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A not so short (and not yet complete!) list of relevant papers:

Molecular signatures of natural selection
By: Nielsen, R
ANNUAL REVIEW OF GENETICS, 39, 197-218
2005

Genomic scans for selective sweeps using SNP data
By: Nielsen, R; Williamson, S; Kim, Y; et al.
GENOME RESEARCH, 15, 1566-1575
2005

Approaches for identifying targets of positive selection
By: Jensen, Jeffrey D.; Wong, Alex; Aquadro, Charles F.
TRENDS IN GENETICS, 23, 568-577
2007

A population genomic approach to map recent positive selection in model species
By: Pavlidis, P.; Hutter, S.; Stephan, W.
MOLECULAR ECOLOGY, 17, 3585-3598
2008

Assessing the evolutionary impact of amino acid mutations in the human genome
By: Boyko, Adam R.; Williamson, Scott H.; Indap, Amit R.; et al.
PLOS GENETICS, 4, e1000083
2008

Natural selection has driven population differentiation in modern humans
By: Barreiro, Luis B.; Laval, Guillaume; Quach, Helene; et al.
NATURE GENETICS, 40 340-345
2008

Patterns of Positive Selection in Six Mammalian Genomes
By: Kosiol, Carolin; Vinar, Tomas; da Fonseca, Rute R.; et al.
PLOS GENETICS, 4, e1000144
2008

An Investigation of the Statistical Power of Neutrality Tests Based on Comparative and Population Genetic Data
By: Zhai, Weiwei; Nielsen, Rasmus; Slatkin, Montgomery
MOLECULAR BIOLOGY AND EVOLUTION, 26, 273-283
2009

Pervasive Natural Selection in the Drosophila Genome?
By: Sella, Guy; Petrov, Dmitri A.; Przeworski, Molly; et al.
PLOS GENETICS, 5, e1000495
2009

Signals of recent positive selection in a worldwide sample of human populations
By: Pickrell, Joseph K.; Coop, Graham; Novembre, John; et al.
GENOME RESEARCH, 19, 826-837
2009

Who believes in whole-genome scans for selection?
By: Hermisson, J.
HEREDITY, 103, 283-284
2009

Darwinian and demographic forces affecting human protein coding genes
By: Nielsen, Rasmus; Hubisz, Melissa J.; Hellmann, Ines; et al.
GENOME RESEARCH, 19, 838-849
2009

Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment
By: Schneider, Adrian; Souvorov, Alexander; Sabath, Niv; et al.
GENOME BIOLOGY AND EVOLUTION, 1, 114-118
2009

Reduced effectiveness of selection caused by a lack of recombination
By: Betancourt, Andrea J.; Welch, John J.; Charlesworth, Brian
CURRENT BIOLOGY, 19, 655-660
2009

The Neutral Theory of Molecular Evolution in the Genomic Era
By: Nei, Masatoshi; Suzuki, Yoshiyuki; Nozawa, Masafumi
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 11, 265-289
2010

Adaptation - not by sweeps alone
By: Pritchard, Jonathan K.; Di Rienzo, Anna
NATURE REVIEWS GENETICS, 11, 665-667
2010

Integrating evolutionary and functional approaches to infer adaptation at specific loci
By: Storz, Jay F.; Wheat, Christopher W.
EVOLUTION, 64, 2489-2509
2010

Statistical methods for detecting natural selection from genomic data
By: Suzuki, Yoshiyuki
GENES & GENETIC SYSTEMS, 85, 359-376
2010

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation
By: Pritchard, Jonathan K.; Pickrell, Joseph K.; Coop, Graham
CURRENT BIOLOGY, 20, 208-215
2010

Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome
By: Lohmueller, Kirk E.; Albrechtsen, Anders; Li, Yingrui; et al.
PLOS GENETICS, 7, e1002326
2011

The genomics of adaptation Introduction
By: Radwan, Jacek; Babik, Wieslaw
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 279, 5024-5028
2012

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs
By: Roesti, Marius; Hendry, Andrew P.; Salzburger, Walter; et al.
MOLECULAR ECOLOGY, 21, 2852-2862
2012

Monitoring adaptive genetic responses to environmental change
By: Hansen, Michael M.; Olivieri, Isabelle; Waller, Donald M.; et al.
MOLECULAR ECOLOGY, 21, 1311-1329
2012

Recent Progress in Polymorphism-Based Population Genetic Inference
By: Crisci, Jessica L.; Poh, Yu-Ping; Bean, Angela; et al.
JOURNAL OF HEREDITY, 103, 287-296
2012

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection
By: Jordan, Gregory; Goldman, Nick
MOLECULAR BIOLOGY AND EVOLUTION, 29, 1125-1139
2012

Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster
By: Kofler, Robert; Betancourt, Andrea J.; Schloetterer, Christian
PLOS GENETICS, 8, e1002487
2012

Detecting Natural Selection in Genomic Data
By: Vitti, Joseph J.; Grossman, Sharon R.; Sabeti, Pardis C.
ANNUAL REVIEW OF GENETICS, 47, 97-120
2013

Thinking too positive? Revisiting current methods of population genetic selection inference
By: Bank, Claudia; Ewing, Gregory B.; Ferrer-Admettla, Anna; et al.
TRENDS IN GENETICS, 30, 540-546
2014

On the unfounded enthusiasm for soft selective sweeps
By: Jensen, Jeffrey D.
NATURE COMMUNICATIONS, 5, 5281
2014

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears
By: Liu, Shiping; Lorenzen, Eline D.; Fumagalli, Matteo; et al.
CELL, 157, 785-794
2014

Prehistoric genomes reveal the genetic foundation and cost of horse domestication
By: Schubert, Mikkel; Jonsson, Hakon; Chang, Dan; et al.
PNAS, 111, E5661-E5669
2014

Comparative genomics reveals insights into avian genome evolution and adaptation
By: Zhang, Guojie; Li, Cai; Li, Qiye; Avian Genome Consortium, et al
SCIENCE, 346, 1311-1320
2014

Detecting balancing selection in genomes: limits and prospects
By: Fijarczyk, Anna; Babik, Wieslaw
MOLECULAR ECOLOGY, 24, 3529-3545
2015

Population Genomics for Understanding Adaptation in Wild Plant Species
By: Weigel, Detlef; Nordborg, Magnus
ANNUAL REVIEW OF GENETICS, 49, 315-338
2015

Genomic Signature of Selective Sweeps Illuminates Adaptation of Medicago truncatula to Root-Associated Microorganisms
By: Bonhomme, Maxime; Boitard, Simon; Clemente, Helen San; et al.
MOLECULAR BIOLOGY AND EVOLUTION, 32, 2097-2110
2015

Inference of evolutionary forces acting on human biological pathways
By: Daub, Josephine T.; Dupanloup, Isabelle; Robinson-Rechavi, Marc; et al.
GENOME BIOLOGY AND EVOLUTION, 7, 1546-1558
2015

Evolutionary genomics and conservation of the endangered Przewalski's horse
By: Sarkissian, Clio Der; Ermini, Luca; Schubert, Mikkel; et al.
CURRENT BIOLOGY, 25, 2577-2583
2015

Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations
By: Pybus, Marc; Luisi, Pierre; Dall'Olio, Giovanni Marco; et al.
BIOINFORMATICS, 31, 3946-3952
2015

The evolution and functional impact of human deletion variants shared with archaic hominin genomes
By: Lin, Yen-Lung; Pavlidis, Pavlos; Karakoc, Emre; et al.
MOLECULAR BIOLOGY AND EVOLUTION, 32, 1008-1019
2015

The genetic consequences of selection in natural populations
By: Thurman, Timothy J.; Barrett, Rowan D. H.
MOLECULAR ECOLOGY, 25, 1429-1448
2016

Detecting Genomic Signatures of Natural Selection with Principal Component Analysis: Application to the 1000 Genomes Data
By: Duforet-Frebourg, Nicolas; Luu, Keurcien; Laval, Guillaume; et al.
MOLECULAR BIOLOGY AND EVOLUTION, 33, 1082-1093
2016

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions
By: Hoban, Sean; Kelley, Joanna L.; Lotterhos, Katie E.; et al.
AMERICAN NATURALIST, 188, 379-397
2016

Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective
By: Malaspinas, Anna-Sapfo
MOLECULAR ECOLOGY, 25, 24-41
2016

Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation
By: Stephan, Wolfgang
MOLECULAR ECOLOGY, 25, 79-88
2016

Deep learning for population genetic inference
By: Sheehan, Sara; Song, Yun S.
PLOS COMPUTATIONAL BIOLOGY, 12, e1004845
2016

1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana
By: Alonso-Blanco, Carlos; Andrade, Jorge; Becker, Claude; 1001 Genomes Consortium; et al.
CELL, 166, 481-491
2016

Detecting recent selective sweeps while controlling for mutation rate and background selection
By: Huber, Christian D.; Degiorgio, Michael; Hellmann, Ines; et al.
MOLECULAR ECOLOGY, 25, 142-156
2016

The past, present and future of genomic scans for selection
By: Jensen, Jeffrey D.; Foll, Matthieu; Bernatchez, Louis
MOLECULAR ECOLOGY, 25, 1-4
2016

Population-genomic inference of the strength and timing of selection against gene flow
By: Aeschbacher, Simon; Selby, Jessica P.; Willis, John H.; Coop Graham
BIORXIV,
2016