@article{Adleman1994,
author = "Leonard M. Adleman",
title = "Molecular Computation of Solutions to Combinatorial Problems",
journal = "Science",
pages = "1021--1024",
volume = 266,
number = 5187,
month = nov,
year = 1994,
comment = Adleman1994.pdf
}

%R. E. Brayton, G. D. Hachtel, C. T. McMullen, A. L. Sangiovanni-Vincentelli, Logic Minimization Algorithms for VLSI Synthesis, Kluwer Academic Publishers, 1984.  

@article{Ball2000,
author = "Philip Ball",
title = "Chemistry meets computing",
journal = "Nature",
pages = "118--120",
volume = 406,
month = jul,
year = 2000,
comment = Ball2000July13-Nature.pdf
}

@Book{brayton1984,
  author = 	 {R. Brayton and G. Hachtel and C. McMullen and A. Sangiovanni-Vincentelli},
  ALTeditor = 	 {},
  title = 	 {Logic Minimization Algorithms for VLSI Synthesis},
  publisher = 	 {Kluwer Academic Publishers},
  year = 	 {1984},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@incollection{ brayton93,
    author = "R.~K.~Brayton and P.~C.~McGeer and J.~V.~Sanghavi and A.~L.~Sangiovanni-Vincentelli",
    title = "A new exact minimizer for two-level logic synthesis",
    booktitle = "Logic Synthesis and Optimization",
    publisher = "Kluwer, Norwell/MA, USA",
    editor = "Tsutomu Sasao",
    pages = "1--32",
    year = "1993",
    url = "citeseer.ist.psu.edu/brayton93new.html" }

@article{Breaker1994,
author = "R. R. Breaker and G. F. Joyce",
title = "A {DNA} Enzyme that Cleaves {RNA}",
journal = "Chemistry and Biology",
pages = "223--229",
volume = 1,
year = 1994
}

@article{Breaker1995,
author = "Ronald R Breaker and Gerald F Joyce",
title = {A {DNA} enzyme with {M}g${}^{2_{+}}$-dependent {RNA} phosphoesterase activity},
journal = {Chemistry \& Biology},
pages = "655--660",
volume = 2,
year = 1995,
abstract = {Abstract:
Backgound


Previously we demonstrated that DNA can act as an enzyme in the Pb2+ -dependent cleavage of an RNA phosphoester. This is a facile reaction, with an uncatalyzed rate for a typical RNA phosphoester of ~10-4 min-1 in the presence of 1 mM Pb(OAc)2 at pH 7.0 and 23°C. The Mg2+-dependent reaction is more difficult, with an uncatalyzed rate of ~10-7 min-1 under comparable conditions. Mg2+-dependent cleavage has special relevance to biology because it is compatible with intracellular conditions. Using in vitro selection, we sought to develop a family of phosphoester-cleaving DNA enzymes that operate in the presence of various divalent metals, focusing particularly on the Mg2+-dependent reaction.
Results


We generated a population of > 1013 DNAs containing 40 random nucleotides and carried out repeated rounds of selective amplification, enriching for molecules that cleave a target RNA phosphoester in the presence of 1 mM Mg2+, Mn2+, Zn2+ or Pb2+. Examination of individual clones from the Mg2+ lineage after the sixth round revealed a catalytic motif comprised of a three-stem junction. This motif was partially randomized and subjected to seven additional rounds of selective amplification, yielding catalysts with a rate of 0.01 min-1. The optimized DNA catalyst was divided into separate substrate and enzyme domains and shown to have a similar level of activity under multiple turnover conditions.
Conclusion


We have generated a Mg2+-dependent DNA enzyme that cleaves a target RNA phosphoester with a catalytic rate ~105 -fold greater than that of the uncatalyzed reaction. This activity is compatible with intracellular conditions, raising the possibility that DNA enzymes might be made to operate in vivo.
}
}


@Book{condon1989,
  author = 	 {Anne Condon},
  ALTeditor = 	 {},
  title = 	 {Computational Models of Games},
  publisher = 	 {The MIT Press},
  year = 	 {1989},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  series = 	 {ACM Distinguished Dissertations},
  address = 	 {Cambridge, Massachusetts},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Cuenoud1995,
author = "Bernard Cuenoud and Jack W. Szostak",
title = "A {DNA} metalloenzyme with {DNA} ligase activity",
journal = "Nature",
pages = "611--614",
volume = 375,
month = jun,
year = 1995
}

@Book{dresher1961,
  author = 	 {Melvin Dresher},
  ALTeditor = 	 {},
  title = 	 {Games of Strategy: Theory and Applications},
  publisher = 	 {Prentice-Hall},
  year = 	 {1961},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  series = 	 {Prentice-Hall Applied Mathematics Series},
  address = 	 {Englewood Cliffs, New Jersey},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@inproceedings{ hlavicka01boom,
    author = "Jan Hlavi\v{c}ka and Petr Fi\v{s}er",
    title = "{BOOM} - A Heuristic Boolean Minimizer",
    booktitle = "{International Conference on Computer Aided Design}",
    pages = "439-442",
    year = "2001",
    url = "citeseer.ist.psu.edu/hlavicka01boom.html" }

%http://www.jesperjuul.dk/ludologist/?p=55

@unpublished{juul,
	author = "Jesper Juul",
	title = "255,168 ways of playing Tic Tac Toe",
	note = "From the author's web page: http://www.jesperjuul.dk/ludologist/?p=55" 
}
	

%M. Karnaugh, "The Map Method for Synthesis of Combinational Logic Circuits," Trans. AIEE, Pt. I, Vol. 79, No. 9, pp. 593--599, 1953.

@InProceedings{karnaugh1953,
  author = 	 {M. Karnaugh},
  title = 	 {The Map Method for Synthesis of Combinational Logic Circuits},
  OPTcrossref =  {},
  OPTkey = 	 {},
  OPTbooktitle = {},
  pages = 	 {593-599},
  year = 	 {1953},
  OPTeditor = 	 {},
  volume = 	 {79},
  number = 	 {9},
  series = 	 {Communications and Electronics},
  OPTaddress = 	 {},
  OPTmonth = 	 {},
  organization = {AIEE},
  OPTpublisher = {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{mccluskey1956,
  author = 	 {E. McCluskey},
  title = 	 {Minimization of {B}oolean Functions},
  journal = 	 {Bell System Technical Journal},
  year = 	 {1956},
  OPTkey = 	 {},
  volume = 	 {35},
  OPTnumber = 	 {},
  pages = 	 {437-457},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}
@inproceedings{mcgeer93minimization,
    author = "Patrick C. McGeer and Jagesh V. Sanghavi and Robert K. Brayton and Alberto L. Sangiovanni-Vincentelli",
    title = "Minimization of Logic Functions Using Essential Signature Sets",
    booktitle = "{VLSI} Design",
    pages = "323-328",
    year = "1993",
    url = "citeseer.ist.psu.edu/178092.html" }

@inproceedings{mcgeer93espressosignature,
    author = "Patrick C. McGeer and Jagesh V. Sanghavi and Robert K. Brayton and Alberto L. Sangiovanni-Vincentelli",
    title = "Espresso-Signature: A New Exact Minimizer for Logic Functions",
    booktitle = "Design Automation Conference",
    pages = "618-624",
    year = "1993",
    url = "citeseer.ist.psu.edu/mcgeer96espressosignature.html" }

@inproceedings{meyer1972,
    author = "A. Meyer and L. Stockmeyer",
    title = "The equivalence problem for regular expressions with squaring requires exponential space",
    booktitle = "Proceedings of the 13th IEEE Symposium on Switching and Automata Theory",
    pages = "125-129",
    year = "1972",
    }

@Book{packel1981,
  author = 	 {Edward W. Packel},
  ALTeditor = 	 {},
  title = 	 {The Mathematics of Games and Gambling},
  publisher = 	 {The Mathematical Association of America},
  year = 	 {1981},
  OPTkey = 	 {},
  volume = 	 {28},
  OPTnumber = 	 {},
  series = 	 {The Mathematical Association of America New Mathematical Library},
  address = 	 {Washington, D.C.},
  edition = 	 {1st},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{quine1952,
  author = 	 {W. Quine},
  title = 	 {The problem of simplifying truth functions},
  journal = 	 {American Mathematical Monthly},
  year = 	 {1952},
  OPTkey = 	 {},
  volume = 	 {59},
  OPTnumber = 	 {},
  pages = 	 {521-531},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{rudell1987,
  author = 	 {R. L. Rudell and A. L. Sangiovanni-Vincentelli},
  title = 	 {Multiple-valued minimization for {PLA} optimization},
  journal = 	 {IEEE Transactions on Computer-Aided Design},
  year = 	 {1987},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTpages = 	 {},
  month = 	 {September},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@PhdThesis{rudell1989,
  author = 	 {R. L. Rudell},
  title = 	 {Logic Synthesis for VLSI Design},
  school = 	 {University of California at Berkeley},
  year = 	 {1989},
  OPTkey = 	 {},
  OPTtype = 	 {},
  OPTaddress = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Stojanovic2001A,
author = "Milan N. Stojanovic and Paloma de Prada and Donald W. Landry",
title = "Catalytic Molecular Beacons",
journal = "ChemBioChem",
pages = "411--415",
volume = 2,
number = 6,
year = 2001,
URL = {http://www.molecular-beacons.org/DOWNLOAD/STOJANOVIC,CEJCB01(2)411.PDF},
comment = Stojanovic2001.pdf
}

@article{Stojanovic2002,
author = "Milan N. Stojanovic and Tiffany Elizabeth Mitchell and Darko Stefanovic",
title = "Deoxyribozyme-Based Logic Gates",
journal = "Journal of the American Chemical Society",
pages = "3555--3561",
volume = 124,
number = 14,
month = apr,
year = 2002,
comment = JACS2002-dblg.pdf
}

@article{Stojanovic2003TicTacToe,
author = "Milan N. Stojanovic and Darko Stefanovic",
title = "A Deoxyribozyme-Based Molecular Automaton",
journal = "Nature Biotechnology",
pages = "1069--1074",
volume = 21,
year = 2003,
comment = Stojanovic2003TicTacToe.pdf,
}

@article{Stojanovic2003HalfAdder,
author = "Milan N. Stojanovic and Darko Stefanovic",
title = "Deoxyribozyme-Based Half Adder",
journal = "Journal of the American Chemical Society",
pages = "6673--6676",
volume = 125,
number = 22,
year = 2003,
comment = "ja0296632.pdf"
}


Turing, A.M., 1936, "On Computable Numbers, with an Application to the Entscheidungsproblem (http://www.abelard.org/turpap2/tp2-ie.asp)", Proceedings of the London Mathematical Society, Series 2, 42 (1936-37), pp.230-265.

@article{Turing1936,
author = "A. M. Turing",
title = "On Computable Numbers, with an Application to the {E}ntscheidungsproblem",
journal = "Proceedings of the London Mathematical Society",
pages = "230-265",
volume = 42,
year = 1936,
}

@Book{vonneumann1944,
  author = 	 {John Von Neumann and Oskar Morgenstern},
  ALTeditor = 	 {},
  title = 	 {Theory of Games and Economic Behavior},
  publisher = 	 {Princeton University Press},
  year = 	 {1944},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  address = 	 {Princeton, New Jersey},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}