (1989).
Excess information at bacteriophage T7 genomic promoters detected by a random cloning technique.
Nucleic Acids Res. 17, 659-674.

Schneider et al., 1986
Schneider, T. D., Stormo, G. D., Gold, L. & Ehrenfeucht, A. (1986).
Information content of binding sites on nucleotide sequences.
J. Mol. Biol. 188, 415-431.

Scott & Smith, 1990
Scott, K. K. & Smith, G. P. (1990).
Searching for peptide ligands with an epitope library.
Science, 249, 386-390.

Shaner et al., 1993
Shaner, M. C., Blair, I. M. & Schneider, T. D. (1993).
Sequence logos: a powerful, yet simple, tool.
In Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences, Volume 1: Architecture and Biotechnology Computing, (Mudge, T. N., Milutinovic, V. & Hunter, L., eds), pp. 813-821, IEEE Computer Society Press, Los Alamitos, CA.
http://www.lecb.ncifcrf.gov//paper/hawaii/.

Shannon, 1948
Shannon, C. E. (1948).
A mathematical theory of communication.
Bell System Tech. J. 27, 379-423, 623-656.
http://cm.bell-labs.com/cm/ms/what/shannonday/paper.html.

Shannon, 1949
Shannon, C. E. (1949).
Communication in the presence of noise.
Proc. IRE, 37, 10-21.

Shannon & Weaver, 1949
Shannon, C. E. & Weaver, W. (1949).
The Mathematical Theory of Communication.
University of Illinois Press, Urbana.

Shenkin et al., 1991
Shenkin, P. S., Erman, B. & Mastrandrea, L. D. (1991).
Information-theoretical entropy as a measure of sequence variability.
Proteins: Structure, Function, and Genetics, 11, 297-313.

Shine & Dalgarno, 1974
Shine, J. & Dalgarno, L. (1974).
The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.
Proc. Natl Acad. Sci. USA, 71, 1342-1346.

Sloane, 1984
Sloane, N. J. A. (1984).
The packing of spheres.
Sci. Am. 250 (1), 116-125.

Sloane & Wyner, 1993
Sloane, N. J. A. & Wyner, A. D. (1993).
Claude Elwood Shannon: Collected Papers.
IEEE Press, Piscataway, NJ.

Smith, 1985
Smith, G. P. (1985).
Filamentous fusion phage: novel expression vectors that display cloned antigens on the viron surface.
Science, 228, 1315-1317.

Southern, 1975
Southern, E. M. (1975).
Detection of specific sequences among DNA fragments separated by gel electrophoresis.
J. Mol. Biol. 98, 503-517.

Stephens & Schneider, 1992
Stephens, R. M. & Schneider, T. D. (1992).
Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites.
J. Mol. Biol. 228, 1124-1136.
http://www.lecb.ncifcrf.gov//paper/splice/.

Stormo, 1990
Stormo, G. D. (1990).
Consensus patterns in DNA.
Meth. Enzym. 183, 211-221.

Stormo et al., 1982a
Stormo, G. D., Schneider, T. D., Gold, L. & Ehrenfeucht, A. (1982a).
Use of the `Perceptron' algorithm to distinguish translational initiation sites in E. coli.
Nucleic Acids Res. 10, 2997-3011.

Stormo et al., 1982b
Stormo, G. D., Schneider, T. D. & Gold, L. M. (1982b).
Characterization of translational initiation sites in E. coli.
Nucleic Acids Res. 10, 2971-2996.

Thomas, 1968
Thomas, G. B. (1968).
Calculus and Analytic Geometry.
fourth edition, Addison-Wesley, Reading, Mass.

Tolman, 1938
Tolman, R. C. (1938).
The Principles of Statistical Mechanics.
Dover Publications, Inc., New York.

Tuerk & Gold, 1990
Tuerk, C. & Gold, L. (1990).
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.
Science, 249, 505-510.

Wait, 1967
Wait, J. V. (1967).
Symbolic logic and practical applications.
In Digital Computer User's Handbook, (Klerer, M. & Korn, G. A., eds), pp. 4-3 to 4-28 show that NAND is sufficient, McGraw-Hill Book Company, Inc., N. Y.

Waldram, 1985
Waldram, J. R. (1985).
The Theory of Thermodynamics.
Cambridge University Press, Cambridge.

Watson et al., 1987
Watson, J. D., Hopkins, N. H., Roberts, J. W., Steitz, J. A. & Weiner, A. M. (1987).
Molecular Biology of the Gene.
fourth edition, The Benjamin/Cummings Publishing Co., Inc., Menlo Park, California.

Weast et al., 1988
Weast, R. C., Astle, M. J. & Beyer, W. H. (1988).
CRC Handbook of Chemistry and Physics.
CRC Press, Inc., Boca Raton, Florida.

Woodhead et al., 1981
Woodhead, J. L., Bhave, N. & Malcolm, A. D. B. (1981).
Cation dependence of restriction endonuclease EcoRI activity.
Eur. J. Biochem, 115, 293-296.



Tom Schneider
2000-10-21