popSim.bib

@article{durvasula2017african,
	Author = {Durvasula, Arun and Fulgione, Andrea and Gutaker, Rafal M and Alacakaptan, Selen Irez and Flood, P{\'a}draic J and Neto, C{\'e}lia and Tsuchimatsu, Takashi and Burbano, Hern{\'a}n A and Pic{\'o}, F Xavier and Alonso-Blanco, Carlos and others},
	Date-Added = {2019-11-25 16:09:47 -0800},
	Date-Modified = {2019-11-25 16:09:47 -0800},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {20},
	Pages = {5213--5218},
	Publisher = {National Acad Sciences},
	Title = {African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana},
	Volume = {114},
	Year = {2017}}

@article{sheehan2016deep,
	Author = {Sheehan, Sara and Song, Yun S},
	Date-Added = {2019-11-25 16:08:27 -0800},
	Date-Modified = {2019-11-25 16:08:27 -0800},
	Journal = {PLoS computational biology},
	Number = {3},
	Pages = {e1004845},
	Publisher = {Public Library of Science},
	Title = {Deep learning for population genetic inference},
	Volume = {12},
	Year = {2016}}

@article{tennessen2012evolution,
	Author = {Tennessen, Jacob A and Bigham, Abigail W and O'Connor, Timothy D and Fu, Wenqing and Kenny, Eimear E and Gravel, Simon and McGee, Sean and Do, Ron and Liu, Xiaoming and Jun, Goo and others},
	Date-Added = {2019-11-25 16:07:39 -0800},
	Date-Modified = {2019-11-25 16:07:39 -0800},
	Journal = {science},
	Number = {6090},
	Pages = {64--69},
	Publisher = {American Association for the Advancement of Science},
	Title = {Evolution and functional impact of rare coding variation from deep sequencing of human exomes},
	Volume = {337},
	Year = {2012}}

@article{kong2010fine,
	Author = {Kong, Augustine and Thorleifsson, Gudmar and Gudbjartsson, Daniel F and Masson, Gisli and Sigurdsson, Asgeir and Jonasdottir, Aslaug and Walters, G Bragi and Jonasdottir, Adalbjorg and Gylfason, Arnaldur and Kristinsson, Kari Th and others},
	Date-Added = {2019-11-25 14:10:27 -0800},
	Date-Modified = {2019-11-25 14:10:27 -0800},
	Journal = {Nature},
	Number = {7319},
	Pages = {1099},
	Publisher = {Nature Publishing Group},
	Title = {Fine-scale recombination rate differences between sexes, populations and individuals},
	Volume = {467},
	Year = {2010}}

@article{international2007second,
	Author = {{International HapMap Consortium} and others},
	Date-Added = {2019-11-25 14:09:36 -0800},
	Date-Modified = {2019-11-25 14:09:36 -0800},
	Journal = {Nature},
	Number = {7164},
	Pages = {851},
	Publisher = {Nature Publishing Group},
	Title = {A second generation human haplotype map of over 3.1 million SNPs},
	Volume = {449},
	Year = {2007}}

@article{beichman2017comparison,
	Author = {Beichman, Annabel C and Phung, Tanya N and Lohmueller, Kirk E},
	Date-Added = {2019-11-25 13:38:43 -0800},
	Date-Modified = {2019-11-25 13:38:43 -0800},
	Journal = {G3: Genes, Genomes, Genetics},
	Number = {11},
	Pages = {3605--3620},
	Publisher = {G3: Genes, Genomes, Genetics},
	Title = {Comparison of single genome and allele frequency data reveals discordant demographic histories},
	Volume = {7},
	Year = {2017}}

@article{gutenkunst2009inferring,
	Author = {Gutenkunst, Ryan N and Hernandez, Ryan D and Williamson, Scott H and Bustamante, Carlos D},
	Date-Added = {2019-11-25 13:36:47 -0800},
	Date-Modified = {2019-11-25 13:36:47 -0800},
	Journal = {PLoS genetics},
	Number = {10},
	Pages = {e1000695},
	Publisher = {Public Library of Science},
	Title = {Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data},
	Volume = {5},
	Year = {2009}}

@article{sugden2018localization,
	Author = {Sugden, Lauren Alpert and Atkinson, Elizabeth G and Fischer, Annie P and Rong, Stephen and Henn, Brenna M and Ramachandran, Sohini},
	Date-Added = {2019-11-22 10:40:22 -0800},
	Date-Modified = {2019-11-22 10:40:22 -0800},
	Journal = {Nature communications},
	Number = {1},
	Pages = {703},
	Publisher = {Nature Publishing Group},
	Title = {Localization of adaptive variants in human genomes using averaged one-dependence estimation},
	Volume = {9},
	Year = {2018}}

@article{kern2018diplos,
	Author = {Kern, Andrew D and Schrider, Daniel R},
	Date-Added = {2019-11-22 10:39:49 -0800},
	Date-Modified = {2019-11-22 10:39:49 -0800},
	Journal = {G3: Genes, Genomes, Genetics},
	Number = {6},
	Pages = {1959--1970},
	Publisher = {G3: Genes, Genomes, Genetics},
	Title = {diploS/HIC: an updated approach to classifying selective sweeps},
	Volume = {8},
	Year = {2018}}

@article{degiorgio2016sweepfinder2,
	Author = {DeGiorgio, Michael and Huber, Christian D and Hubisz, Melissa J and Hellmann, Ines and Nielsen, Rasmus},
	Date-Added = {2019-11-22 10:38:45 -0800},
	Date-Modified = {2019-11-22 10:38:45 -0800},
	Journal = {Bioinformatics},
	Number = {12},
	Pages = {1895--1897},
	Publisher = {Oxford University Press},
	Title = {SweepFinder2: increased sensitivity, robustness and flexibility},
	Volume = {32},
	Year = {2016}}

@article{alachiotis2012omegaplus,
	Author = {Alachiotis, Nikolaos and Stamatakis, Alexandros and Pavlidis, Pavlos},
	Date-Added = {2019-11-22 10:38:11 -0800},
	Date-Modified = {2019-11-22 10:38:11 -0800},
	Journal = {Bioinformatics},
	Number = {17},
	Pages = {2274--2275},
	Publisher = {Oxford University Press},
	Title = {OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets},
	Volume = {28},
	Year = {2012}}

@article{eyre2009estimating,
	Author = {Eyre-Walker, Adam and Keightley, Peter D},
	Date-Added = {2019-11-22 10:34:54 -0800},
	Date-Modified = {2019-11-22 10:34:54 -0800},
	Journal = {Molecular biology and evolution},
	Number = {9},
	Pages = {2097--2108},
	Publisher = {Oxford University Press},
	Title = {Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change},
	Volume = {26},
	Year = {2009}}

@article{kim2017inference,
	Author = {Kim, Bernard Y and Huber, Christian D and Lohmueller, Kirk E},
	Date-Added = {2019-11-22 10:34:02 -0800},
	Date-Modified = {2019-11-22 10:34:02 -0800},
	Journal = {Genetics},
	Number = {1},
	Pages = {345--361},
	Publisher = {Genetics Soc America},
	Title = {Inference of the distribution of selection coefficients for new nonsynonymous mutations using large samples},
	Volume = {206},
	Year = {2017}}

@article{terhorst2017robust,
	Author = {Terhorst, Jonathan and Kamm, John A and Song, Yun S},
	Date-Added = {2019-11-22 10:32:59 -0800},
	Date-Modified = {2019-11-22 10:32:59 -0800},
	Journal = {Nature genetics},
	Number = {2},
	Pages = {303},
	Publisher = {Nature Publishing Group},
	Title = {Robust and scalable inference of population history from hundreds of unphased whole genomes},
	Volume = {49},
	Year = {2017}}

@article{liu2015exploring,
	Author = {Liu, Xiaoming and Fu, Yun-Xin},
	Date-Added = {2019-11-22 10:32:41 -0800},
	Date-Modified = {2019-11-22 10:32:41 -0800},
	Journal = {Nature genetics},
	Number = {5},
	Pages = {555},
	Publisher = {Nature Publishing Group},
	Title = {Exploring population size changes using SNP frequency spectra},
	Volume = {47},
	Year = {2015}}

@article{schiffels2014inferring,
	Author = {Schiffels, Stephan and Durbin, Richard},
	Date-Added = {2019-11-22 10:32:22 -0800},
	Date-Modified = {2019-11-22 10:32:22 -0800},
	Journal = {Nature genetics},
	Number = {8},
	Pages = {919},
	Publisher = {Nature Publishing Group},
	Title = {Inferring human population size and separation history from multiple genome sequences},
	Volume = {46},
	Year = {2014}}

@article{li2011inference,
	Author = {Li, Heng and Durbin, Richard},
	Date-Added = {2019-11-22 10:32:04 -0800},
	Date-Modified = {2019-11-22 10:32:04 -0800},
	Journal = {Nature},
	Number = {7357},
	Pages = {493},
	Publisher = {Nature Publishing Group},
	Title = {Inference of human population history from individual whole-genome sequences},
	Volume = {475},
	Year = {2011}}

@article{haller2019tree,
	Author = {Haller, Benjamin C and Galloway, Jared and Kelleher, Jerome and Messer, Philipp W and Ralph, Peter L},
	Journal = {Molecular ecology resources},
	Number = {2},
	Pages = {552--566},
	Publisher = {Wiley Online Library},
	Title = {Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes},
	Volume = {19},
	Year = {2019}}

@article{kelleher2018efficient,
	Abstract = {Author summary Sexually reproducing organisms are related to the others in their species by the complex web of parent-offspring relationships that constitute the pedigree. In this paper, we describe a way to record all of these relationships, as well as how genetic material is passed down through the pedigree, during a forwards-time population genetic simulation. To make effective use of this information, we describe both efficient storage methods for this embellished pedigree as well as a way to remove all information that is irrelevant to the genetic history of a given set of individuals, which dramatically reduces the required amount of storage space. Storing this information allows us to produce whole-genome sequence from simulations of large populations in which we have not explicitly recorded new genomic mutations; we find that this results in computational run times of up to 50 times faster than simulations forced to explicitly carry along that information.},
	Added-At = {2018-12-09T17:30:18.000+0100},
	Author = {Kelleher, Jerome and Thornton, Kevin R. and Ashander, Jaime and Ralph, Peter L.},
	Biburl = {https://www.bibsonomy.org/bibtex/2a4f12f0bb2d13faee628fec0fc2679b8/peter.ralph},
	Description = {Efficient pedigree recording for fast population genetics simulation},
	Doi = {10.1371/journal.pcbi.1006581},
	Interhash = {b855fb1dfdb8542b91b86dff2be80c63},
	Intrahash = {a4f12f0bb2d13faee628fec0fc2679b8},
	Journal = {PLOS Computational Biology},
	Keywords = {ARG methods myown simulation software tree_sequence},
	Month = {11},
	Number = 11,
	Pages = {1-21},
	Publisher = {Public Library of Science},
	Timestamp = {2018-12-09T17:30:18.000+0100},
	Title = {Efficient pedigree recording for fast population genetics simulation},
	Url = {https://doi.org/10.1371/journal.pcbi.1006581},
	Volume = 14,
	Year = 2018,
	Bdsk-Url-1 = {https://doi.org/10.1371/journal.pcbi.1006581}}

@article{Adrion662247,
	Abstract = {Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim in genomics, as patterns of linkage influence everything from genetic mapping to understanding evolutionary history. Here we describe ReLERNN, a deep learning method for accurately estimating a genome-wide recombination landscape using as few as four samples. Rather than use summaries of linkage disequilibrium as its input, ReLERNN considers columns from a genotype alignment, which are then modeled as a sequence across the genome using a recurrent neural network. We demonstrate that ReLERNN improves accuracy and reduces bias relative to existing methods and maintains high accuracy in the face of demographic model misspecification. We apply ReLERNN to natural populations of African Drosophila melanogaster and show that genome-wide recombination landscapes, while largely correlated among populations, exhibit important population-specific differences. Lastly, we connect the inferred patterns of recombination with the frequencies of major inversions segregating in natural Drosophila populations.},
	Author = {Adrion, Jeffrey R. and Galloway, Jared G. and Kern, Andrew D.},
	Doi = {10.1101/662247},
	Elocation-Id = {662247},
	Eprint = {https://www.biorxiv.org/content/early/2019/06/06/662247.full.pdf},
	Journal = {bioRxiv},
	Publisher = {Cold Spring Harbor Laboratory},
	Title = {Inferring the landscape of recombination using recurrent neural networks},
	Url = {https://www.biorxiv.org/content/early/2019/06/06/662247},
	Year = {2019},
	Bdsk-Url-1 = {https://www.biorxiv.org/content/early/2019/06/06/662247},
	Bdsk-Url-2 = {https://doi.org/10.1101/662247}}

@article{kelleher2016efficient,
	Author = {Kelleher, Jerome and Etheridge, Alison M and McVean, Gilean},
	Date-Added = {2018-11-09 11:18:34 -0800},
	Date-Modified = {2018-11-09 11:18:34 -0800},
	Journal = {PLoS computational biology},
	Number = {5},
	Pages = {e1004842},
	Publisher = {Public Library of Science},
	Title = {Efficient coalescent simulation and genealogical analysis for large sample sizes},
	Volume = {12},
	Year = {2016}}

@article{lin2013fast,
	Author = {Lin, Kao and Futschik, Andreas and Li, Haipeng},
	Date-Added = {2018-11-09 10:35:44 -0800},
	Date-Modified = {2018-11-09 10:35:44 -0800},
	Journal = {Genetics},
	Pages = {genetics--113},
	Publisher = {Genetics Soc America},
	Title = {A fast estimate for the population recombination rate based on regression},
	Year = {2013}}

@article{chan2012genome,
	Author = {Chan, Andrew H and Jenkins, Paul A and Song, Yun S},
	Date-Added = {2018-11-09 10:29:39 -0800},
	Date-Modified = {2018-11-09 10:29:39 -0800},
	Journal = {PLoS genetics},
	Number = {12},
	Pages = {e1003090},
	Publisher = {Public Library of Science},
	Title = {Genome-wide fine-scale recombination rate variation in Drosophila melanogaster},
	Volume = {8},
	Year = {2012}}


@article{haller2018tree,
	Author = {Haller, Benjamin C and Galloway, Jared and Kelleher, Jerome and Messer, Philipp W and Ralph, Peter L},
	Journal = {Molecular ecology resources},
	Publisher = {Wiley Online Library},
	Title = {Tree-sequence recording in {SLiM} opens new horizons for forward-time simulation of whole genomes},
	Year = {2018}}

@article{kelleher2019inferring,
	Added-At = {2019-09-11T22:02:19.000+0200},
	Author = {Kelleher, Jerome and Wong, Yan and Wohns, Anthony W. and Fadil, Chaimaa and Albers, Patrick K. and McVean, Gil},
	Biburl = {https://www.bibsonomy.org/bibtex/2d3c11b81ec3003c314454ff82fc67927/peter.ralph},
	Doi = {10.1038/s41588-019-0483-y},
	Interhash = {595cf803356d1c356a806a7eb973190e},
	Intrahash = {d3c11b81ec3003c314454ff82fc67927},
	Issn = {15461718},
	Journal = {Nature Genetics},
	Keywords = {methods tree_sequence tree_sequence_inference},
	Number = 9,
	Pages = {1330--1338},
	Refid = {Kelleher2019},
	Timestamp = {2019-09-11T22:02:19.000+0200},
	Title = {Inferring whole-genome histories in large population datasets},
	Url = {https://doi.org/10.1038/s41588-019-0483-y},
	Volume = 51,
	Year = 2019,
	Bdsk-Url-1 = {https://doi.org/10.1038/s41588-019-0483-y}}

@article{haller2019slim,
	Author = {Haller, Benjamin C and Messer, Philipp W},
	Journal = {Molecular biology and evolution},
	Number = {3},
	Pages = {632--637},
	Publisher = {Oxford University Press},
	Title = {{SLiM} 3: forward genetic simulations beyond the {Wright--Fisher} model},
	Volume = {36},
	Year = {2019}}

@article{ragsdale2019models,
  title={Models of archaic admixture and recent history from two-locus statistics},
  author={Ragsdale, Aaron P and Gravel, Simon},
  journal={PLoS genetics},
  volume={15},
  number={6},
  pages={e1008204},
  year={2019},
  publisher={Public Library of Science}
}

@article{browning2018ancestry,
  title={Ancestry-specific recent effective population size in the Americas},
  author={Browning, Sharon R and Browning, Brian L and Daviglus, Martha L and Durazo-Arvizu, Ramon A and Schneiderman, Neil and Kaplan, Robert C and Laurie, Cathy C},
  journal={PLoS genetics},
  volume={14},
  number={5},
  pages={e1007385},
  year={2018},
  publisher={Public Library of Science}
}

@article{li2006inferring,
  title={Inferring the demographic history and rate of adaptive substitution in Drosophila},
  author={Li, Haipeng and Stephan, Wolfgang},
  journal={PLoS genetics},
  volume={2},
  number={10},
  pages={e166},
  year={2006},
  publisher={Public Library of Science}
}

@article{koster2012snakemake,
  title={Snakemake---a scalable bioinformatics workflow engine},
  author={K{\"o}ster, Johannes and Rahmann, Sven},
  journal={Bioinformatics},
  volume={28},
  number={19},
  pages={2520--2522},
  year={2012},
  publisher={Oxford University Press}
}

@article{comeron2012many,
  title={The many landscapes of recombination in {\textit{Drosophila} melanogaster}},
  author={Comeron, Josep M and Ratnappan, Ramesh and Bailin, Samuel},
  journal={PLoS genetics},
  volume={8},
  number={10},
  pages={e1002905},
  year={2012},
  publisher={Public Library of Science}
}

@article{excoffier2013robust,
  title={Robust Demographic Inference from Genomic and {SNP} Data},
  author={Excoffier, Laurent and Dupanloup, Isabelle and Huerta-S\'anchez, Emilia, and Sousa, Vitor C and Foll, Matthieu},
  journal={PLoS genetics},
  volume={9},
  issue={10},
  pages={e1003905},
  year={2013},
  publisher={Public Library of Science}
}

@article{danecek20111000,
  title={1000 Genomes Project Analysis Group (2011)},
  author={Danecek, Petr and Auton, Adam and Abecasis, Goncalo and Albers, Cornelis A and Banks, Eric and DePristo, Mark A and Handsaker, Robert E and Lunter, Gerton and Marth, Gabor T and Sherry, Stephen T and others},
  journal={The variant call format and VCFtools. Bioinformatics},
  volume={27},
  number={15},
  pages={2156--2158},
  year={2011}
}

@article{langley2012genomic,
  title={Genomic variation in natural populations of Drosophila melanogaster},
  author={Langley, Charles H and Stevens, Kristian and Cardeno, Charis and Lee, Yuh Chwen G and Schrider, Daniel R and Pool, John E and Langley, Sasha A and Suarez, Charlyn and Corbett-Detig, Russell B and Kolaczkowski, Bryan and others},
  journal={Genetics},
  volume={192},
  number={2},
  pages={533--598},
  year={2012},
  publisher={Genetics Soc America}
}

@article{moult1995large,
  title={A large-scale experiment to assess protein structure prediction methods},
  author={Moult, John and Pedersen, Jan T and Judson, Richard and Fidelis, Krzysztof},
  journal={Proteins: Structure, Function, and Bioinformatics},
  volume={23},
  number={3},
  pages={ii--iv},
  year={1995},
  publisher={Wiley Online Library}
}

@article{russakovsky2015imagenet,
  title={Imagenet large scale visual recognition challenge},
  author={Russakovsky, Olga and Deng, Jia and Su, Hao and Krause, Jonathan and Satheesh, Sanjeev and Ma, Sean and Huang, Zhiheng and Karpathy, Andrej and Khosla, Aditya and Bernstein, Michael and others},
  journal={International journal of computer vision},
  volume={115},
  number={3},
  pages={211--252},
  year={2015},
  publisher={Springer}
}