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@BOOK{Abramowitz1972,
  title = {Handbook of Mathematical Functions: With Formulas, Graphs and Mathematical
	Tables},
  publisher = {John Wiley \& Sons, Incorporated},
  year = {1972},
  author = {Abramowitz, M. and Stegun, I.A.},
  series = {A Wiley-Interscience publication},
  isbn = {9780471800071},
  owner = {jakirkham},
  timestamp = {2013.08.20},
  url = {http://books.google.com/books?id=fDfHQgAACAAJ}
}

@ARTICLE{Arutyunov2013,
  author = {Denis Arutyunov and Laura S. Frost},
  title = {F conjugation: Back to the beginning},
  journal = {Plasmid },
  year = {2013},
  pages = { - },
  number = {0},
  doi = {10.1016/j.plasmid.2013.03.010},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Arutyunov D, Frost LS -- F conjugation- Back to the beginning.pdf:PDF},
  issn = {0147-619X},
  keywords = {Conjugation},
  owner = {jakirkham},
  timestamp = {2013.05.15},
  url = {http://www.sciencedirect.com/science/article/pii/S0147619X13000395}
}

@BOOK{Balakrishnan2004,
  title = {A Primer on Statistical Distributions},
  publisher = {Wiley},
  year = {2004},
  author = {Balakrishnan, N. and Nevzorov, V.B.},
  isbn = {9780471722212},
  owner = {jakirkham},
  timestamp = {2013.08.19},
  url = {http://books.google.com/books?id=JIfk5kBdLGIC}
}

@ARTICLE{Barton1998,
  author = {Barton, N. H. and Charlesworth, B.},
  title = {Why Sex and Recombination?},
  journal = {Science},
  year = {1998},
  volume = {281},
  pages = {1986-1990},
  number = {5385},
  abstract = {REVIEWMost higher organisms reproduce sexually, despite the automatic
	reproductive advantage experienced by asexual variants. This implies
	the operation of selective forces that confer an advantage to sexuality
	and genetic recombination, at either the population or individual
	level. The effect of sex and recombination in breaking down negative
	correlations between favorable variants at different genetic loci,
	which increases the efficiency of natural selection, is likely to
	be a major factor favoring their evolution and maintenance. Various
	processes that can cause such an effect have been studied theoretically.
	It has, however, so far proved hard to discriminate among them empirically.},
  doi = {10.1126/science.281.5385.1986},
  eprint = {http://www.sciencemag.org/content/281/5385/1986.full.pdf},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Barton, Charlesworth -- Why Sex and Recombination.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.sciencemag.org/content/281/5385/1986.abstract}
}

@ARTICLE{Bedau2003,
  author = {Mark A Bedau and Norman H Packard},
  title = {Evolution of evolvability via adaptation of mutation rates },
  journal = {Biosystems },
  year = {2003},
  volume = {69},
  pages = {143 - 162},
  doi = {http://dx.doi.org/10.1016/S0303-2647(02)00137-5},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Bedau and Packard -- Evolution of evolvability via adaptation of mutation rates.pdf:PDF},
  issn = {0303-2647},
  keywords = {Evolvability},
  owner = {jakirkham},
  timestamp = {2013.10.10},
  url = {http://www.sciencedirect.com/science/article/pii/S0303264702001375}
}

@INCOLLECTION{Black2006,
  author = {Paul E. Black},
  title = {Hamming distance},
  booktitle = {Dictionary of Algorithms and Data Structures [online]},
  publisher = {U.S. National Institute of Standards and Technology},
  year = {2006},
  editor = {Paul E. Black},
  address = {http://www.nist.gov/dads/HTML/HammingDistance.html},
  owner = {jakirkham},
  timestamp = {2013.09.28}
}

@ARTICLE{Bonhoeffer1993,
  author = {Sebastian Bonhoeffer and Peter F. Stadler},
  title = {Error Thresholds on Correlated Fitness Landscapes},
  journal = {Journal of Theoretical Biology },
  year = {1993},
  volume = {164},
  pages = {359 - 372},
  number = {3},
  doi = {http://dx.doi.org/10.1006/jtbi.1993.1160},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Bonhoeffer and Stadler -- Error Thresholds on Correlated Fitness Landscapes.pdf:PDF},
  issn = {0022-5193},
  owner = {jakirkham},
  timestamp = {2013.10.08},
  url = {http://www.sciencedirect.com/science/article/pii/S0022519383711604}
}

@ARTICLE{Cairns1988,
  author = {Cairns, John and Overbaugh, Julie and Miller, Stephan},
  title = {The origin of mutants},
  journal = {Nature},
  year = {1988},
  volume = {335},
  pages = {142--145},
  number = {6186},
  month = sep,
  comment = {10.1038/335142a0},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Cairns, et al -- The origin of mutants.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.10.10},
  url = {http://dx.doi.org/10.1038/335142a0}
}

@ARTICLE{Chen2005,
  author = {Chen, Inês and Christie, Peter J. and Dubnau, David},
  title = {The Ins and Outs of DNA Transfer in Bacteria},
  journal = {Science},
  year = {2005},
  volume = {310},
  pages = {1456-1460},
  number = {5753},
  abstract = {Transformation and conjugation permit the passage of DNA through the
	bacterial membranes and represent dominant modes for the transfer
	of genetic information between bacterial cells or between bacterial
	and eukaryotic cells. As such, they are responsible for the spread
	of fitness-enhancing traits, including antibiotic resistance. Both
	processes usually involve the recognition of double-stranded DNA,
	followed by the transfer of single strands. Elaborate molecular machines
	are responsible for negotiating the passage of macromolecular DNA
	through the layers of the cell surface. All or nearly all the machine
	components involved in transformation and conjugation have been identified,
	and here we present models for their roles in DNA transport.},
  doi = {10.1126/science.1114021},
  eprint = {http://www.sciencemag.org/content/310/5753/1456.full.pdf},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Chen, et al -- The Ins and Outs of DNA Transfer in Bacteria.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.09},
  url = {http://www.sciencemag.org/content/310/5753/1456.abstract}
}

@ARTICLE{Chen2004,
  author = {Chen, Ines and Dubnau, David},
  title = {DNA uptake during bacterial transformation},
  journal = {Nat Rev Micro},
  year = {2004},
  volume = {2},
  pages = {241--249},
  number = {3},
  month = mar,
  comment = {10.1038/nrmicro844},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Chen and Dubnau -- DNA uptake during bacterial transformation.pdf:PDF},
  issn = {1740-1526},
  owner = {jakirkham},
  timestamp = {2013.11.09},
  url = {http://dx.doi.org/10.1038/nrmicro844}
}

@ARTICLE{Christiansen1998,
  author = {Freddy B. Christiansen and Sarah P. Otto and Aviv Bergman and Marcus
	W. Feldman},
  title = {Waiting with and without Recombination: The Time to Production of
	a Double Mutant },
  journal = {Theoretical Population Biology },
  year = {1998},
  volume = {53},
  pages = {199 - 215},
  number = {3},
  doi = {http://dx.doi.org/10.1006/tpbi.1997.1358},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Christiansen, et al -- Waiting with and without Recombination- The Time to Production of a Double Mutant.pdf:PDF},
  issn = {0040-5809},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.sciencedirect.com/science/article/pii/S0040580997913587}
}

@ARTICLE{Clark1973,
  author = {Clark, Alvin J},
  title = {Recombination deficient mutants of E. coli and other bacteria},
  journal = {Annual review of genetics},
  year = {1973},
  volume = {7},
  pages = {67--86},
  number = {1},
  doi = {10.1146/annurev.ge.07.120173.000435},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Clark -- Recombination Deficient Mutants of E. Coli and Other Bacteria.pdf:PDF},
  owner = {jakirkham},
  publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139,
	USA},
  timestamp = {2013.05.13},
  url = {http://www.annualreviews.org.proxy.library.emory.edu/doi/abs/10.1146/annurev.ge.07.120173.000435}
}

@ARTICLE{Clark1965,
  author = {Clark, Alvin J. and Margulies, Ann Dee},
  title = {Isolation and Characterization of Recombination-Deficient Mutants
	of Escherichia Coli K12},
  journal = {Proceedings of the National Academy of Sciences},
  year = {1965},
  volume = {53},
  pages = {451-459},
  number = {2},
  eprint = {http://www.pnas.org/content/53/2/451.full.pdf+html},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Clark and Margulies -- Isolation and Characterization of Recombination-Deficient Mutants of Escherichia Coli K12.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.08},
  url = {http://www.pnas.org/content/53/2/451.short}
}

@ARTICLE{Clarke2008,
  author = {Clarke, Margaret and Maddera, Lucinda and Harris, Robin L. and Silverman,
	Philip M.},
  title = {F-pili dynamics by live-cell imaging},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2008},
  volume = {105},
  pages = {17978-17981},
  number = {46},
  abstract = {Bacteria have evolved numerous mechanisms for cell–cell communication,
	many of which have important consequences for human health. Among
	these is conjugation, the direct transfer of DNA from one cell to
	another. For Gram-negative bacteria, conjugation requires thin, flexible
	filaments (conjugative pili) that are elaborated by DNA donor cells.
	The structure, function, and especially the dynamics of conjugative
	pili are poorly understood. Here, we have applied live-cell imaging
	to characterize the dynamics of F-pili (conjugative pili encoded
	by the F plasmid of Escherichia coli). We establish that F-pili normally
	undergo cycles of extension and retraction in the absence of any
	obvious triggering event, such as contact with a recipient cell.
	When made, such contacts are able to survive the shear forces felt
	by bacteria in liquid media. Our data emphasize the role of F-pilus
	flexibility both in efficiently sampling a large volume surrounding
	donor cells in liquid culture and in establishing and maintaining
	cell–cell contact. Additionally and unexpectedly, we infer that
	extension and retraction are accompanied by rotation about the long
	axis of the filament.},
  doi = {10.1073/pnas.0806786105},
  eprint = {http://www.pnas.org/content/105/46/17978.full.pdf+html},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Clarke, et al -- F-pili dynamics by live-cell imaging.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.05.15},
  url = {http://www.pnas.org/content/105/46/17978.abstract}
}

@ARTICLE{Cohan2002,
  author = {Cohan, Frederick M},
  title = {What are bacterial species?},
  journal = {Annual Reviews in Microbiology},
  year = {2002},
  volume = {56},
  pages = {457--487},
  number = {1},
  doi = {10.1146/annurev.micro.56.012302.160634},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Cohan -- What are Bacterial Species?.pdf:PDF},
  owner = {jakirkham},
  publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139,
	USA},
  timestamp = {2013.05.13},
  url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.micro.56.012302.160634}
}

@ARTICLE{Cohen2005,
  author = {Cohen, Elisheva and Kessler, David A. and Levine, Herbert},
  title = {Recombination Dramatically Speeds Up Evolution of Finite Populations},
  journal = {Phys. Rev. Lett.},
  year = {2005},
  volume = {94},
  pages = {098102},
  month = {Mar},
  doi = {10.1103/PhysRevLett.94.098102},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Cohen, et al -- Recombination Dramatically Speeds Up Evolution of Finite Populations.pdf:PDF},
  issue = {9},
  numpages = {4},
  owner = {jakirkham},
  publisher = {American Physical Society},
  timestamp = {2013.11.09},
  url = {http://link.aps.org/doi/10.1103/PhysRevLett.94.098102}
}

@ARTICLE{Conrad2011,
  author = {Conrad, Tom M and Lewis, Nathan E and Palsson, Bernhard O},
  title = {Microbial laboratory evolution in the era of genome-scale science},
  journal = {Mol Syst Biol},
  year = {2011},
  volume = {7},
  pages = {--},
  month = jul,
  doi = {10.1038/msb.2011.42},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Conrad, et al -- Microbial laboratory evolution in the era of genome-scale science.pdf:PDF},
  owner = {jakirkham},
  publisher = {EMBO and Macmillan Publishers Limited},
  timestamp = {2013.05.15},
  url = {http://dx.doi.org/10.1038/msb.2011.42}
}

@ELECTRONIC{Cooke,
  author = {Rosa-Lee Cooke},
  address = {http://water.me.vccs.edu/courses/env108/},
  url = {http://water.me.vccs.edu/courses/env108/},
  owner = {jakirkham},
  timestamp = {2013.05.15}
}

@ELECTRONIC{Cordoba2012,
  author = {Carlos Cordoba},
  year = {2012},
  title = {Spyder is the Scientific PYthon Development EnviRonment},
  howpublished = {online},
  address = {http://code.google.com/p/spyderlib/},
  url = {http://code.google.com/p/spyderlib/},
  owner = {jakirkham},
  timestamp = {2013.11.08}
}

@ARTICLE{Cox1976,
  author = {Cox, Edward C},
  title = {Bacterial mutator genes and the control of spontaneous mutation},
  journal = {Annual review of genetics},
  year = {1976},
  volume = {10},
  pages = {135--156},
  number = {1},
  doi = {10.1146/annurev.ge.10.120176.001031},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Cox -- Bacterial Mutator Genes and the Control of Spontaneous Mutation.pdf:PDF},
  owner = {jakirkham},
  publisher = {Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139,
	USA},
  timestamp = {2013.10.10},
  url = {http://dx.doi.org/10.1146/annurev.ge.10.120176.001031}
}

@ARTICLE{Cruz2000,
  author = {Fernando de la Cruz and Julian Davies},
  title = {Horizontal gene transfer and the origin of species: lessons from
	bacteria },
  journal = {Trends in Microbiology },
  year = {2000},
  volume = {8},
  pages = {128 - 133},
  number = {3},
  doi = {http://dx.doi.org/10.1016/S0966-842X(00)01703-0},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/de la Cruz and Davies -- Horizontal gene transfer and the origin of species- lessons from bacteria.pdf:PDF},
  issn = {0966-842X},
  keywords = {Bacterial evolution},
  owner = {jakirkham},
  timestamp = {2013.10.10},
  url = {http://www.sciencedirect.com/science/article/pii/S0966842X00017030}
}

@ARTICLE{Didelot2010,
  author = {Xavier Didelot and Martin C.J. Maiden},
  title = {Impact of recombination on bacterial evolution},
  journal = {Trends in Microbiology },
  year = {2010},
  volume = {18},
  pages = {315 - 322},
  number = {7},
  doi = {10.1016/j.tim.2010.04.002},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Didelot and Maiden -- Impact of recombination on bacterial evolution.pdf:PDF},
  issn = {0966-842X},
  owner = {jakirkham},
  timestamp = {2013.04.23},
  url = {http://www.sciencedirect.com/science/article/pii/S0966842X10000594}
}

@ARTICLE{Drake1999,
  author = {Drake, John W.},
  title = {The Distribution of Rates of Spontaneous Mutation over Viruses, Prokaryotes,
	and Eukaryotes},
  journal = {Annals of the New York Academy of Sciences},
  year = {1999},
  volume = {870},
  pages = {100--107},
  number = {1},
  doi = {10.1111/j.1749-6632.1999.tb08870.x},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Drake -- The Distribution of Rates of Spontaneous Mutation over Viruses, Prokaryotes, and Eukaryotes.pdf:PDF},
  issn = {1749-6632},
  owner = {jakirkham},
  publisher = {Blackwell Publishing Ltd},
  timestamp = {2013.05.16},
  url = {http://dx.doi.org/10.1111/j.1749-6632.1999.tb08870.x}
}

@ARTICLE{Drake1991,
  author = {Drake, J W},
  title = {Spontaneous Mutation},
  journal = {Annual Review of Genetics},
  year = {1991},
  volume = {25},
  pages = {125-146},
  number = {1},
  note = {PMID: 1812804},
  doi = {10.1146/annurev.ge.25.120191.001013},
  eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ge.25.120191.001013},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Drake -- Spontaneous mutation.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ge.25.120191.001013}
}

@ARTICLE{Drake1998,
  author = {Drake, John W and Charlesworth, Brian and Charlesworth, Deborah and
	Crow, James F},
  title = {Rates of spontaneous mutation},
  journal = {Genetics},
  year = {1998},
  volume = {148},
  pages = {1667--1686},
  number = {4},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Drake, et al -- Rates of spontaneous mutation.pdf:PDF},
  owner = {jakirkham},
  publisher = {Genetics Soc America},
  timestamp = {2013.05.16},
  url = {http://www.genetics.org/content/148/4/1667.short}
}

@ARTICLE{Drossel2001,
  author = {Drossel, Barbara},
  title = {Biological evolution and statistical physics},
  journal = {Advances in Physics},
  year = {2001},
  volume = {50},
  pages = {209-295},
  number = {2},
  abstract = { This review is an introduction to theoretical models and mathematical
	calculations for biological evolution, aimed at physicists. The methods
	in the field are naturally very similar to those used in statistical
	physics, although the majority of publications have appeared in biology
	journals. The review has three parts, which can be read independently.
	The first part deals with evolution in fitness landscapes and includes
	Fisher's theorem, adaptive walks, quasispecies models, effects of
	finite population sizes, and neutral evolution. The second part studies
	models of coevolution, including evolutionary game theory, kin selection,
	group selection, sexual selection, speciation, and coevolution of
	hosts and parasites. The third part discusses models for networks
	of interacting species and their extinction avalanches. Throughout
	the review, attention is paid to giving the necessary biological
	information, and to pointing out the assumptions underlying the models,
	and their limits of validity. },
  doi = {10.1080/00018730110041365},
  eprint = {http://www.tandfonline.com/doi/pdf/10.1080/00018730110041365},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Drossel -- Biological evolution and statistical physics.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.tandfonline.com/doi/abs/10.1080/00018730110041365}
}

@ARTICLE{Eigen1988,
  author = {Eigen, Manfred and McCaskill, John and Schuster, Peter},
  title = {Molecular quasi-species},
  journal = {The Journal of Physical Chemistry},
  year = {1988},
  volume = {92},
  pages = {6881--6891},
  number = {24},
  doi = {10.1002/9780470141243.ch4},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Eigen, et al -- Molecular quasi-species.pdf:PDF},
  owner = {jakirkham},
  publisher = {ACS Publications},
  timestamp = {2013.10.08},
  url = {http://onlinelibrary.wiley.com/doi/10.1002/9780470141243.ch4/summary}
}

@ARTICLE{Ewens1989,
  author = {Ewens, W.J.},
  title = {An interpretation and proof of the fundamental theorem of natural
	selection},
  journal = {Theoretical Population Biology},
  year = {1989},
  volume = {36},
  pages = {167--180},
  number = {2},
  month = oct,
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Ewens -- An interpretation and proof of the fundamental theorem of natural selection.pdf:PDF},
  issn = {0040-5809},
  owner = {jakirkham},
  timestamp = {2013.10.08},
  url = {http://www.sciencedirect.com/science/article/pii/0040580989900282}
}

@ARTICLE{Felsenstein1974,
  author = {Felsenstein, Joseph},
  title = {The Evolutionary Advantage of Recombination},
  journal = {Genetics},
  year = {1974},
  volume = {78},
  pages = {737-756},
  number = {2},
  abstract = {The controversy over the evolutionary advantage of recombination initially
	discovered by Fisher and by Muller is reviewed. Those authors whose
	models had finite-population effects found an advantage of recombination,
	and those whose models had infinite populations found none. The advantage
	of recombination is that it breaks down random linkage disequilibrium
	generated by genetic drift. Hill and Robertson found that the average
	effect of this randomly-generated linkage disequilibrium was to cause
	linked loci to interfere with each other's response to selection,
	even where there was no gene interaction between the loci. This effect
	is shown to be identical to the original argument of Fisher and Muller.
	It also predicts the "ratchet mechanism" discovered by Muller, who
	pointed out that deleterious mutants would more readily increase
	in a population without recombination. Computer simulations of substitution
	of favorable mutants and of the long-term increase of deleterious
	mutants verified the essential correctness of the original Fisher-Muller
	argument and the reality of the Muller ratchet mechanism. It is argued
	that these constitute an intrinsic advantage of recombination capable
	of accounting for its persistence in the face of selection for tighter
	linkage between interacting polymorphisms, and possibly capable of
	accounting for its origin.},
  eprint = {http://www.genetics.org/content/78/2/737.full.pdf+html},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Felsenstein -- The Evolutionary Advantage of Recombination.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.08.13},
  url = {http://www.genetics.org/content/78/2/737.abstract}
}

@ARTICLE{Fisher2013,
  author = {Daniel Fisher and Michael L\"{a}ssig and Boris Shraiman},
  title = {Evolutionary dynamics and statistical physics},
  journal = {Journal of Statistical Mechanics: Theory and Experiment},
  year = {2013},
  volume = {2013},
  pages = {N01001},
  number = {01},
  __markedentry = {[jakirkham:6]},
  abstract = {This introductory article provides the background to and motivation
	for this special issue and the relationship between evolutionary
	dynamics and statistical physics.},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Fisher, et al -- Evolutionary dynamics and statistical physics.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.11},
  url = {http://stacks.iop.org/1742-5468/2013/i=01/a=N01001}
}

@BOOK{fisher1999genetical,
  title = {The genetical theory of natural selection: a complete variorum edition},
  publisher = {Oxford University Press},
  year = {1999},
  author = {Fisher, Ronald Aylmer},
  owner = {jakirkham},
  timestamp = {2013.11.10}
}

@ARTICLE{Fontana1993,
  author = {Fontana, Walter and Stadler, Peter F. and Bornberg-Bauer, Erich G.
	and Griesmacher, Thomas and Hofacker, Ivo L. and Tacker, Manfred
	and Tarazona, Pedro and Weinberger, Edward D. and Schuster, Peter},
  title = {RNA folding and combinatory landscapes},
  journal = {Phys. Rev. E},
  year = {1993},
  volume = {47},
  pages = {2083--2099},
  month = {Mar},
  doi = {10.1103/PhysRevE.47.2083},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Fontana, et al -- RNA folding and combinatory landscapes.pdf:PDF},
  issue = {3},
  owner = {jakirkham},
  publisher = {American Physical Society},
  timestamp = {2013.10.08},
  url = {http://link.aps.org/doi/10.1103/PhysRevE.47.2083}
}

@ARTICLE{Fraser2009,
  author = {Fraser, Christophe and Alm, Eric J. and Polz, Martin F. and Spratt,
	Brian G. and Hanage, William P.},
  title = {The Bacterial Species Challenge: Making Sense of Genetic and Ecological
	Diversity},
  journal = {Science},
  year = {2009},
  volume = {323},
  pages = {741-746},
  number = {5915},
  abstract = {The Bacteria and Archaea are the most genetically diverse superkingdoms
	of life, and techniques for exploring that diversity are only just
	becoming widespread. Taxonomists classify these organisms into species
	in much the same way as they classify eukaryotes, but differences
	in their biology--including horizontal gene transfer between distantly
	related taxa and variable rates of homologous recombination--mean
	that we still do not understand what a bacterial species is. This
	is not merely a semantic question; evolutionary theory should be
	able to explain why species exist at all levels of the tree of life,
	and we need to be able to define species for practical applications
	in industry, agriculture, and medicine. Recent studies have emphasized
	the need to combine genetic diversity and distinct ecology in an
	attempt to define species in a coherent and convincing fashion. The
	resulting data may help to discriminate among the many theories of
	prokaryotic species that have been produced to date.},
  doi = {10.1126/science.1159388},
  eprint = {http://www.sciencemag.org/content/323/5915/741.full.pdf},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Fraser, et al -- The Bacterial Species Challenge- Making Sense of Genetic and Ecological Diversity.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.10.10},
  url = {http://www.sciencemag.org/content/323/5915/741.abstract}
}

@BOOK{Gentle2003,
  title = {Random Number Generation and Monte Carlo Methods},
  publisher = {Springer},
  year = {2003},
  author = {Gentle, J.E.},
  series = {Statistics and Computing},
  isbn = {9780387001784},
  lccn = {2003042437},
  owner = {jakirkham},
  timestamp = {2013.08.27},
  url = {http://books.google.com/books?id=ERSSDBDcYOIC}
}

@BOOK{Gillespie2010,
  title = {Population genetics: a concise guide},
  publisher = {JHU Press},
  year = {2010},
  author = {Gillespie, John H},
  owner = {jakirkham},
  timestamp = {2013.10.09}
}

@ARTICLE{Gogarten2005,
  author = {Gogarten, J. Peter and Townsend, Jeffrey P.},
  title = {Horizontal gene transfer, genome innovation and evolution},
  journal = {Nat Rev Micro},
  year = {2005},
  volume = {3},
  pages = {679--687},
  number = {9},
  month = sep,
  comment = {10.1038/nrmicro1204},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Gogarten and Townsend -- Horizontal gene transfer, genome innovation and evolution.pdf:PDF},
  issn = {1740-1526},
  owner = {jakirkham},
  publisher = {Nature Publishing Group},
  timestamp = {2013.11.10},
  url = {http://dx.doi.org/10.1038/nrmicro1204}
}

@ARTICLE{Goodman2002,
  author = {Goodman, Myron F.},
  title = {Error-prone repair DNA polymerases in prokaryotes and eukaryotes},
  journal = {Annual Review of Biochemistry},
  year = {2002},
  volume = {71},
  pages = {17-50},
  number = {1},
  note = {PMID: 12045089},
  doi = {10.1146/annurev.biochem.71.083101.124707},
  eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.biochem.71.083101.124707},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Goodman -- Error-prone repair DNA polymerases in prokaryotes and eukaryotes.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.05.16},
  url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.biochem.71.083101.124707}
}

@ARTICLE{Hamilton1980,
  author = {Hamilton, William D.},
  title = {Sex versus Non-Sex versus Parasite},
  journal = {Oikos},
  year = {1980},
  volume = {35},
  pages = {pp. 282-290},
  number = {2},
  abstract = {Pressure of parasites that are short-lived and rapid-evolving compared
	to the hosts they attack could be an evolutionary factor sufficiently
	general to account for sex wherever it exists. To be such a factor,
	parasites must show virulences specific to differing genotypes. Models
	are set up on this basis (one-locus diploid-selection and two-locus
	haploid-selection) in which the rapid demographic reactivity of parasite
	strains to abundance of susceptible hosts becomes represented in
	a single frequency-dependent fitness function which applies to every
	host genotype. It is shown that with frequency dependence sufficiently
	intense such models generate cycles, and that in certain states of
	cycling sexual species easily obtain higher long-term geometric mean
	fitness than any competing monotypic asexual species or mixture of
	such. In the successful cycle of the two-locus model, it is seen
	that both population size and gene frequencies may be steady while
	only oscillating linkage disequilibrium reflects the intense selection
	by parasites. High levels of recombination work best. Fecundity in
	the models can be low and no incidence of competition of siblings
	or other relatives is required.},
  copyright = {Copyright © 1980 Nordic Society Oikos},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Hamilton -- Sex versus Non-Sex versus Parasite.pdf:PDF},
  issn = {00301299},
  jstor_articletype = {research-article},
  jstor_formatteddate = {Oct., 1980},
  language = {English},
  owner = {jakirkham},
  publisher = {Wiley on behalf of Nordic Society Oikos},
  timestamp = {2013.11.11},
  url = {http://www.jstor.org/stable/3544435}
}

@ARTICLE{Hamilton1990,
  author = {Hamilton, W D and Axelrod, R and Tanese, R},
  title = {Sexual reproduction as an adaptation to resist parasites (a review)},
  journal = {Proceedings of the National Academy of Sciences},
  year = {1990},
  volume = {87},
  pages = {3566-3573},
  number = {9},
  __markedentry = {[jakirkham:]},
  abstract = {Darwinian theory has yet to explain adequately the fact of sex. If
	males provide little or no aid to offspring, a high (up to 2-fold)
	extra average fitness has to emerge as a property of a sexual parentage
	if sex is to be stable. The advantage must presumably come from recombination
	but has been hard to identify. It may well lie in the necessity to
	recombine defenses to defeat numerous parasites. A model demonstrating
	this works best for contesting hosts whose defense polymorphisms
	are constrained to low mutation rates. A review of the literature
	shows that the predictions of parasite coevolution fit well with
	the known ecology of sex. Moreover, parasite coevolution is superior
	to previous models of the evolution of sex by supporting the stability
	of sex under the following challenging conditions: very low fecundity,
	realistic patterns of genotype fitness and changing environment,
	and frequent mutation to parthenogenesis, even while sex pays the
	full 2-fold cost.},
  eprint = {http://www.pnas.org/content/87/9/3566.full.pdf+html},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Hamilton, et al -- Sexual reproduction as an adaptation to resist parasites (a review).pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.11},
  url = {http://www.pnas.org/content/87/9/3566.abstract}
}

@ARTICLE{Hartfield2012,
  author = {Hartfield, Matthew and Keightley, Peter D.},
  title = {Current hypotheses for the evolution of sex and recombination},
  journal = {Integrative Zoology},
  year = {2012},
  volume = {7},
  pages = {192--209},
  number = {2},
  abstract = {The evolution of sex is one of the most important and controversial
	problems in evolutionary biology. Although sex is almost universal
	in higher animals and plants, its inherent costs have made its maintenance
	difficult to explain. The most famous of these is the twofold cost
	of males, which can greatly reduce the fecundity of a sexual population,
	compared to a population of asexual females. Over the past century,
	multiple hypotheses, along with experimental evidence to support
	these, have been put forward to explain widespread costly sex. In
	this review, we outline some of the most prominent theories, along
	with the experimental and observational evidence supporting these.
	Historically, there have been 4 classes of theories: the ability
	of sex to fix multiple novel advantageous mutants (Fisher–Muller
	hypothesis); sex as a mechanism to stop the build-up of deleterious
	mutations in finite populations (Muller's ratchet); recombination
	creating novel genotypes that can resist infection by parasites (Red
	Queen hypothesis); and the ability of sex to purge bad genomes if
	deleterious mutations act synergistically (mutational deterministic
	hypothesis). Current theoretical and experimental evidence seems
	to favor the hypothesis that sex breaks down selection interference
	between new mutants, or it acts as a mechanism to shuffle genotypes
	in order to repel parasitic invasion. However, there is still a need
	to collect more data from natural populations and experimental studies,
	which can be used to test different hypotheses.},
  doi = {10.1111/j.1749-4877.2012.00284.x},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Hartfield, Keightley -- Current hypotheses for the evolution of sex and recombination.pdf:PDF},
  issn = {1749-4877},
  keywords = {evolution of sex, fitness-associated sex, Hill–Robertson interference,
	mutational deterministic hypothesis, Red Queen hypothesis},
  owner = {jakirkham},
  publisher = {Blackwell Publishing Ltd},
  timestamp = {2013.11.10},
  url = {http://dx.doi.org/10.1111/j.1749-4877.2012.00284.x}
}

@ELECTRONIC{Heesch2013,
  author = {Dimitri van Heesch},
  month = {August},
  year = {2013},
  title = {Doxygen},
  language = {English},
  howpublished = {Online},
  address = {www.doxygen.org},
  url = {www.doxygen.org},
  owner = {jakirkham},
  timestamp = {2013.09.26}
}

@ARTICLE{Higgs1995,
  author = {Higgs, PaulG. and Woodcock, Glenn},
  title = {The accumulation of mutations in asexual populations and the structure
	of genealogical trees in the presence of selection},
  journal = {Journal of Mathematical Biology},
  year = {1995},
  volume = {33},
  pages = {677-702},
  number = {7},
  doi = {10.1007/BF00184644},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Higgs and Woodcock -- The accumulation of mutations in asexual populations and the structure of genealogical trees in the presence of selection.pdf:PDF},
  issn = {0303-6812},
  keywords = {Muller's ratchet; Neutral evolution; Mutation-selection balance; Genealogical
	trees},
  language = {English},
  owner = {jakirkham},
  publisher = {Springer-Verlag},
  timestamp = {2013.10.09},
  url = {http://dx.doi.org/10.1007/BF00184644}
}

@ARTICLE{Hill1966,
  author = {Hill,W. G. and Robertson,Alan},
  title = {The effect of linkage on limits to artificial selection},
  journal = {Genetics Research},
  year = {1966},
  volume = {8},
  pages = {269--294},
  month = {12},
  doi = {10.1017/S0016672300010156},
  issn = {1469-5073},
  issue = {03},
  numpages = {26},
  owner = {jakirkham},
  timestamp = {2013.11.11},
  url = {http://journals.cambridge.org/article_S0016672300010156}
}

@ARTICLE{Hunter2007,
  author = {John D. Hunter},
  title = {Matplotlib: A 2D Graphics Environment},
  journal = {Computing In Science and Engineering},
  year = {2007},
  volume = {9},
  pages = {90--95},
  number = {3},
  abstract = {Matplotlib is a 2D graphics package used for Python for application
	development, interactive scripting, and publication-quality image
	generation across user interfaces and operating systems.},
  address = {Los Alamitos, CA, USA},
  doi = {10.1109/MCSE.2007.55},
  issn = {1521-9615},
  owner = {jakirkham},
  publisher = {IEEE Computer Society},
  timestamp = {2013.10.05},
  url = {http://doi.ieeecomputersociety.org/10.1109/MCSE.2007.55}
}

@MISC{Jones2001--,
  author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
  title = {{SciPy}: Open source scientific tools for {Python}},
  year = {2001--},
  owner = {jakirkham},
  timestamp = {2013.10.05},
  url = {http://www.scipy.org/}
}

@ARTICLE{Kashtan2007,
  author = {Kashtan, Nadav and Noor, Elad and Alon, Uri},
  title = {Varying environments can speed up evolution},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2007},
  volume = {104},
  pages = {13711-13716},
  number = {34},
  abstract = {Simulations of biological evolution, in which computers are used to
	evolve systems toward a goal, often require many generations to achieve
	even simple goals. It is therefore of interest to look for generic
	ways, compatible with natural conditions, in which evolution in simulations
	can be speeded. Here, we study the impact of temporally varying goals
	on the speed of evolution, defined as the number of generations needed
	for an initially random population to achieve a given goal. Using
	computer simulations, we find that evolution toward goals that change
	over time can, in certain cases, dramatically speed up evolution
	compared with evolution toward a fixed goal. The highest speedup
	is found under modularly varying goals, in which goals change over
	time such that each new goal shares some of the subproblems with
	the previous goal. The speedup increases with the complexity of the
	goal: the harder the problem, the larger the speedup. Modularly varying
	goals seem to push populations away from local fitness maxima, and
	guide them toward evolvable and modular solutions. This study suggests
	that varying environments might significantly contribute to the speed
	of natural evolution. In addition, it suggests a way to accelerate
	optimization algorithms and improve evolutionary approaches in engineering.},
  doi = {10.1073/pnas.0611630104},
  eprint = {http://www.pnas.org/content/104/34/13711.full.pdf+html},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Kashtan, et al -- Varying environments can speed up evolution.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.pnas.org/content/104/34/13711.abstract}
}

@ARTICLE{Kauffman1989,
  author = {Stuart A. Kauffman and Edward D. Weinberger},
  title = {The \{NK\} model of rugged fitness landscapes and its application
	to maturation of the immune response },
  journal = {Journal of Theoretical Biology },
  year = {1989},
  volume = {141},
  pages = {211 - 245},
  number = {2},
  doi = {http://dx.doi.org/10.1016/S0022-5193(89)80019-0},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Kauffman and Weinberger -- The NK model of rugged fitness landscapes and its application to maturation of the immune response.pdf:PDF},
  issn = {0022-5193},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.sciencedirect.com/science/article/pii/S0022519389800190}
}

@ARTICLE{Kauffman1987,
  author = {Stuart Kauffman and Simon Levin},
  title = {Towards a general theory of adaptive walks on rugged landscapes },
  journal = {Journal of Theoretical Biology },
  year = {1987},
  volume = {128},
  pages = {11 - 45},
  number = {1},
  doi = {http://dx.doi.org/10.1016/S0022-5193(87)80029-2},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Kauffman and Levin -- Towards a general theory of adaptive walks on rugged landscapes.pdf:PDF},
  issn = {0022-5193},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.sciencedirect.com/science/article/pii/S0022519387800292}
}

@BOOK{Kimball1994,
  title = {Biology},
  publisher = {Wm. C. Brown Publishers},
  year = {1994},
  author = {John W. Kimball},
  isbn = {9780697202840},
  lccn = {93070167},
  owner = {jakirkham},
  timestamp = {2013.10.10},
  url = {http://books.google.com/books?id=RoG7QgAACAAJ}
}

@MISC{Krug2012,
  author = {Joachim Krug},
  title = {Statistical Physics of Biological Evolution},
  howpublished = {Published in the Proceedings of the 4th Warsaw School of Statistical
	Physics, ed. by B. Cichocki, M. Napiorkowski and J. Piasecki (Warsaw
	University Press, 2012), pp. 123-129},
  year = {2012},
  eprint = {arXiv:1204.2661}
}

@ARTICLE{Landy1989,
  author = {Landy, A},
  title = {Dynamic, Structural, and Regulatory Aspects of lambda Site-Specific
	Recombination},
  journal = {Annual Review of Biochemistry},
  year = {1989},
  volume = {58},
  pages = {913-941},
  number = {1},
  note = {PMID: 2528323},
  doi = {10.1146/annurev.bi.58.070189.004405},
  eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.bi.58.070189.004405},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Landy -- Dynamic, Structural, and Regulatory Aspects of lambda Site-Specific Recombination.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.09},
  url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.bi.58.070189.004405}
}

@ARTICLE{Lenski1989,
  author = {Lenski, R E and Slatkin, M and Ayala, F J},
  title = {Mutation and selection in bacterial populations: alternatives to
	the hypothesis of directed mutation},
  journal = {Proceedings of the National Academy of Sciences},
  year = {1989},
  volume = {86},
  pages = {2775-2778},
  number = {8},
  abstract = {Bacterial populations have served as model systems for studying evolutionary
	processes ever since the classic experiments of Luria and Delbrück,
	which demonstrated the occurrence of mutations prior to selection
	for the traits they conferred. However, several authors have recently
	presented experiments suggesting that bacteria may have mechanisms
	for directing which mutations occur, such that the rate of adaptive
	mutations is enhanced. Before the hypothesis of directed mutation
	is accepted, it is imperative to consider alternative hypotheses
	that might account for the same observations. To this end, we expand
	upon existing mathematical theory of the dynamics of mutation and
	selection in clonal populations for two cases of particular interest.
	The first case concerns selection against mutants before plating;
	this selection occurs as the result of differences in growth rate
	between mutants and nonmutants. We demonstrate that this selection
	model gives rise to distributions of mutants, obtained by plating
	from sister cultures, that are very similar to those expected when
	some mutations are induced by the selective environment. The second
	case concerns the sequential incorporation of two mutations as the
	result of selection for an intermediate genotype after plating. We
	demonstrate that this two-step mutation model also yields distributions
	that are similar to those expected when some mutations are induced
	by the selective environment. These two cases therefore provide alternatives
	to the hypothesis of directed mutation. We suggest experiments that
	might be used to examine our alternative hypotheses. We also contrast
	the hypothesis of directed mutation with the notion of inheritance
	of acquired characteristics.},
  eprint = {http://www.pnas.org/content/86/8/2775.full.pdf+html},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Lenski, et al -- Mutation and selection in bacterial populations- alternatives to the hypothesis of directed mutation.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.09},
  url = {http://www.pnas.org/content/86/8/2775.abstract}
}

@ARTICLE{Leuthaeusser1987,
  author = {Leuthäusser, Ira},
  title = {Statistical mechanics of Eigen's evolution model},
  journal = {Journal of Statistical Physics},
  year = {1987},
  volume = {48},
  pages = {343-360},
  number = {1-2},
  doi = {10.1007/BF01010413},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Leuthausser -- Statistical mechanics of Eigen's evolution model.pdf:PDF},
  issn = {0022-4715},
  keywords = {Macromolecular evolution; inhomogeneous; random Ising systems; replication
	number landscape; error threshold; quasispecies},
  language = {English},
  owner = {jakirkham},
  publisher = {Kluwer Academic Publishers-Plenum Publishers},
  timestamp = {2013.10.08},
  url = {http://dx.doi.org/10.1007/BF01010413}
}

@ARTICLE{Levin2000,
  author = {Levin, Bruce R. and Bergstrom, Carl T.},
  title = {Bacteria are different: Observations, interpretations, speculations,
	and opinions about the mechanisms of adaptive evolution in prokaryotes},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2000},
  volume = {97},
  pages = {6981-6985},
  number = {13},
  abstract = {To some extent, the genetic theory of adaptive evolution in bacteria
	is a simple extension of that developed for sexually reproducing
	eukaryotes. In other, fundamental ways, the process of adaptive evolution
	in bacteria is quantitatively and qualitatively different from that
	of organisms for which recombination is an integral part of the reproduction
	process. In this speculative and opinionated discussion, we explore
	these differences. In particular, we consider (i) how, as a consequence
	of the low rates of recombination, “ordinary� chromosomal gene
	evolution in bacteria is different from that in organisms where recombination
	is frequent and (ii) the fundamental role of the horizontal transmission
	of genes and accessory genetic elements as sources of variation in
	bacteria. We conclude with speculations about the evolution of accessory
	elements and their role in the adaptive evolution of bacteria.},
  doi = {10.1073/pnas.97.13.6981},
  eprint = {http://www.pnas.org/content/97/13/6981.full.pdf+html},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Levin and Bergstrom -- Bacteria are different- Observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.05.16},
  url = {http://www.pnas.org/content/97/13/6981.abstract}
}

@ARTICLE{Levin2000a,
  author = {Levin, Bruce R. and Perrot, Véronique and Walker, Nina},
  title = {Compensatory Mutations, Antibiotic Resistance and the Population
	Genetics of Adaptive Evolution in Bacteria},
  journal = {Genetics},
  year = {2000},
  volume = {154},
  pages = {985-997},
  number = {3},
  abstract = {In the absence of the selecting drugs, chromosomal mutations for resistance
	to antibiotics and other chemotheraputic agents commonly engender
	a cost in the fitness of microorganisms. Recent in vivo and in vitro
	experimental studies of the adaptation to these "costs of resistance"
	in Escherichia coli, HIV, and Salmonella typhimurium found that evolution
	in the absence of these drugs commonly results in the ascent of mutations
	that ameliorate these costs, rather than higher-fitness, drug-sensitive
	revertants. To ascertain the conditions under which this compensatory
	evolution, rather than reversion, will occur, we did computer simulations,
	in vitro experiments, and DNA sequencing studies with low-fitness
	rpsL (streptomycin-resistant) mutants of E. coli with and without
	mutations that compensate for the fitness costs of these ribosomal
	protein mutations. The results of our investigation support the hypothesis
	that in these experiments, the ascent of intermediate-fitness compensatory
	mutants, rather than high-fitness revertants, can be attributed to
	higher rates of compensatory mutations relative to that of reversion
	and to the numerical bottlenecks associated with serial passage.
	We argue that these bottlenecks are intrinsic to the population dynamics
	of parasitic and commensal microbes and discuss the implications
	of these results to the problem of drug resistance and adaptive evolution
	in parasitic and commmensal microorganisms in general.},
  eprint = {http://www.genetics.org/content/154/3/985.full.pdf+html},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Levin, et al -- Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.genetics.org/content/154/3/985.abstract}
}

@ARTICLE{Li1967,
  author = {Li, C. C.},
  title = {Fundamental Theorem of Natural Selection},
  journal = {Nature},
  year = {1967},
  volume = {214},
  pages = {505--506},
  number = {5087},
  month = apr,
  comment = {10.1038/214505a0},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Li -- Fundamental Theorem of Natural Selection.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.10.08},
  url = {http://dx.doi.org/10.1038/214505a0}
}

@ARTICLE{Low1978,
  author = {Low, K B and Porter, D D},
  title = {Modes of Gene Transfer and Recombination in Bacteria},
  journal = {Annual Review of Genetics},
  year = {1978},
  volume = {12},
  pages = {249-287},
  number = {1},
  note = {PMID: 106767},
  doi = {10.1146/annurev.ge.12.120178.001341},
  eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ge.12.120178.001341},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Low and Porter -- Modes of Gene Transfer and Recombination in Bacteria.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.10.09},
  url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ge.12.120178.001341}
}

@ARTICLE{Luria1943,
  author = {Luria, S. E. and Delbrück, M.},
  title = {Mutations of Bacteria from Virus Sensitivity to Virus Resistance},
  journal = {Genetics},
  year = {1943},
  volume = {28},
  pages = {491-511},
  number = {6},
  eprint = {http://www.genetics.org/content/28/6/491.full.pdf+html},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Luria and Delbrück -- Mutations of Bacteria from Virus Sensitivity to Virus Resistance.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.09},
  url = {http://www.genetics.org/content/28/6/491.short}
}

@ARTICLE{Marks2012,
  author = {Marks, Laura R and Reddinger, Ryan M and Hakansson, Anders P},
  title = {High levels of genetic recombination during nasopharyngeal carriage
	and biofilm formation in Streptococcus pneumoniae},
  journal = {mBio},
  year = {2012},
  volume = {3},
  number = {5},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Marks, et al -- High Levels of Genetic Recombination during Nasopharyngeal Carriage and Biofilm Formation in Streptococcus pneumoniae.pdf:PDF},
  owner = {jakirkham},
  publisher = {Am Soc Microbiol},
  timestamp = {2013.05.15},
  url = {http://mbio.asm.org/content/3/5/e00200-12.short}
}

@ARTICLE{Matic1996,
  author = {Ivan Matic and François Taddei and Miroslav Radman},
  title = {Genetic barriers among bacteria},
  journal = {Trends in Microbiology },
  year = {1996},
  volume = {4},
  pages = {69 - 73},
  number = {2},
  doi = {http://dx.doi.org/10.1016/0966-842X(96)81514-9},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Matic, et al -- Genetic barriers among bacteria.pdf:PDF},
  issn = {0966-842X},
  owner = {jakirkham},
  timestamp = {2013.10.10},
  url = {http://www.sciencedirect.com/science/article/pii/0966842X96815149}
}

@ARTICLE{Matsumoto1998,
  author = {Matsumoto, Makoto and Nishimura, Takuji},
  title = {Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random
	number generator},
  journal = {ACM Trans. Model. Comput. Simul.},
  year = {1998},
  volume = {8},
  pages = {3--30},
  number = {1},
  month = jan,
  acmid = {272995},
  address = {New York, NY, USA},
  doi = {10.1145/272991.272995},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Matsumoto and Nishimura -- Mersenne twister- a 623-dimensionally equidistributed uniform pseudo-random number generator.pdf:PDF},
  issn = {1049-3301},
  issue_date = {Jan. 1998},
  keywords = {<italic>k</italic>-distribution, <italic>m</italic>-sequences, GFSR,
	MT19937, Mersenne primes, Mersenne twister, TGFSR, finite fields,
	incomplete array, inversive-decimation method, multiple-recursive
	matrix method, primitive polynomials, random number generation, tempering},
  numpages = {28},
  owner = {jakirkham},
  publisher = {ACM},
  timestamp = {2013.08.26},
  url = {http://doi.acm.org/10.1145/272991.272995}
}

@BOOK{Michod1988,
  title = {The Evolution of sex : an examination of current ideas},
  publisher = {Sinauer Associates},
  year = {1988},
  author = {Michod, Richard and Levin, Bruce},
  address = {Sunderland, Mass},
  isbn = {0878934596},
  owner = {jakirkham},
  timestamp = {2013.04.23}
}

@ARTICLE{Michod2008,
  author = {Richard E. Michod and Harris Bernstein and Aurora M. Nedelcu},
  title = {Adaptive value of sex in microbial pathogens },
  journal = {Infection, Genetics and Evolution },
  year = {2008},
  volume = {8},
  pages = {267 - 285},
  number = {3},
  doi = {http://dx.doi.org/10.1016/j.meegid.2008.01.002},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Michod, et al -- Adaptive value of sex in microbial pathogens.pdf:PDF},
  issn = {1567-1348},
  keywords = {Recombination},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.sciencedirect.com/science/article/pii/S156713480800004X}
}

@ARTICLE{Modrich1991,
  author = {Modrich, P},
  title = {Mechanisms and Biological Effects of Mismatch Repair},
  journal = {Annual Review of Genetics},
  year = {1991},
  volume = {25},
  pages = {229-253},
  number = {1},
  note = {PMID: 1812808},
  doi = {10.1146/annurev.ge.25.120191.001305},
  eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ge.25.120191.001305},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Modrich -- Mechanisms and Biological Effects of Mismatch Repair.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ge.25.120191.001305}
}

@ELECTRONIC{Moran2007,
  author = {Laurence A. Moran},
  month = {July},
  year = {2007},
  title = {Mutation Rates},
  howpublished = {Blog},
  address = {http://sandwalk.blogspot.com/2007/07/mutation-rates.html},
  url = {http://sandwalk.blogspot.com/2007/07/mutation-rates.html},
  owner = {jakirkham},
  timestamp = {2013.05.16}
}

@ARTICLE{Muller1964,
  author = {H.J. Muller},
  title = {The relation of recombination to mutational advance},
  journal = {Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis},
  year = {1964},
  volume = {1},
  pages = {2 - 9},
  number = {1},
  doi = {http://dx.doi.org/10.1016/0027-5107(64)90047-8},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Muller -- The relation of recombination to mutational advance.pdf:PDF},
  issn = {0027-5107},
  owner = {jakirkham},
  timestamp = {2013.11.09},
  url = {http://www.sciencedirect.com/science/article/pii/0027510764900478}
}

@ARTICLE{Muller1932,
  author = {Muller, H. J.},
  title = {Some Genetic Aspects of Sex},
  journal = {The American Naturalist},
  year = {1932},
  volume = {66},
  pages = {pp. 118-138},
  number = {703},
  copyright = {Copyright © 1932 The University of Chicago},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Muller -- Some Genetic Aspects of Sex.pdf:PDF},
  issn = {00030147},
  jstor_articletype = {research-article},
  jstor_formatteddate = {Mar. - Apr., 1932},
  language = {English},
  owner = {jakirkham},
  publisher = {The University of Chicago Press for The American Society of Naturalists},
  timestamp = {2013.11.09},
  url = {http://www.jstor.org/stable/2456922}
}

@ARTICLE{Mustonen2010,
  author = {Mustonen, Ville and Lässig, Michael},
  title = {Fitness flux and ubiquity of adaptive evolution},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2010},
  volume = {107},
  pages = {4248-4253},
  number = {9},
  abstract = {Natural selection favors fitter variants in a population, but actual
	evolutionary processes may decrease fitness by mutations and genetic
	drift. How is the stochastic evolution of molecular biological systems
	shaped by natural selection? Here, we derive a theorem on the fitness
	flux in a population, defined as the selective effect of its genotype
	frequency changes. The fitness-flux theorem generalizes Fisher's
	fundamental theorem of natural selection to evolutionary processes
	including mutations, genetic drift, and time-dependent selection.
	It shows that a generic state of populations is adaptive evolution:
	there is a positive fitness flux resulting from a surplus of beneficial
	over deleterious changes. In particular, stationary nonequilibrium
	evolution processes are predicted to be adaptive. Under specific
	nonstationary conditions, notably during a decrease in population
	size, the average fitness flux can become negative. We show that
	these predictions are in accordance with experiments in bacteria
	and bacteriophages and with genomic data in Drosophila. Our analysis
	establishes fitness flux as a universal measure of adaptation in
	molecular evolution.},
  doi = {10.1073/pnas.0907953107},
  eprint = {http://www.pnas.org/content/107/9/4248.full.pdf+html},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Mustonen and Lässig - From fitness landscapes to seascapes- non-equilibrium dynamics of selection and adaptation.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.10.08},
  url = {http://www.pnas.org/content/107/9/4248.abstract}
}

@ARTICLE{Mustonen2009,
  author = {Mustonen, Ville and Lässig, Michael},
  title = {From fitness landscapes to seascapes: non-equilibrium dynamics of
	selection and adaptation},
  journal = {Trends in Genetics},
  year = {2009},
  volume = {25},
  pages = {111--119},
  number = {3},
  month = mar,
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Mustonen and Lässig - Fitness flux and ubiquity of adaptive evolution.pdf:PDF;SI:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Mustonen and Lässig - Fitness flux and ubiquity of adaptive evolution (Supplementary Information).pdf:PDF},
  issn = {0168-9525},
  owner = {jakirkham},
  timestamp = {2013.10.08},
  url = {http://www.sciencedirect.com/science/article/pii/S0168952509000250}
}

@ARTICLE{Munoz2008,
  author = {Muñoz, Enrique and Park, Jeong-Man and Deem, Michael W.},
  title = {Quasispecies theory for horizontal gene transfer and recombination},
  journal = {Phys. Rev. E},
  year = {2008},
  volume = {78},
  pages = {061921},
  month = {Dec},
  doi = {10.1103/PhysRevE.78.061921},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Muñoz, et al -- Quasispecies theory for horizontal gene transfer and recombination.pdf:PDF},
  issue = {6},
  numpages = {37},
  owner = {jakirkham},
  publisher = {American Physical Society},
  timestamp = {2013.03.18},
  url = {http://link.aps.org/doi/10.1103/PhysRevE.78.061921}
}

@ARTICLE{Neher2011,
  author = {Neher, Richard A. and Shraiman, Boris I.},
  title = {Statistical genetics and evolution of quantitative traits},
  journal = {Rev. Mod. Phys.},
  year = {2011},
  volume = {83},
  pages = {1283--1300},
  month = {Nov},
  doi = {10.1103/RevModPhys.83.1283},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Neher and Shraiman -- Statistical genetics and evolution of quantitative traits.pdf:PDF},
  issue = {4},
  owner = {jakirkham},
  publisher = {American Physical Society},
  timestamp = {2013.11.10},
  url = {http://link.aps.org/doi/10.1103/RevModPhys.83.1283}
}

@ARTICLE{Ochman2000,
  author = {Ochman, Howard and Lawrence, Jeffrey G. and Groisman, Eduardo A.},
  title = {Lateral gene transfer and the nature of bacterial innovation},
  journal = {Nature},
  year = {2000},
  volume = {405},
  pages = {299--304},
  number = {6784},
  month = may,
  comment = {10.1038/35012500},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Ochman, et al -- Lateral gene transfer and the nature of bacterial innovation.pdf:PDF},
  issn = {0028-0836},
  owner = {jakirkham},
  publisher = {Macmillian Magazines Ltd.},
  timestamp = {2013.11.10},
  url = {http://dx.doi.org/10.1038/35012500}
}

@ARTICLE{Ohta1992,
  author = {Ohta, Tomoko},
  title = {The Nearly Neutral Theory of Molecular Evolution},
  journal = {Annual Review of Ecology and Systematics},
  year = {1992},
  volume = {23},
  pages = {263--286},
  month = jan,
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Ohta -- The Nearly Neutral Theory of Molecular Evolution.pdf:PDF},
  issn = {00664162},
  owner = {jakirkham},
  publisher = {Annual Reviews},
  timestamp = {2013.11.09},
  url = {http://www.jstor.org/stable/2097289}
}

@ARTICLE{Oliphant2007,
  author = {Travis E. Oliphant},
  title = {Python for Scientific Computing},
  journal = {Computing in Science \& Engineering},
  year = {2007},
  volume = {9},
  pages = {10-20},
  number = {3},
  doi = {10.1109/MCSE.2007.58},
  keywords = {high level languages; natural sciences computing},
  owner = {jakirkham},
  publisher = {IEEE},
  timestamp = {2013.10.05},
  url = {http://doi.ieeecomputersociety.org.proxy.library.emory.edu/10.1109/MCSE.2007.58}
}

@ARTICLE{Otto2002,
  author = {Otto, Sarah P. and Lenormand, Thomas},
  title = {Resolving the paradox of sex and recombination},
  journal = {Nat Rev Genet},
  year = {2002},
  volume = {3},
  pages = {252--261},
  number = {4},
  month = apr,
  comment = {10.1038/nrg761},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Otto and Lenormand -- Evolution of sex- Resolving the paradox of sex and recombination.pdf:PDF},
  issn = {1471-0056},
  owner = {jakirkham},
  timestamp = {2013.11.09},
  url = {http://dx.doi.org/10.1038/nrg761}
}

@ARTICLE{Panicker1985,
  author = {Panicker, Mitradas M and Minkley, EG},
  title = {DNA transfer occurs during a cell surface contact stage of F sex
	factor-mediated bacterial conjugation.},
  journal = {Journal of bacteriology},
  year = {1985},
  volume = {162},
  pages = {584--590},
  number = {2},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Panicker and Minkley, Jr -- DNA transfer occurs during a cell surface contact stage of F sex factor-mediated bacterial conjugation.pdf:PDF},
  owner = {jakirkham},
  publisher = {Am Soc Microbiol},
  timestamp = {2013.05.15},
  url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC218888/}
}

@ARTICLE{Park2010,
  author = {Park, Su-Chan and Simon, Damien and Krug, Joachim},
  title = {The Speed of Evolution in Large Asexual Populations},
  journal = {Journal of Statistical Physics},
  year = {2010},
  volume = {138},
  pages = {381-410},
  doi = {10.1007/s10955-009-9915-x},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Park, Simon, et al -- The Speed of Evolution in Large Asexual Populations.pdf:PDF},
  issn = {0022-4715},
  issue = {1-3},
  keywords = {Evolutionary dynamics; Wright-Fisher model; Clonal interference; Traveling
	waves},
  language = {English},
  owner = {jakirkham},
  publisher = {Springer US},
  timestamp = {2013.03.18},
  url = {http://dx.doi.org/10.1007/s10955-009-9915-x}
}

@ARTICLE{Perez2007,
  author = {Fernando Perez and Brian E. Granger},
  title = {IPython: A System for Interactive Scientific Computing},
  journal = {Computing in Science and Engineering},
  year = {2007},
  volume = {9},
  pages = {21-29},
  number = {3},
  address = {Los Alamitos, CA, USA},
  doi = {10.1109/MCSE.2007.53},
  issn = {1521-9615},
  keywords = {natural sciences computing; interactive systems; high level languages},
  owner = {jakirkham},
  publisher = {IEEE},
  timestamp = {2013.10.05},
  url = {http://doi.ieeecomputersociety.org/10.1109/MCSE.2007.53}
}

@ARTICLE{Pigliucci2008,
  author = {Pigliucci, Massimo},
  title = {Is evolvability evolvable?},
  journal = {Nat Rev Genet},
  year = {2008},
  volume = {9},
  pages = {75--82},
  number = {1},
  month = jan,
  comment = {10.1038/nrg2278},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Pigliucci -- Is evolvability evolvable.pdf:PDF},
  issn = {1471-0056},
  owner = {jakirkham},
  publisher = {Nature Publishing Group},
  timestamp = {2013.10.10},
  url = {http://dx.doi.org/10.1038/nrg2278}
}

@ARTICLE{Prugel-Bennett1997,
  author = {Adam Pr\"{u}gel-Bennett and Jonathan L. Shapiro},
  title = {The dynamics of a Genetic Algorithm for simple random Ising systems
	},
  journal = {Physica D: Nonlinear Phenomena },
  year = {1997},
  volume = {104},
  pages = {75 - 114},
  number = {1},
  doi = {http://dx.doi.org/10.1016/S0167-2789(96)00163-7},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Prügel-Bennett, Shapiro -- The dynamics of a Genetic Algorithm for simple random Ising systems.pdf:PDF},
  issn = {0167-2789},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.sciencedirect.com/science/article/pii/S0167278996001637}
}

@ARTICLE{Radding1973,
  author = {Radding, C M},
  title = {Molecular Mechanisms in Genetic Recombination},
  journal = {Annual Review of Genetics},
  year = {1973},
  volume = {7},
  pages = {87-111},
  number = {1},
  note = {PMID: 4593311},
  doi = {10.1146/annurev.ge.07.120173.000511},
  eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ge.07.120173.000511},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Radding -- Molecular Mechanisms in Genetic Recombination.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.11.10},
  url = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ge.07.120173.000511}
}

@ARTICLE{Redfield2001,
  author = {Redfield, Rosemary J.},
  title = {Do bacteria have sex?},
  journal = {Nat Rev Genet},
  year = {2001},
  volume = {2},
  pages = {634--639},
  number = {8},
  month = aug,
  comment = {10.1038/35084593},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Redfield -- Do bacteria have sex.pdf:PDF},
  issn = {1471-0056},
  owner = {jakirkham},
  timestamp = {2013.11.09},
  url = {http://dx.doi.org/10.1038/35084593}
}

@ARTICLE{Rosenberg2001,
  author = {Rosenberg, Susan M.},
  title = {Evolving responsively: adaptive mutation},
  journal = {Nat Rev Genet},
  year = {2001},
  volume = {2},
  pages = {504--515},
  number = {7},
  month = jul,
  comment = {10.1038/35080556},
  doi = {10.1038/35080556},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Rosenberg -- Evolving responsively- adaptive mutation.pdf:PDF},
  issn = {1471-0056},
  owner = {jakirkham},
  timestamp = {2013.10.10},
  url = {http://dx.doi.org/10.1038/35080556}
}

@BOOK{Roth2006,
  title = {Introduction to Coding Theory},
  publisher = {Cambridge University Press},
  year = {2006},
  author = {Roth, R.},
  isbn = {9780521845045},
  lccn = {2006280936},
  owner = {jakirkham},
  timestamp = {2013.09.08},
  url = {http://books.google.com/books?id=fk7u8awR0hIC}
}

@ARTICLE{Salathe2008,
  author = {Salath\'{e}, Marcel and Kouyos, Roger D. and Regoes, Roland R. and
	Bonhoeffer, Sebastian and Van Baalen, M.},
  title = {Rapid Parasite Adaptation Drives Selection for High Recombination
	Rates},
  journal = {Evolution},
  year = {2008},
  volume = {62},
  pages = {295--300},
  number = {2},
  month = feb,
  booktitle = {Evolution},
  comment = {doi: 10.1111/j.1558-5646.2007.00265.x},
  doi = {10.1111/j.1558-5646.2007.00265.x},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Salathé, et al -- Rapid Parasite Adaptation Drives Selection for High Recombination Rates.pdf:PDF},
  issn = {0014-3820},
  owner = {jakirkham},
  publisher = {The Society for the Study of Evolution},
  timestamp = {2013.11.10},
  url = {http://dx.doi.org/10.1111/j.1558-5646.2007.00265.x}
}

@ARTICLE{Sasaki1987,
  author = {Sasaki and Iwasa},
  title = {Optimal recombination rate in fluctuating environments.},
  year = {1987},
  pages = {--},
  number = {0016-6731 (Linking)},
  month = {Feb},
  abstract = {The optimal recombination rate which maximizes the long-term geometric
	average of the population fitness is studied for a two-locus haploid
	model, assuming that the fitnesses of genotypes AB, Ab, aB and ab
	are 1 + s(t), 1 - s(t), 1 - s(t), and 1 + s(t), respectively, where
	s(t) follows various stationary stochastic processes with the average
	zero. With positive recombination, the polymorphism is stably maintained
	at both loci. After an initial transient phase, the dynamics are
	reduced to one dimension, and are analyzed for weak selection limit,
	strong selection limit, and selection with two state Markovian jump.
	Results are: (1) If the environmental fluctuation has a predominant
	periodic component, ropt is approximately inversely proportional
	to the period irrespective of selection intensity. (2) If the fluctuation
	is a superposition of many periodic components, the one with the
	longest period is the most effective in determining ropt because
	the genetic dynamics cannot track very quick fluctuations (low pass
	filter effect). (3) If the power spectrum density is decreasing with
	the frequency, as in pink, or 1/f noises, ropt is small when selection
	is weak, and increases with the selection intensity. Numerical calculation
	of the genetic dynamics of a recombination modifier supports all
	these predictions for the evolutionarily stable recombination rate.
	FAU - Sasaki, A},
  doi = {http://www.ncbi.nlm.nih.gov/pubmed/3557117},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Sasaki and Iwasa -- Optimal Recombination Rate in Fluctuating Environments.pdf:PDF},
  owner = {jakirkham},
  timestamp = {2013.08.14},
  url = {http://www.genetics.org/content/115/2/377.long}
}

@ARTICLE{Sniegowski2000,
  author = {Sniegowski, Paul D. and Gerrish, Philip J. and Johnson, Toby and
	Shaver, Aaron},
  title = {The evolution of mutation rates: separating causes from consequences},
  journal = {BioEssays},
  year = {2000},
  volume = {22},
  pages = {1057--1066},
  number = {12},
  doi = {10.1002/1521-1878(200012)22:12<1057::AID-BIES3>3.0.CO;2-W},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Sniegowski, et al -- The evolution of mutation rates- separating causes from consequences.pdf:PDF},
  issn = {1521-1878},
  owner = {jakirkham},
  publisher = {John Wiley \& Sons, Inc.},
  timestamp = {2013.10.10},
  url = {http://dx.doi.org/10.1002/1521-1878(200012)22:12<1057::AID-BIES3>3.0.CO;2-W}
}

@ARTICLE{Sniegowski1997,
  author = {Sniegowski, Paul D. and Gerrish, Philip J. and Lenski, Richard E.},
  title = {Evolution of high mutation rates in experimental populations of E.
	coli},
  journal = {Nature},
  year = {1997},
  volume = {387},
  pages = {703--705},
  number = {6634},
  month = jun,
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Sniegowski, et al -- Evolution of high mutation rates in experimental populations of E coli.pdf:PDF},
  issn = {0028-0836},
  owner = {jakirkham},
  timestamp = {2013.10.10},
  url = {http://www.nature.com/nature/journal/v387/n6634/full/387703a0.html}
}

@ARTICLE{Spratt2001,
  author = {Brian G Spratt and William P Hanage and Edward J Feil},
  title = {The relative contributions of recombination and point mutation to
	the diversification of bacterial clones },
  journal = {Current Opinion in Microbiology },
  year = {2001},
  volume = {4},
  pages = {602 - 606},
  number = {5},
  doi = {http://dx.doi.org/10.1016/S1369-5274(00)00257-5},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Spratt, et al -- The relative contributions of recombination and point mutation to the diversification of bacterial clones.pdf:PDF},
  issn = {1369-5274},
  keywords = {recombination rate},
  owner = {jakirkham},
  timestamp = {2013.10.09},
  url = {http://www.sciencedirect.com/science/article/pii/S1369527400002575}
}

@ARTICLE{Tago2005,
  author = {Yu-ichiro Tago and Masaru Imai and Makoto Ihara and Hironari Atofuji
	and Yuki Nagata and Kazuo Yamamoto},
  title = {Escherichia coli Mutator $\Delta$ polA is Defective in Base Mismatch
	Correction: The Nature of in Vivo \{DNA\} Replication Errors},
  journal = {Journal of Molecular Biology },
  year = {2005},
  volume = {351},
  pages = {299 - 308},
  number = {2},
  doi = {10.1016/j.jmb.2005.06.014},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Tago, et al -- Escherichia coli Mutator delta polA is Defective in Base Mismatch Correction- The Nature of in Vivo DNA Replication Errors.pdf:PDF},
  issn = {0022-2836},
  keywords = {\{SOS\} polymerases},
  owner = {jakirkham},
  timestamp = {2013.05.16},
  url = {http://www.sciencedirect.com/science/article/pii/S0022283605006637}
}

@ARTICLE{Tan2004,
  author = {Tan, Taison and Bogarad, LeonardD. and Deem, MichaelW.},
  title = {Modulation of Base-Specific Mutation and Recombination Rates EnablesFunctional
	Adaptation Within the Context of the Genetic Code},
  journal = {Journal of Molecular Evolution},
  year = {2004},
  volume = {59},
  pages = {385-399},
  doi = {10.1007/s00239-004-2633-8},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Tan, et al -- Modulation of Base-Specific Mutation and Recombination Rates EnablesFunctional Adaptation Within the Context of the Genetic Code.pdf:PDF},
  issn = {0022-2844},
  issue = {3},
  keywords = {Codon usage; Codon mutation matrix; Mutation rate; Recombination rate},
  language = {English},
  owner = {jakirkham},
  publisher = {Springer-Verlag},
  timestamp = {2013.03.18},
  url = {http://dx.doi.org/10.1007/s00239-004-2633-8}
}

@ARTICLE{Tarazona1992,
  author = {Tarazona, P.},
  title = {Error thresholds for molecular quasispecies as phase transitions:
	From simple landscapes to spin-glass models},
  journal = {Phys. Rev. A},
  year = {1992},
  volume = {45},
  pages = {6038--6050},
  month = {Apr},
  doi = {10.1103/PhysRevA.45.6038},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Tarazona -- Error thresholds for molecular quasispecies as phase transitions- From simple landscapes to spin-glass models.pdf:PDF},
  issue = {8},
  owner = {jakirkham},
  publisher = {American Physical Society},
  timestamp = {2013.10.08},
  url = {http://link.aps.org/doi/10.1103/PhysRevA.45.6038}
}

@MANUAL{Team2008,
  title = {SymPy: Python library for symbolic mathematics},
  author = {SymPy Development Team},
  year = {2008},
  owner = {jakirkham},
  timestamp = {2013.10.05},
  url = {http://www.sympy.org}
}

@ARTICLE{Thomas2005,
  author = {Thomas, Christopher M. and Nielsen, Kaare M.},
  title = {Mechanisms of, and Barriers to, Horizontal Gene Transfer between
	Bacteria},
  journal = {Nat Rev Micro},
  year = {2005},
  volume = {3},
  pages = {711--721},
  number = {9},
  month = sep,
  comment = {10.1038/nrmicro1234},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Thomas and Nielsen -- Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria.pdf:PDF},
  issn = {1740-1526},
  owner = {jakirkham},
  publisher = {Nature Publishing Group},
  timestamp = {2013.04.23},
  url = {http://dx.doi.org/10.1038/nrmicro1234}
}

@ARTICLE{Vladar2011,
  author = {Harold P. de Vladar and Nicholas H. Barton},
  title = {The contribution of statistical physics to evolutionary biology },
  journal = {Trends in Ecology \& Evolution },
  year = {2011},
  volume = {26},
  pages = {424 - 432},
  number = {8},
  doi = {10.1016/j.tree.2011.04.002},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/de Vladar and Barton -- The contribution of statistical physics to evolutionary biology.pdf:PDF;Appendices:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/de Vladar and Barton -- The contribution of statistical physics to evolutionary biology, Appendices.pdf:PDF},
  issn = {0169-5347},
  owner = {jakirkham},
  timestamp = {2013.05.13},
  url = {http://www.sciencedirect.com/science/article/pii/S0169534711001108}
}

@ARTICLE{Vos2009,
  author = {Vos, Michiel},
  title = {Why do bacteria engage in homologous recombination?},
  journal = {Trends Microbiol},
  year = {2009},
  volume = {17},
  pages = {226--232},
  number = {6},
  month = jun,
  abstract = {Microbiologists have long recognized that the uptake and incorporation
	of homologous DNA from outside the cell is a common feature of bacteria,
	with important implications for their evolution. However, the exact
	reasons why bacteria engage in homologous recombination remain elusive.
	This Opinion article aims to reinvigorate the debate by examining
	the costs and benefits that homologous recombination could engender
	in natural populations of bacteria. It specifically focuses on the
	hypothesis that homologous recombination is selectively maintained
	because the genetic variation it generates improves the response
	of bacterial populations to natural selection, analogous to sex in
	eukaryotes.},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Vos, Michiel -- Why do bacteria engage in homologous recombination.pdf:PDF},
  issn = {0966-842X},
  owner = {jakirkham},
  publisher = {Elsevier Trends Journals},
  refid = {S0966-842X(09)00086-9 DOI - 10.1016/j.tim.2009.03.001},
  timestamp = {2013.08.14},
  url = {http://linkinghub.elsevier.com/retrieve/pii/S0966842X09000869}
}

@ARTICLE{Wagner1996,
  author = {Wagner, Gunter P. and Altenberg, Lee},
  title = {Perspective: Complex Adaptations and the Evolution of Evolvability},
  journal = {Evolution},
  year = {1996},
  volume = {50},
  pages = {pp. 967-976},
  number = {3},
  abstract = {The problem of complex adaptations is studied in two largely disconnected
	research traditions: evolutionary biology and evolutionary computer
	science. This paper summarizes the results from both areas and compares
	their implications. In evolutionary computer science it was found
	that the Darwinian process of mutation, recombination and selection
	is not universally effective in improving complex systems like computer
	programs or chip designs. For adaptation to occur, these systems
	must possess "evolvability," i.e., the ability of random variations
	to sometimes produce improvement. It was found that evolvability
	critically depends on the way genetic variation maps onto phenotypic
	variation, an issue known as the representation problem. The genotype-phenotype
	map determines the variability of characters, which is the propensity
	to vary Variability needs to be distinguished from variations, which
	are the actually realized differences between individuals. The genotype-phenotype
	map is the common theme underlying such varied biological phenomena
	as genetic canalization, developmental constraints, biological versatility,
	developmental dissociability, and morphological integration. For
	evolutionary biology the representation problem has important implications:
	how is it that extant species acquired a genotype-phenotype map which
	allows improvement by mutation and selection? Is the genotype-phenotype
	map able to change in evolution? What are the selective forces, if
	any, that shape the genotype-phenotype map? We propose that the genotype-phenotype
	map can evolve by two main routes: epistatic mutations, or the creation
	of new genes. A common result for organismic design is inodularity
	By modularity we mean a genotype-phenotype map in which there are
	few pleiotropic effects among characters serving different functions,
	with pleiotropic effects falling mainly among characters that are
	part of a single functional complex. Such a design is expected to
	improve evolvability by limiting the interference between the adaptation
	of different functions. Several population genetic models are reviewed
	that are intended to explain the evolutionary origin of a modular
	design. While our current knowledge is insufficient to assess the
	plausibility of these models, they form the beginning of a framework
	for understanding the evolution of the genotype-phenotype map.},
  copyright = {Copyright © 1996 Society for the Study of Evolution},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Wagner and Altenberg -- Perspective- Complex Adaptations and the Evolution of Evolvability.pdf:PDF},
  issn = {00143820},
  jstor_articletype = {research-article},
  jstor_formatteddate = {Jun., 1996},
  language = {English},
  owner = {jakirkham},
  publisher = {Society for the Study of Evolution},
  timestamp = {2013.10.10},
  url = {http://www.jstor.org/stable/2410639}
}

@ARTICLE{Wang2009,
  author = {Ying A. Wang and Xiong Yu and Philip M. Silverman and Robin L. Harris
	and Edward H. Egelman},
  title = {The Structure of F-Pili },
  journal = {Journal of Molecular Biology },
  year = {2009},
  volume = {385},
  pages = {22 - 29},
  number = {1},
  doi = {10.1016/j.jmb.2008.10.054},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Wang, et al -- The Structure of F-Pili.pdf:PDF},
  issn = {0022-2836},
  keywords = {helical polymers},
  owner = {jakirkham},
  timestamp = {2013.05.15},
  url = {http://www.sciencedirect.com/science/article/pii/S0022283608013430}
}

@ARTICLE{West1999,
  author = {West and Lively and Read},
  title = {A pluralist approach to sex and recombination},
  journal = {Journal of Evolutionary Biology},
  year = {1999},
  volume = {12},
  pages = {1003--1012},
  number = {6},
  abstract = {One of the greatest challenges for evolutionary biology is explaining
	the widespread occurrence of sexual reproduction and the associated
	process of genetic recombination. A large number of theories have
	been developed that provide a sufficient short-term advantage for
	sex to offset its two-fold cost. These theories can be broadly classified
	into environmental (or ecological) and mutation-based models. Traditionally,
	the different theories have been viewed as competing, and empirical
	work has attempted to distinguish between them. Here we highlight
	the advantages that may be gained from considering that multiple
	mechanisms (environmental and mutational) may be at work, and that
	interactions between the theories may be very important.},
  doi = {10.1046/j.1420-9101.1999.00119.x},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/West, et al -- A pluralist approach to sex and recombination.pdf:PDF},
  issn = {1420-9101},
  keywords = {mutation, parasites, recombination, Red Queen, sex},
  owner = {jakirkham},
  publisher = {Blackwell Science Ltd},
  timestamp = {2013.11.10},
  url = {http://dx.doi.org/10.1046/j.1420-9101.1999.00119.x}
}

@ARTICLE{Wilke1999,
  author = {Wilke, Claus O. and Martinetz, Thomas},
  title = {Adaptive walks on time-dependent fitness landscapes},
  journal = {Phys. Rev. E},
  year = {1999},
  volume = {60},
  pages = {2154--2159},
  month = {Aug},
  doi = {10.1103/PhysRevE.60.2154},
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Wilke and Martinetz -- Adaptive walks on time-dependent fitness landscapes.pdf:PDF},
  issue = {2},
  owner = {jakirkham},
  publisher = {American Physical Society},
  timestamp = {2013.11.10},
  url = {http://link.aps.org/doi/10.1103/PhysRevE.60.2154}
}

@ELECTRONIC{Winning2006,
  author = {Dr. Bob Winning},
  year = {2006},
  title = {Recombination in Bacteria},
  address = {http://www.emunix.emich.edu/~rwinning/genetics},
  url = {http://www.emunix.emich.edu/~rwinning/genetics/bactrec.htm},
  owner = {jakirkham},
  timestamp = {2013.05.15}
}

@ELECTRONIC{WolframResearch2001,
  author = {Wolfram Research, Inc.},
  month = {10},
  year = {2001},
  title = {Inverse error function: Series representations (formula 06.29.06.0002)},
  organization = {Wolfram Research, Inc.},
  address = {http://functions.wolfram.com/GammaBetaErf/InverseErf/06/02/0001/},
  url = {http://functions.wolfram.com/GammaBetaErf/InverseErf/06/02/0001/},
  owner = {jakirkham},
  timestamp = {2013.11.11}
}

@ARTICLE{Woodcock1996,
  author = {Woodcock, Glenn and Higgs, Paul G.},
  title = {Population Evolution on a Multiplicative Single-Peak Fitness Landscape},
  journal = {Journal of Theoretical Biology},
  year = {1996},
  volume = {179},
  pages = {61--73},
  number = {1},
  month = mar,
  file = {:/Users/jakirkham/Documents/School/Emory/2012-2013/Summer 2013/Masters Thesis/Papers/Woodcock and Higgs -- Population Evolution on a Multiplicative Single-Peak Fitness Landscape.pdf:PDF},
  issn = {0022-5193},
  owner = {jakirkham},
  timestamp = {2013.10.08},
  url = {http://www.sciencedirect.com/science/article/pii/S0022519396900491}
}

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