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Bibliography

1
T. D. Schneider.
Some lessons for molecular biology from information theory.
In J. Kacprzyk, editor, Entropy Measures, Maximum Entropy Principle and Emerging Applications. Special Series on Studies in Fuzziness and Soft Computing. (Festschrift Volume in honour of Professor J.N. Kapour, Jawaharlal Nehru University, India), volume 119, pages 229-237, New York, 2003. Springer-Verlag.
Errata to the book: the two figures given in the paper are missing from the book!

2
T. D. Schneider, 2000.
http://www.lecb.ncifcrf.gov//.

3
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.
http://www.lecb.ncifcrf.gov//paper/nano2/.

4
T. D. Schneider.
Information Theory Primer.
http://www.lecb.ncifcrf.gov//paper/primer/, 1995.

5
C. E. Shannon.
A mathematical theory of communication.
Bell System Tech. J., 27:379-423, 623-656, 1948.
http://cm.bell-labs.com/cm/ms/what/shannonday/paper.html.

6
J. R. Pierce.
An Introduction to Information Theory: Symbols, Signals and Noise.
Dover Publications, Inc., New York, second edition, 1980.

7
C. E. Shannon.
Communication in the presence of noise.
Proc. IRE, 37:10-21, 1949.

8
W. Gappmair.
Claude E. Shannon: The 50th anniversary of information theory.
IEEE Communications Magazine, 37(4):102-105, April 1999.

9
S. Verdú and Steven W. McLaughlin.
Information Theory: 50 Years of Discovery.
IEEE Press, New York, 1998.

10
H. Nyquist.
Thermal agitation of electric charge in conductors.
Physical Review, 32:110-113, 1928.

11
J. B. Johnson.
Thermal agitation of electricity in conductors.
Physical Review, 32:97-109, 1928.

12
T. D. Schneider.
Theory of molecular machines. I. Channel capacity of molecular machines.
J. Theor. Biol., 148:83-123, 1991.
http://www.lecb.ncifcrf.gov//paper/ccmm/.

13
L. Brillouin.
Science and Information Theory.
Academic Press, Inc., New York, second edition, 1962.

14
H. B. Callen.
Thermodynamics and an Introduction to Thermostatistics.
John Wiley & Sons, Ltd., N. Y., second edition, 1985.

15
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.
http://www.lecb.ncifcrf.gov//paper/schneider1986/.

16
R. M. Stephens and T. D. Schneider.
Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites.
J. Mol. Biol., 228:1124-1136, 1992.
http://www.lecb.ncifcrf.gov//paper/splice/.

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

18
Y. Hayakawa, T. Murotsu, and K. Matsubara.
Mini-F protein that binds to a unique region for partition of mini-F plasmid DNA.
J. Bacteriol., 163:349-354, 1985.

19
N. D. Herman and T. D. Schneider.
High information conservation implies that at least three proteins bind independently to F plasmid incD repeats.
J. Bacteriol., 174:3558-3560, 1992.

20
P. P. Papp, D. K. Chattoraj, and T. D. Schneider.
Information analysis of sequences that bind the replication initiator RepA.
J. Mol. Biol., 233:219-230, 1993.

21
N. C. Seeman, J. M. Rosenberg, and A. Rich.
Sequence-specific recognition of double helical nucleic acids by proteins.
Proc. Natl. Acad. Sci. USA, 73:804-808, 1976.

22
T. D. Schneider.
Reading of DNA sequence logos: Prediction of major groove binding by information theory.
Meth. Enzym., 274:445-455, 1996.
http://www.lecb.ncifcrf.gov//paper/oxyr/.

23
T. D. Schneider.
Evolution of biological information.
Nucleic Acids Res., 28(14):2794-2799, 2000.
http://www.lecb.ncifcrf.gov//paper/ev/.

24
T. D. Schneider.
Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences.
Nucleic Acids Res., 25:4408-4415, 1997.
http://www.lecb.ncifcrf.gov//paper/walker/, erratum: NAR 26(4): 1135, 1998.

25
P. N. Hengen, S. L. Bartram, L. E. Stewart, and T. D. Schneider.
Information analysis of Fis binding sites.
Nucleic Acids Res., 25(24):4994-5002, 1997.
http://www.lecb.ncifcrf.gov//paper/fisinfo/.

26
P. K. Rogan and T. D. Schneider.
Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites.
Human Mutation, 6:74-76, 1995.
http://www.lecb.ncifcrf.gov//paper/colonsplice/.

27
P. K. Rogan, B. M. Faux, and T. D. Schneider.
Information analysis of human splice site mutations.
Human Mutation, 12:153-171, 1998.
http://www.lecb.ncifcrf.gov//paper/rfs/.

28
C. Kannabiran, P. K. Rogan, L. Olmos, S. Basti, G. N. Rao, M. Kaiser-Kupfer, and J. F. Hejtmancik.
Autosomal dominant zonular cataract with sutural opacities is associated with a splice mutation in the betaA3/A1-crystallin gene.
Mol Vis, 4:21, 1998.

29
R. Allikmets, W. W. Wasserman, A. Hutchinson, P. Smallwood, J. Nathans, P. K. Rogan, T. D. Schneider, and M. Dean.
Organization of the ABCR gene: analysis of promoter and splice junction sequences.
Gene, 215:111-122, 1998.
http://www.lecb.ncifcrf.gov//paper/abcr/.

30
S. G. Khan, H. L. Levy, R. Legerski, E. Quackenbush, J. T. Reardon, S. Emmert, A. Sancar, L. Li, T. D. Schneider, J. E. Cleaver, and K. H. Kraemer.
Xeroderma Pigmentosum Group C splice mutation associated with mutism and hypoglycinemia - A new syndrome?
J. Investigative Dermatology, 111:791-796, 1998.

31
C. Speck, C. Weigel, and W. Messer.
From footprint to toeprint: a close-up of the DnaA box, the binding site for the bacterial initiator protein DnaA.
Nucleic Acids Res., 25:3242-3247, 1997.

32
V. S. Ramachandran and Sandra Blakeslee.
Phantoms in the Brain: Probing the Mysteries of the Human Mind.
William Morrow & Co, New York, 1998.

33
T. D. Schneider and R. M. Stephens.
Sequence logos: A new way to display consensus sequences.
Nucleic Acids Res., 18:6097-6100, 1990.
http://www.lecb.ncifcrf.gov//paper/logopaper/.

34
T. D. Schneider.
Information content of individual genetic sequences.
J. Theor. Biol., 189(4):427-441, 1997.
http://www.lecb.ncifcrf.gov//paper/ri/.



Tom Schneider
2003-04-04

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