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Volumn 12, Issue 3, 2016, Pages

Deep Learning for Population Genetic Inference

Author keywords

[No Author keywords available]

Indexed keywords

DEEP LEARNING; GENES; MULTILAYER NEURAL NETWORKS; POPULATION DYNAMICS; POPULATION STATISTICS;

EID: 84962045150     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004845     Document Type: Article
Times cited : (193)

References (72)
  • 1
    • 84892142922 scopus 로고    scopus 로고
    • Computer science: The learning machines
    • 24402264, .;()
    • Jones N, Computer science: The learning machines. Nature. 2014;505(7482):146. doi: 10.1038/505146a24402264
    • (2014) Nature , vol.505 , Issue.7482 , pp. 146
    • Jones, N.1
  • 2
    • 84155170973 scopus 로고    scopus 로고
    • Joint analysis of demography and selection in population genetics: where do we stand and where could we go?
    • .;():
    • Li J, Li H, Jakobsson M, Li S, Sjödin P, Lascoux M, Joint analysis of demography and selection in population genetics: where do we stand and where could we go?Molecular Ecology. 2012;21(1):28–44.
    • (2012) Molecular Ecology , vol.21 , Issue.1 , pp. 28-44
    • Li, J.1    Li, H.2    Jakobsson, M.3    Li, S.4    Sjödin, P.5    Lascoux, M.6
  • 3
    • 84871785145 scopus 로고    scopus 로고
    • Demographic inference reveals African and European admixture in the North American Drosophila melanogaster population
    • 23150605, .;():
    • Duchen P, Živković D, Hutter S, Stephan W, Laurent S, Demographic inference reveals African and European admixture in the North American Drosophila melanogaster population. Genetics. 2013;193(1):291–301. doi: 10.1534/genetics.112.14591223150605
    • (2013) Genetics , vol.193 , Issue.1 , pp. 291-301
    • Duchen, P.1    Živković, D.2    Hutter, S.3    Stephan, W.4    Laurent, S.5
  • 4
    • 60149111297 scopus 로고    scopus 로고
    • Inferring the Strength of Selection in Drosophila under Complex Demographic Models
    • 19033258, .;():
    • González J, Macpherson JM, Messer PW, Petrov DA, Inferring the Strength of Selection in Drosophila under Complex Demographic Models. Molecular Biology and Evolution. 2009;26(3):513–526. doi: 10.1093/molbev/msn27019033258
    • (2009) Molecular Biology and Evolution , vol.26 , Issue.3 , pp. 513-526
    • González, J.1    Macpherson, J.M.2    Messer, P.W.3    Petrov, D.A.4
  • 5
    • 67651050074 scopus 로고    scopus 로고
    • Pervasive natural selection in the Drosophila genome?
    • 19503600, .;()
    • Sella G, Petrov DA, Przeworski M, Andolfatto P, Pervasive natural selection in the Drosophila genome?PLoS Genetics. 2009;5(6):e1000495. doi: 10.1371/journal.pgen.100049519503600
    • (2009) PLoS Genetics , vol.5 , Issue.6 , pp. 1000495
    • Sella, G.1    Petrov, D.A.2    Przeworski, M.3    Andolfatto, P.4
  • 6
    • 84924966448 scopus 로고    scopus 로고
    • The Drosophila Genome Nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population
    • 25631317, ..;():
    • Lack JB, Cardeno CM, Crepeau MW, Taylor W, Corbett-Detig RB, Stevens KA, et al. The Drosophila Genome Nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population. Genetics. 2015;199(4):1229–1241. doi: 10.1534/genetics.115.17466425631317
    • (2015) Genetics , vol.199 , Issue.4 , pp. 1229-1241
    • Lack, J.B.1    Cardeno, C.M.2    Crepeau, M.W.3    Taylor, W.4    Corbett-Detig, R.B.5    Stevens, K.A.6
  • 7
    • 77955759338 scopus 로고    scopus 로고
    • Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations
    • 20407129, .;:
    • Pavlidis P, Jensen JD, Stephan W, Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics. 2010;185:907–922. doi: 10.1534/genetics.110.11645920407129
    • (2010) Genetics , vol.185 , pp. 907-922
    • Pavlidis, P.1    Jensen, J.D.2    Stephan, W.3
  • 8
    • 84883252048 scopus 로고    scopus 로고
    • SweeD: likelihood-based detection of selective sweeps in thousands of genomes
    • 23777627, .;():
    • Pavlidis P, Živković D, Stamatakis A, Alachiotis N, SweeD: likelihood-based detection of selective sweeps in thousands of genomes. Molecular Biology and Evolution. 2013;30(9):2224–2224. doi: 10.1093/molbev/mst11223777627
    • (2013) Molecular Biology and Evolution , vol.30 , Issue.9 , pp. 2224
    • Pavlidis, P.1    Živković, D.2    Stamatakis, A.3    Alachiotis, N.4
  • 9
    • 84883794892 scopus 로고    scopus 로고
    • Learning natural selection from the site frequency spectrum
    • 23770700, .;:
    • Ronen R, Udpa N, Halperin E, Bafna V, Learning natural selection from the site frequency spectrum. Genetics. 2013;195:181–193. doi: 10.1534/genetics.113.15258723770700
    • (2013) Genetics , vol.195 , pp. 181-193
    • Ronen, R.1    Udpa, N.2    Halperin, E.3    Bafna, V.4
  • 10
    • 78951472188 scopus 로고    scopus 로고
    • Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics
    • 21041556, .;:
    • Lin K, Li H, Schlötterer C, Futschik A, Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics. Genetics. 2011;187:229–244. doi: 10.1534/genetics.110.12261421041556
    • (2011) Genetics , vol.187 , pp. 229-244
    • Lin, K.1    Li, H.2    Schlötterer, C.3    Futschik, A.4
  • 11
    • 84878616246 scopus 로고    scopus 로고
    • A fast estimate for the population recombination rate based on regression
    • 23589457, .;:
    • Lin K, Futschik A, Li H, A fast estimate for the population recombination rate based on regression. Genetics. 2013;194:473–484. doi: 10.1534/genetics.113.15020123589457
    • (2013) Genetics , vol.194 , pp. 473-484
    • Lin, K.1    Futschik, A.2    Li, H.3
  • 12
    • 84950272772 scopus 로고    scopus 로고
    • Hierarchical Boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations
    • 26315912, ..;In pres
    • Pybus M, Luisi P, Dall’Olio G, Uzkundun M, Laayouni H, Bertranpetit J, et al. Hierarchical Boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations. Bioinformatics. 2015;In press. doi: 10.1093/bioinformatics/btv49326315912
    • (2015) Bioinformatics
    • Pybus, M.1    Luisi, P.2    Dall’Olio, G.3    Uzkundun, M.4    Laayouni, H.5    Bertranpetit, J.6
  • 13
    • 79960914105 scopus 로고    scopus 로고
    • Inference of human population history from individual whole-genome sequences
    • 21753753, .;:
    • Li H, Durbin R, Inference of human population history from individual whole-genome sequences. Nature. 2011;475:493–496. doi: 10.1038/nature1023121753753
    • (2011) Nature , vol.475 , pp. 493-496
    • Li, H.1    Durbin, R.2
  • 14
    • 84879621036 scopus 로고    scopus 로고
    • Estimating variable effective population sizes from multiple genomes: A sequentially Markov conditional sampling distribution approach
    • 23608192, .;():
    • Sheehan S, Harris K, Song YS, Estimating variable effective population sizes from multiple genomes: A sequentially Markov conditional sampling distribution approach. Genetics. 2013;194(3):647–662. doi: 10.1534/genetics.112.14909623608192
    • (2013) Genetics , vol.194 , Issue.3 , pp. 647-662
    • Sheehan, S.1    Harris, K.2    Song, Y.S.3
  • 15
    • 84962082415 scopus 로고    scopus 로고
    • Steinrücken M, Kamm JA, Song YS. Inference of complex population histories using whole-genome sequences from multiple populations; 2015. BioRxiv preprin
    • Steinrücken M, Kamm JA, Song YS. Inference of complex population histories using whole-genome sequences from multiple populations; 2015. BioRxiv preprint, http://dx.doi.org/10.1101/026591.
  • 16
    • 84905572361 scopus 로고    scopus 로고
    • Inferring human population size and separation history from multiple genome sequences
    • 24952747, .;:
    • Schiffels S, Durbin R, Inferring human population size and separation history from multiple genome sequences. Nature Genetics. 2014;46:919–925. doi: 10.1038/ng.301524952747
    • (2014) Nature Genetics , vol.46 , pp. 919-925
    • Schiffels, S.1    Durbin, R.2
  • 17
    • 0034086970 scopus 로고    scopus 로고
    • Detecting bottlenecks and selective sweeps from DNA sequence polymorphism
    • 10835415, .;:
    • Galtier N, Depaulis F, Barton NH, Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics. 2000;155:981–987. 10835415
    • (2000) Genetics , vol.155 , pp. 981-987
    • Galtier, N.1    Depaulis, F.2    Barton, N.H.3
  • 18
    • 83455243192 scopus 로고    scopus 로고
    • Quantifying the variation in the effective population size within a genome
    • 21954163, .;:
    • Gossmann TI, Woolfit M, Eyre-Walker A, Quantifying the variation in the effective population size within a genome. Genetics. 2011;189:1389–1402. doi: 10.1534/genetics.111.13265421954163
    • (2011) Genetics , vol.189 , pp. 1389-1402
    • Gossmann, T.I.1    Woolfit, M.2    Eyre-Walker, A.3
  • 19
    • 0032735986 scopus 로고    scopus 로고
    • Population growth of human Y chromosomes: a study of Y chromosome microsatellites
    • 10605120, .;():
    • Pritchard JK, Seielstad MT, Perez-Lezaun A, Feldman MW, Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Molecular Biology and Evolution. 1999;16(12):1791–1798. doi: 10.1093/oxfordjournals.molbev.a02609110605120
    • (1999) Molecular Biology and Evolution , vol.16 , Issue.12 , pp. 1791-1798
    • Pritchard, J.K.1    Seielstad, M.T.2    Perez-Lezaun, A.3    Feldman, M.W.4
  • 20
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian Computation in Population Genetics
    • 12524368, .;():
    • Beaumont MA, Zhang W, Balding DJ, Approximate Bayesian Computation in Population Genetics. Genetics. 2002;162(4):2025–2035. 12524368
    • (2002) Genetics , vol.162 , Issue.4 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 21
    • 34948847222 scopus 로고    scopus 로고
    • A new approach to estimate parameters of speciation models with application to apes
    • 17712021, .;():
    • Becquet C, Przeworski M, A new approach to estimate parameters of speciation models with application to apes. Genome Res. 2007;17(10):1505–19. doi: 10.1101/gr.640970717712021
    • (2007) Genome Res , vol.17 , Issue.10 , pp. 1505-1519
    • Becquet, C.1    Przeworski, M.2
  • 22
    • 52949128377 scopus 로고    scopus 로고
    • An approximate Bayesian estimator suggests strong, recurrent selective sweeps in Drosophila
    • 18802463, .;()
    • Jensen JD, Thornton KR, Andolfatto P, An approximate Bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLoS Genetics. 2008;4(9):e1000198. doi: 10.1371/journal.pgen.100019818802463
    • (2008) PLoS Genetics , vol.4 , Issue.9 , pp. 1000198
    • Jensen, J.D.1    Thornton, K.R.2    Andolfatto, P.3
  • 23
    • 84868152411 scopus 로고    scopus 로고
    • Distinguishing between selective sweeps from standing variation and from a de novo mutation
    • 23071458, .;()
    • Peter BM, Huerta-Sanchez E, Nielsen R, Distinguishing between selective sweeps from standing variation and from a de novo mutation. PLoS Genetics. 2012;8(10):e1003011. doi: 10.1371/journal.pgen.100301123071458
    • (2012) PLoS Genetics , vol.8 , Issue.10 , pp. 1003011
    • Peter, B.M.1    Huerta-Sanchez, E.2    Nielsen, R.3
  • 24
    • 0346734143 scopus 로고    scopus 로고
    • Markov chain Monte Carlo without likelihoods
    • 14663152, .;():
    • Marjoram P, Molitor J, Plagnol V, Tavare S, Markov chain Monte Carlo without likelihoods. PNAS. 2003;100(26):15324–8. doi: 10.1073/pnas.030689910014663152
    • (2003) PNAS , vol.100 , Issue.26 , pp. 15324-15328
    • Marjoram, P.1    Molitor, J.2    Plagnol, V.3    Tavare, S.4
  • 26
    • 51449104123 scopus 로고    scopus 로고
    • Approximately sufficient statistics and Bayesian computation
    • 18764775, .;()
    • Joyce P, Marjoram P, Approximately sufficient statistics and Bayesian computation. Statistical Applications in Genetics and Molecular Biology. 2008;7(1):Article26. doi: 10.2202/1544-6115.138918764775
    • (2008) Statistical Applications in Genetics and Molecular Biology , vol.7 , Issue.1 , pp. 26
    • Joyce, P.1    Marjoram, P.2
  • 27
    • 71249121103 scopus 로고    scopus 로고
    • Adaptive approximate Bayesian computation
    • .;():
    • Beaumont MA, Cornuet JM, Marin JM, Robert CP, Adaptive approximate Bayesian computation. Biometrika. 2009;96(4):983–990. doi: 10.1093/biomet/asp052
    • (2009) Biometrika , vol.96 , Issue.4 , pp. 983-990
    • Beaumont, M.A.1    Cornuet, J.M.2    Marin, J.M.3    Robert, C.P.4
  • 28
    • 73549122582 scopus 로고    scopus 로고
    • Non-linear regression models for Approximate Bayesian Computation
    • .;():
    • Blum MGB, François O, Non-linear regression models for Approximate Bayesian Computation. Statistics and Computing. 2010;20(1):63–73. doi: 10.1007/s11222-009-9116-0
    • (2010) Statistics and Computing , vol.20 , Issue.1 , pp. 63-73
    • Blum, M.G.B.1    François, O.2
  • 29
    • 77957728670 scopus 로고    scopus 로고
    • On optimal selection of summary statistics for approximate Bayesian computation
    • .;()
    • Nunes MA, Balding DJ, On optimal selection of summary statistics for approximate Bayesian computation. Statistical Applications in Genetics and Molecular Biology. 2010;9(1):34. doi: 10.2202/1544-6115.1576
    • (2010) Statistical Applications in Genetics and Molecular Biology , vol.9 , Issue.1 , pp. 34
    • Nunes, M.A.1    Balding, D.J.2
  • 31
    • 84861111043 scopus 로고    scopus 로고
    • Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation
    • .;():
    • Fearnhead P, Prangle D, Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation. Journal of the Royal Statistical Society: Series B (Statistical Methodology). 2012;74(3):419–474. doi: 10.1111/j.1467-9868.2011.01010.x
    • (2012) Journal of the Royal Statistical Society: Series B (Statistical Methodology) , vol.74 , Issue.3 , pp. 419-474
    • Fearnhead, P.1    Prangle, D.2
  • 32
    • 78149388939 scopus 로고    scopus 로고
    • Approximate Bayesian computation in evolution and ecology
    • .;:
    • Beaumont MA, Approximate Bayesian computation in evolution and ecology. Annual Review of Ecology, Evolution, and Systematics. 2010;41:379–406. doi: 10.1146/annurev-ecolsys-102209-144621
    • (2010) Annual Review of Ecology, Evolution, and Systematics , vol.41 , pp. 379-406
    • Beaumont, M.A.1
  • 33
    • 77955508453 scopus 로고    scopus 로고
    • Likelihood-Free Inference of Population Structure and Local Adaptation in a Bayesian Hierarchical Model
    • 20382835, .;():
    • Bazin E, Dawson KJ, Beaumont MA, Likelihood-Free Inference of Population Structure and Local Adaptation in a Bayesian Hierarchical Model. Genetics. 2010;185(2):587–602. doi: 10.1534/genetics.109.11239120382835
    • (2010) Genetics , vol.185 , Issue.2 , pp. 587-602
    • Bazin, E.1    Dawson, K.J.2    Beaumont, M.A.3
  • 34
    • 0020118274 scopus 로고
    • Neural networks and physical systems with emergent collective computational abilities
    • 6953413, .;():
    • Hopfield JJ, Neural networks and physical systems with emergent collective computational abilities. PNAS. 1982;79(8):2554–2558. doi: 10.1073/pnas.79.8.25546953413
    • (1982) PNAS , vol.79 , Issue.8 , pp. 2554-2558
    • Hopfield, J.J.1
  • 35
    • 0024861871 scopus 로고
    • Approximations by superpositions of sigmoidal functions
    • .;():
    • Cybenko G, Approximations by superpositions of sigmoidal functions. Mathematics of Control, Signals, and Systems. 1989;2(4):303–314. doi: 10.1007/BF02551274
    • (1989) Mathematics of Control, Signals, and Systems , vol.2 , Issue.4 , pp. 303-314
    • Cybenko, G.1
  • 36
    • 0025751820 scopus 로고
    • Approximation Capabilities of Multilayer Feedforward Networks
    • .;():
    • Hornik K, Approximation Capabilities of Multilayer Feedforward Networks. Neural Networks. 1991;4(2):251–257. doi: 10.1016/0893-6080(91)90009-T
    • (1991) Neural Networks , vol.4 , Issue.2 , pp. 251-257
    • Hornik, K.1
  • 37
    • 33746600649 scopus 로고    scopus 로고
    • Reducing the dimensionality of data with neural networks
    • 16873662, .;():
    • Hinton GE, Salakhutdinov RR, Reducing the dimensionality of data with neural networks. Science. 2006;313(5786):504–507. doi: 10.1126/science.112764716873662
    • (2006) Science , vol.313 , Issue.5786 , pp. 504-507
    • Hinton, G.E.1    Salakhutdinov, R.R.2
  • 38
    • 0022471098 scopus 로고
    • Learning representations by back-propagating errors
    • .;():
    • Rumelhart DE, Hinton GE, Williams RJ, Learning representations by back-propagating errors. Nature. 1986;323(9):533–536. doi: 10.1038/323533a0
    • (1986) Nature , vol.323 , Issue.9 , pp. 533-536
    • Rumelhart, D.E.1    Hinton, G.E.2    Williams, R.J.3
  • 39
    • 80051654263 scopus 로고    scopus 로고
    • Acoustics
    • Mohamed Ar, Sainath TN, Dahl G, Ramabhadran B, Hinton GE, Picheny MA. Deep belief networks using discriminative features for phone recognition. In: Acoustics, Speech and Signal Processing (ICASSP), 2011 IEEE International Conference on; 2011. p. 5060–5063.
    • Speech and Signal Processing (ICASSP), 2011 IEEE International Conference on , vol.2011 , pp. 5060-5063
  • 42
    • 84962090675 scopus 로고    scopus 로고
    • Hinton GE, Srivastava N, Krizhevsky A, Sutskever I, Salakhutdinov RR. Improving neural networks by preventing co-adaptation of feature detectors; 2012. ArXiv preprin
    • Hinton GE, Srivastava N, Krizhevsky A, Sutskever I, Salakhutdinov RR. Improving neural networks by preventing co-adaptation of feature detectors; 2012. ArXiv preprint, http://arxiv.org/abs/1207.0580.
  • 44
    • 84900523778 scopus 로고    scopus 로고
    • Space-time wiring specificity supports direction selectivity in the retina
    • 24805243, ..;():
    • Kim JS, Greene MJ, Zlateski A, Lee K, Richardson M, Turaga SC, et al. Space-time wiring specificity supports direction selectivity in the retina. Nature. 2014;509(7500):331–336. doi: 10.1038/nature1324024805243
    • (2014) Nature , vol.509 , Issue.7500 , pp. 331-336
    • Kim, J.S.1    Greene, M.J.2    Zlateski, A.3    Lee, K.4    Richardson, M.5    Turaga, S.C.6
  • 45
    • 84858841519 scopus 로고    scopus 로고
    • A unified multitask architecture for predicting local protein properties
    • 22461885, .;()
    • Qi Y, Oja M, Weston J, Noble WS, A unified multitask architecture for predicting local protein properties. PLoS One. 2012;7(3):e32235. doi: 10.1371/journal.pone.003223522461885
    • (2012) PLoS One , vol.7 , Issue.3 , pp. 32235
    • Qi, Y.1    Oja, M.2    Weston, J.3    Noble, W.S.4
  • 46
    • 84902462761 scopus 로고    scopus 로고
    • Deep learning of the tissue-regulated splicing code
    • 24931975, .;():
    • Leung MKK, Xiong HY, Lee LJ, Frey BJ, Deep learning of the tissue-regulated splicing code. Bioinformatics. 2014;30(12):i121–i129. doi: 10.1093/bioinformatics/btu27724931975
    • (2014) Bioinformatics , vol.30 , Issue.12 , pp. 121-129
    • Leung, M.K.K.1    Xiong, H.Y.2    Lee, L.J.3    Frey, B.J.4
  • 47
    • 84923276179 scopus 로고    scopus 로고
    • The human splicing code reveals new insights into the genetic determinants of disease
    • 25525159, ..;(
    • Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Ryan et al. The human splicing code reveals new insights into the genetic determinants of disease. Science. 2015;347 (6218). doi: 10.1126/science.125480625525159
    • (2015) Science , vol.347 , Issue.6218
    • Xiong, H.Y.1    Alipanahi, B.2    Lee, L.J.3    Bretschneider, H.4    Merico, D.5
  • 48
    • 84938888109 scopus 로고    scopus 로고
    • Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
    • 26213851, .;:
    • Alipanahi B, Delong A, Weirauch MT, Frey BJ, Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nature Biotechnology. 2015;33:831–838. doi: 10.1038/nbt.330026213851
    • (2015) Nature Biotechnology , vol.33 , pp. 831-838
    • Alipanahi, B.1    Delong, A.2    Weirauch, M.T.3    Frey, B.J.4
  • 49
    • 84962079156 scopus 로고    scopus 로고
    • Jiang B, Wu T, Zheng C, Wong WH. Learning Summary Statistic for Approximate Bayesian Computation via Deep Neural Network; 2015. ArXiv preprint
    • Jiang B, Wu T, Zheng C, Wong WH. Learning Summary Statistic for Approximate Bayesian Computation via Deep Neural Network; 2015. ArXiv preprint: http://arxiv.org/abs/1510.02175.
  • 50
    • 0031014291 scopus 로고    scopus 로고
    • Inferring Coalescence Times From DNA Sequence Data
    • 9071603, .;:
    • Tavaré S, Balding DJ, Griffiths JRC, Donnelly P, Inferring Coalescence Times From DNA Sequence Data. Genetics. 1997;145:505–518. 9071603
    • (1997) Genetics , vol.145 , pp. 505-518
    • Tavaré, S.1    Balding, D.J.2    Griffiths, J.R.C.3    Donnelly, P.4
  • 51
    • 84869057921 scopus 로고    scopus 로고
    • A novel approach for choosing summary statistics in approximate Bayesian computation
    • 22960215, .;():
    • Aeschbacher S, Beaumont MA, Futschik A, A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027–1047. doi: 10.1534/genetics.112.14316422960215
    • (2012) Genetics , vol.192 , Issue.3 , pp. 1027-1047
    • Aeschbacher, S.1    Beaumont, M.A.2    Futschik, A.3
  • 53
    • 84878991573 scopus 로고    scopus 로고
    • A comparative review of dimension reduction methods in approximate Bayesian computation
    • .;():
    • Blum MGB, Nunes MA, Prangle D, Sisson SA, A comparative review of dimension reduction methods in approximate Bayesian computation. Statistical Science. 2013;28(2):189–208. doi: 10.1214/12-STS406
    • (2013) Statistical Science , vol.28 , Issue.2 , pp. 189-208
    • Blum, M.G.B.1    Nunes, M.A.2    Prangle, D.3    Sisson, S.A.4
  • 54
    • 77951177432 scopus 로고    scopus 로고
    • ABCtoolbox: a versatile toolkit for approximate Bayesian computations
    • 20202215, .;
    • Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L, ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics. 2010;11:116. doi: 10.1186/1471-2105-11-11620202215
    • (2010) BMC Bioinformatics , vol.11 , pp. 116
    • Wegmann, D.1    Leuenberger, C.2    Neuenschwander, S.3    Excoffier, L.4
  • 55
    • 84962079148 scopus 로고    scopus 로고
    • Elyashiv E, Sattath S, Hu TT, Strustovsky A, McVicker G, Andolfatto P, et al. A genomic map of the effects of linked selection in; 2014. ArXiv preprin
    • Elyashiv E, Sattath S, Hu TT, Strustovsky A, McVicker G, Andolfatto P, et al. A genomic map of the effects of linked selection in Drosophila; 2014. ArXiv preprint, http://arxiv.org/abs/1408.5461.
  • 56
    • 77955381733 scopus 로고    scopus 로고
    • MSMS: A Coalescent Simulation Program Including Recombination, Demographic Structure, and Selection at a Single Locus
    • 20591904, .;:
    • Ewing G, Hermisson J, MSMS: A Coalescent Simulation Program Including Recombination, Demographic Structure, and Selection at a Single Locus. Bioinformatics. 2010;26:2064–2065. doi: 10.1093/bioinformatics/btq32220591904
    • (2010) Bioinformatics , vol.26 , pp. 2064-2065
    • Ewing, G.1    Hermisson, J.2
  • 57
    • 33846047594 scopus 로고    scopus 로고
    • Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila
    • 17203060, ..;:
    • Haag-Liautard C, Dorris M, Maside X, Macaskill S, Halligan DL, Charlesworth B, et al. Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature. 2007;445:82–85. doi: 10.1038/nature0538817203060
    • (2007) Nature , vol.445 , pp. 82-85
    • Haag-Liautard, C.1    Dorris, M.2    Maside, X.3    Macaskill, S.4    Halligan, D.L.5    Charlesworth, B.6
  • 58
    • 33644763127 scopus 로고    scopus 로고
    • Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster
    • 16299396, .;():
    • Thornton K, Andolfatto P, Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics. 2006;172(3):1607–1619. doi: 10.1534/genetics.105.04822316299396
    • (2006) Genetics , vol.172 , Issue.3 , pp. 1607-1619
    • Thornton, K.1    Andolfatto, P.2
  • 59
    • 22344444998 scopus 로고    scopus 로고
    • Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations
    • 15930491, .;:
    • Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P, Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Research. 2005;15:790–799. doi: 10.1101/gr.354100515930491
    • (2005) Genome Research , vol.15 , pp. 790-799
    • Haddrill, P.R.1    Thornton, K.R.2    Charlesworth, B.3    Andolfatto, P.4
  • 60
    • 0033828706 scopus 로고    scopus 로고
    • A Genome-Wide Departure From the Standard Neutral Model in Natural Populations of Drosophila
    • 10978290, .;:
    • Andolfatto P, Przeworski M, A Genome-Wide Departure From the Standard Neutral Model in Natural Populations of Drosophila. Genetics. 2000;156:257–268. 10978290
    • (2000) Genetics , vol.156 , pp. 257-268
    • Andolfatto, P.1    Przeworski, M.2
  • 61
    • 84887482933 scopus 로고    scopus 로고
    • Adaptive divergence of a transcriptional enhancer between populations of Drosophila melanogaster
    • 24218636, .;()
    • Glaser-Schmitt A, Catalán A, Parsch J, Adaptive divergence of a transcriptional enhancer between populations of Drosophila melanogaster. Philos Trans R Soc Lond B Biol Sci. 2013;368(1632):20130024. doi: 10.1098/rstb.2013.002424218636
    • (2013) Philos Trans R Soc Lond B Biol Sci , vol.368 , Issue.1632 , pp. 20130024
    • Glaser-Schmitt, A.1    Catalán, A.2    Parsch, J.3
  • 62
    • 26444439223 scopus 로고    scopus 로고
    • Cross-Species Comparison of Drosophila Male Accessory Gland Protein Genes
    • 15944345, ..;():
    • Mueller JL, Ram KR, McGraw LA, Qazi MCB, Siggia ED, Clark AG, et al. Cross-Species Comparison of Drosophila Male Accessory Gland Protein Genes. Genetics. 2005;171(1):131–143. doi: 10.1534/genetics.105.04384415944345
    • (2005) Genetics , vol.171 , Issue.1 , pp. 131-143
    • Mueller, J.L.1    Ram, K.R.2    McGraw, L.A.3    Qazi, M.C.B.4    Siggia, E.D.5    Clark, A.G.6
  • 63
    • 6944221222 scopus 로고    scopus 로고
    • Kruppel is a gap gene in the intermediate germband insect Oncopeltus fasciatus and is required for development of both blastoderm and germband-derived segments
    • 15342481, .;:
    • Liu PZ, Kaufman TC, Kruppel is a gap gene in the intermediate germband insect Oncopeltus fasciatus and is required for development of both blastoderm and germband-derived segments. Development. 2004;131:4567–4579. doi: 10.1242/dev.0131115342481
    • (2004) Development , vol.131 , pp. 4567-4579
    • Liu, P.Z.1    Kaufman, T.C.2
  • 64
    • 84901748239 scopus 로고    scopus 로고
    • Reproductive hacking: A male seminal protein acts through intact reproductive pathways in female Drosophila
    • 25483253, .;():
    • Rubinstein CD, Wolfner MF, Reproductive hacking: A male seminal protein acts through intact reproductive pathways in female Drosophila. Fly. 2014;8(2):80–85. doi: 10.4161/fly.2839625483253
    • (2014) Fly , vol.8 , Issue.2 , pp. 80-85
    • Rubinstein, C.D.1    Wolfner, M.F.2
  • 65
    • 84902108866 scopus 로고    scopus 로고
    • The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila
    • 24906153, .;():
    • Mohn F, Sienski G, Handler D, Brennecke J, The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila. Cell. 2014;157(6):1364–1379. doi: 10.1016/j.cell.2014.04.03124906153
    • (2014) Cell , vol.157 , Issue.6 , pp. 1364-1379
    • Mohn, F.1    Sienski, G.2    Handler, D.3    Brennecke, J.4
  • 66
    • 84962062761 scopus 로고    scopus 로고
    • Zhou H, Hu S, Matveev R, Yu Q, Li J, Khaitovich P, et al. A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years; 2015. BioRxiv preprin
    • Zhou H, Hu S, Matveev R, Yu Q, Li J, Khaitovich P, et al. A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years; 2015. BioRxiv preprint, http://dx.doi.org/10.1101/018929.
  • 67
    • 84929000155 scopus 로고    scopus 로고
    • Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps
    • 25716978, .;():
    • Schrider DR, Mendes FK, Hahn MW, Kern AD, Soft Shoulders Ahead: Spurious Signatures of Soft and Partial Selective Sweeps Result from Linked Hard Sweeps. Genetics. 2015;200(1):267–284. doi: 10.1534/genetics.115.17491225716978
    • (2015) Genetics , vol.200 , Issue.1 , pp. 267-284
    • Schrider, D.R.1    Mendes, F.K.2    Hahn, M.W.3    Kern, A.D.4
  • 68
    • 84962089063 scopus 로고    scopus 로고
    • Ng A, Ngiam J, Foo CY, Mai Y, Suen C. Unsupervised Feature Learning and Deep Learning Tutorial; 201
    • Ng A, Ngiam J, Foo CY, Mai Y, Suen C. Unsupervised Feature Learning and Deep Learning Tutorial; 2013. http://ufldl.stanford.edu/wiki/index.php/UFLDL_Tutorial.
  • 69
    • 84962079822 scopus 로고    scopus 로고
    • Dodier R. LBFGS optimization routine, Java translation; 199
    • Dodier R. LBFGS optimization routine, Java translation; 1999. http://riso.sourceforge.net/.
  • 71
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
    • 2513255, .;():
    • Tajima F, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123(3):585–595. 2513255
    • (1989) Genetics , vol.123 , Issue.3 , pp. 585-595
    • Tajima, F.1
  • 72
    • 84924411185 scopus 로고    scopus 로고
    • Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps
    • 25706129, .;()
    • Garud NR, Messer PW, Buzbas EO, Petrov DA, Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLoS Genetics. 2015;11(2):e1005004. doi: 10.1371/journal.pgen.100500425706129
    • (2015) PLoS Genetics , vol.11 , Issue.2 , pp. 1005004
    • Garud, N.R.1    Messer, P.W.2    Buzbas, E.O.3    Petrov, D.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.