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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.
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-
Pierce, J. R. (1980)
An Introduction to Information Theory: Symbols, Signals and Noise,
Dover Publications, Inc., New York second edition.
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Gappmair, W. (April, 1999)
Claude E. Shannon: The 50th anniversary of information theory.
IEEE Communications Magazine, 37(4), 102-105.
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Schneider, T. D., Stormo, G. D., Gold, L., and Ehrenfeucht, A. (1986)
Information content of binding sites on nucleotide sequences.
J. Mol. Biol., 188, 415-431
http://www.lecb.ncifcrf.gov/~toms/paper/schneider1986/.
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Schneider, T. D. and Stephens, R. M. (1990)
Sequence logos: A new way to display consensus sequences.
Nucleic Acids Res., 18, 6097-6100
http://www.lecb.ncifcrf.gov/~toms/paper/logopaper/.
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Stephens, R. M. and 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/~toms/paper/splice/.
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Schneider, T. D. (1997)
Information content of individual genetic sequences.
J. Theor. Biol., 189(4), 427-441
http://www.lecb.ncifcrf.gov/~toms/paper/ri/.
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Schneider, T. D. (1997)
Sequence walkers: a graphical method to display how binding proteins interact
with DNA or RNA sequences.
Nucleic Acids Res., 25, 4408-4415
http://www.lecb.ncifcrf.gov/~toms/paper/walker/, erratum: NAR 26(4):
1135, 1998.
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Schneider, T. D. (1996)
Reading of DNA sequence logos: Prediction of major groove binding by
information theory.
Meth. Enzym., 274, 445-455
http://www.lecb.ncifcrf.gov/~toms/paper/oxyr/.
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Shultzaberger, R. K. and Schneider, T. D. (1999)
Using sequence logos and information analysis of Lrp DNA binding sites to
investigate discrepancies between natural selection and SELEX.
Nucleic Acids Res., 27(3), 882-887
http://www.lecb.ncifcrf.gov/~toms/paper/lrp/.
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Zheng, M., Doan, B., Schneider, T. D., and Storz, G. (1999)
OxyR and SoxRS regulation of fur.
J. Bacteriol., 181, 4639-4643.
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Schneider, T. D. (1988)
Information and entropy of patterns in genetic switches.
In G. J. Erickson and C. R. Smith, (ed.), Maximum-Entropy and Bayesian Methods
in Science and Engineering, volume 2, Dordrecht, The Netherlands:
Kluwer Academic Publishers
pp. 147-154.
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Laughlin, R. B., Pines, D., Schmalian, J., Stojkovic, B. P., and Wolynes, P.
(2000)
The middle way.
Proc. Natl. Acad. Sci. USA, 97, 32-37.
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Schneider, T. D. (1994)
Sequence logos, machine/channel capacity, Maxwell's demon, and molecular
computers: a review of the theory of molecular machines.
Nanotechnology, 5, 1-18
http://www.lecb.ncifcrf.gov/~toms/paper/nano2/.
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Stormo, G. D., Schneider, T. D., Gold, L., and Ehrenfeucht, A. (1982)
Use of the `Perceptron' algorithm to distinguish translational initiation
sites in E. coli.
Nucleic Acids Res., 10, 2997-3011.
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Schneider, T. D. (1991)
Theory of molecular machines. I. Channel capacity of molecular machines.
J. Theor. Biol., 148, 83-123
http://www.lecb.ncifcrf.gov/~toms/paper/ccmm/.
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Loeb, L. A., Essigmann, J. M., Kazazi, F., Zhang, J., Rose, K. D., and Mullins,
J. I. (1999)
Lethal mutagenesis of HIV with mutagenic nucleoside analogs.
Proc. Natl. Acad. Sci. USA, 96, 1492-1497.
- 18
-
Gould, S. J. (1977)
Is the cambrian explosion a sigmoid fraud?.
In Ever Since Darwin, Reflections in Natural History N. Y.: W. W. Norton & Co.
pp. 126-133.
- 19
-
Gould, S. J. and Eldredge, N. (1993)
Punctuated equilibrium comes of age.
Nature, 366, 223-227.
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Dawkins, R. (1986)
The Blind Watchmaker,
W. W. Norton & Co., New York.
- 21
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Lenski, R. E., Ofria, C., Collier, T. C., and Adami, C. (1999)
Genome complexity, robustness and genetic interactions in digital organisms.
Nature, 400, 661-664
http://www.krl.caltech.edu/avida/.
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Ray, T. S. (1994)
Evolution, Complexity, Entropy, and Artificial Reality.
Physica D, 75, 239-263
http://www.hip.atr.co.jp/~ray/pubs/oji/ojihtml.html.
- 23
-
Jaynes, E. T. (1988)
The evolution of Carnot's principle.
In G. J. Erickson and C. R. Smith, (ed.), Maximum-Entropy and Bayesian Methods
in Science and Engineering, volume 1, Dordrecht, The Netherlands:
Kluwer Academic Publishers
http://bayes.wustl.edu/etj/articles/ccarnot.ps.gz
http://bayes.wustl.edu/etj/articles/ccarnot.pdf
pp. 267-281.
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Schneider, T. D. (1991)
Theory of molecular machines. II. Energy dissipation from molecular machines.
J. Theor. Biol., 148, 125-137
http://www.lecb.ncifcrf.gov/~toms/paper/edmm/.
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-
Haldane, J. B. S. (1949)
Suggestions as to quantitative measurement of rates of evolution.
Evolution, 3, 51-56.
- 26
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Hendry, A. P. and Kinnison, M. T. (2000)
Perspective: the pace of modern life: measuring rates of contemporary
microevolution.
Evolution, 53, 1637-1653.
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Huey, R. B., Gilchrist, G. W., Carlson, M. L., Berrigan, D., and Serra, L.
(2000)
Rapid evolution of a geographic cline in size in an introduced fly.
Science, 287, 308-309.
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Schneider, T. D. and Stormo, G. D. (1989)
Excess information at bacteriophage T7 genomic promoters detected by a random
cloning technique.
Nucleic Acids Res., 17, 659-674.
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Herman, N. D. and 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.
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Stormo, G. D. (1998)
Information Content and Free Energy in DNA-Protein Interactions.
J. Theor. Biol., 195, 135-137.
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Schneider, T. D. (1999)
Measuring molecular information.
J. Theor. Biol., 201, 87-92
http://www.lecb.ncifcrf.gov/~toms/paper/ridebate/.
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Spetner, L. M. (1998)
NOT BY CHANCE! Shattering the Modern Theory of Evolution,
Judaica Press, New York.
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Dawkins, R. (December, 1998)
The ``Information Challenge''.
The Skeptic, 18(4), 21-25
http://www.onthenet.com.au/~stear/dawkinschallenge.htm
and
http://www.skeptics.com.au/journal/dawkins1.htm.
- 34
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Behe, M. J. (1996)
Darwin's Black Box: The Biochemical Challenge to Evolution,
The Free Press, New York.
- 35
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Perelson, A. S., Neumann, A. U., Markowitz, M., Leonard, J. M., and Ho, D. D.
(1996)
HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and
viral generation time.
Science, 271, 1582-1586.
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Spetner, L. M. (1964)
Natural selection: an information-transmission mechanism for evolution.
J. Theor. Biol., 7, 412-429.
Tom Schneider
2001-11-07