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@Article{ harris2020array,
title = {Array programming with {NumPy}},
author = {Charles R. Harris and K. Jarrod Millman and St{\'{e}}fan J.
van der Walt and Ralf Gommers and Pauli Virtanen and David
Cournapeau and Eric Wieser and Julian Taylor and Sebastian
Berg and Nathaniel J. Smith and Robert Kern and Matti Picus
and Stephan Hoyer and Marten H. van Kerkwijk and Matthew
Brett and Allan Haldane and Jaime Fern{\'{a}}ndez del
R{\'{i}}o and Mark Wiebe and Pearu Peterson and Pierre
G{\'{e}}rard-Marchant and Kevin Sheppard and Tyler Reddy and
Warren Weckesser and Hameer Abbasi and Christoph Gohlke and
Travis E. Oliphant},
year = {2020},
month = sep,
journal = {Nature},
volume = {585},
number = {7825},
pages = {357--362},
doi = {10.1038/s41586-020-2649-2},
publisher = {Springer Science and Business Media {LLC}},
url = {https://doi.org/10.1038/s41586-020-2649-2}
}
@article{boi2021,
title={Gene banks as reservoirs to detect recent selection: the example of the Asturiana de los Valles bovine breed},
author={Boitard, Simon and Paris, Cyriel and Sevane, Natalia and Servin, Bertrand and Bazi-Kabbaj, Kenza and Dunner, Susana},
journal={Frontiers in genetics},
volume={12},
year={2021},
publisher={Frontiers Media SA}
}
@article{boi2023,
title={Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines},
author={Boitard, Simon and Liaubet, Laurence and Paris, Cyriel and F{\`e}ve, Katia and Dehais, Patrice and Bouquet, Alban and Riquet, Juliette and Mercat, Marie-Jos{\'e}},
journal={Genetics Selection Evolution},
volume={55},
number={1},
pages={13},
year={2023},
publisher={Springer}
}
@article{bol2008,
author = "Bollback, Jonathan P. and York, Thomas L. and Nielsen, Rasmus",
journal = "Genetics",
localfile = "Source/Estimation of 2Nes from temporal allele frequency data - Bollback (2008).pdf",
title = "{Estimation of $2N_es$ from temporal allele frequency data}",
x-color = "#009966",
year = "2008"
}
@misc{compareHMM,
author = {Paris, Cyriel and Servin, Bertrand and Boitard, Simon},
title = {compareHMM},
year = {2019},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/CyrielParis/compareHMM}
}
@article{fag2019,
author = "{Fages Antoine} and {Hangh{\o}j Kristian} and {Khan Naveed} and {Gaunitz Charleen} and {Seguin-Orlando Andaine} and {Leonardi Michela} and {McCrory Constantz Christian} and {Gamba Cristina} and {Al-Rasheid Khaled A.S.} and {Albizuri Silvia} and {Alfarhan Ahmed H.} and {Allentoft Morten} and {Alquraishi Saleh} and {Anthony David} and {Baimukhanov Nurbol} and {Barrett James H.} and {Bayarsaikhan Jamsranjav} and {Benecke Norbert} and {Bern{\'a}ldez-S{\'a}nchez Elo{\'i}sa} and {Berrocal-Rangel Luis} and {Biglari Fereidoun} and {Boessenkool Sanne} and {Boldgiv Bazartseren} and {Brem Gottfried} and {Brown Dorcas} and {Burger Joachim} and {Crub{\'e}zy Eric} and {Daugnora Linas} and {Davoudi Hossein} and Peter, de Barros Damgaard and Mar{\'i}a, de los {\'A}ngeles de Chorro y de Villa-Ceballos and {Deschler-Erb Sabine} and {Detry Cleia} and {Dill Nadine} and Maria, do Mar Oom and {Dohr Anna} and {Ellingv{\aa}g Sturla} and {Erdenebaatar Diimaajav} and {Fathi Homa} and {Felkel Sabine} and {Fern{\'a}ndez-Rodr{\'i}guez Carlos} and {Garc{\'i}a-Vi{\~n}as Esteban} and {Germonpr{\'e} Mietje} and {Granado Jos{\'e} D.} and {Hallsson J{\'o}n H.} and {Hemmer Helmut} and {Hofreiter Michael} and {Kasparov Aleksei} and {Khasanov Mutalib} and {Khazaeli Roya} and {Kosintsev Pavel} and {Kristiansen Kristian} and {Kubatbek Tabaldiev} and {Kuderna Lukas} and {Kuznetsov Pavel} and {Laleh Haeedeh} and {Leonard Jennifer A.} and {Lhuillier Johanna} and {Liesau von Lettow-Vorbeck Corina} and {Logvin Andrey} and {Lõugas Lembi} and {Ludwig Arne} and {Luis Cristina} and {Arruda Ana Margarida} and {Marques-Bonet Tomas} and {Matoso Silva Raquel} and {Merz Victor} and {Mijiddorj Enkhbayar} and {Miller Bryan K.} and {Monchalov Oleg} and {Mohaseb Fatemeh A.} and {Morales Arturo} and {Nieto-Espinet Ariadna} and {Nistelberger Heidi} and {Onar Vedat} and {P{\'a}lsd{\'o}ttir Alb{\'i}na H.} and {Pitulko Vladimir} and {Pitskhelauri Konstantin} and {Pruvost M{\'e}lanie} and {Rajic Sikanjic Petra} and {Rapan Pape\v{s}a Anita} and {Roslyakova Natalia} and {Sardari Alireza} and {Sauer Eberhard} and {Schafberg Renate} and {Scheu Amelie} and {Schibler J{\"o}rg} and {Schlumbaum Angela} and {Serrand Nathalie} and {Serres-Armero Aitor} and {Shapiro Beth} and {Sheikhi Seno Shiva} and {Shevnina Irina} and {Shidrang Sonia} and {Southon John} and {Star Bastiaan} and {Sykes Naomi} and {Taheri Kamal} and {Taylor William} and {Teegen Wolf-R{\"u}diger} and {Trbojevi{\'c} Vuki\v{c}evi{\'c} Tajana} and {Trixl Simon} and {Tumen Dashzeveg} and {Undrakhbold Sainbileg} and {Usmanova Emma} and {Vahdati Ali} and {Valenzuela-Lamas Silvia} and {Viegas Catarina} and {Wallner Barbara} and {Weinstock Jaco} and {Zaibert Victor} and {Clavel Benoit} and {Lepetz S{\'e}bastien} and {Mashkour Marjan} and {Helgason Agnar} and {Stef{\'a}nsson K{\'a}ri} and {Barrey Eric} and {Willerslev Eske} and {Outram Alan K.} and {Librado Pablo} and {Orlando Ludovic}",
issn = "0092-8674",
journal = "Cell",
number = "6",
pages = "1419--1435.e31",
publisher = "Elsevier",
title = "{Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series}",
volume = "177",
year = "2019"
}
@article{hui2015,
author = "Hui, Tin-Yu J. and Burt, Austin",
issn = "0016-6731",
journal = "Genetics",
number = "1",
pages = "285--293",
publisher = "Genetics",
title = "{Estimating Effective Population Size from Temporally Spaced Samples with a Novel, Efficient Maximum-Likelihood Algorithm}",
volume = "200",
year = "2015"
}
@article{lon2015,
title={Elucidating the molecular architecture of adaptation via evolve and resequence experiments},
author={Long, Anthony and Liti, Gianni and Luptak, Andrej and Tenaillon, Olivier},
journal={Nature Reviews Genetics},
volume={16},
number={10},
pages={567--582},
year={2015},
publisher={Nature Publishing Group UK London}
}
@article{mal2015,
author = "Malaspinas, Anna-Sapfo",
journal = "Molecular Ecology",
month = nov,
number = "1",
pages = "24--41",
title = "{Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective}",
volume = "25",
year = "2015"
}
@misc{nb,
author = {"Hui, Tin-Yu J."},
title = {NB: Maximum Likelihood method in estimating effective population size from genetic data},
year = {2014},
publisher = {CRAN},
journal = {CRAN repository},
url = {https://cran.r-project.org/web/packages/NB}
}
@article{par2019,
title={Inference of selection from genetic time series using various parametric approximations to the Wright-Fisher model},
author={Paris, Cyriel and Servin, Bertrand and Boitard, Simon},
journal={G3: Genes, Genomes, Genetics},
volume={9},
number={12},
pages={4073--4086},
year={2019},
publisher={Oxford University Press}
}
@article{tat2015,
author = "Tataru, Paula and Bataillon, Thomas and Hobolth, Asger",
doi = "10.1534/genetics.115.179606",
eprint = "https://www.genetics.org/content/201/3/1133.full.pdf",
issn = "0016-6731",
journal = "Genetics",
number = "3",
pages = "1133--1141",
publisher = "Genetics",
title = "{Inference under a wright-fisher model using an accurate beta approximation}",
url = "https://www.genetics.org/content/201/3/1133",
volume = "201",
year = 2015
}