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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 = {k-distribution, m-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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