Recent novel approaches for population genomics data analysis

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

(2013) Paul A. Hohenlohe et al.   MOLECULAR ECOLOGY

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Simple life-history traits explain key effective population size ratios across diverse taxa

(2013) R. S. Waples et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Alternative forms for genomic clines

(2013) Benjamin M. Fitzpatrick   Ecology and Evolution

ezRAD: a simplified method for genomic genotyping in non-model organisms

(2013) Robert J. Toonen et al.   PeerJ

Estimating ancestry and heterozygosity of hybrids using molecular markers

(2012) Benjamin M Fitzpatrick   BMC EVOLUTIONARY BIOLOGY

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

(2012) Ke Bi et al.   BMC GENOMICS

Environmental selection on transcriptome-derived SNPs in a high gene flow marine fish, the Atlantic herring (Clupea harengus)

(2012) MORTEN T. LIMBORG et al.   MOLECULAR ECOLOGY

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

2b-RAD: a simple and flexible method for genome-wide genotyping

(2012) Shi Wang et al.   NATURE METHODS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data

(2012) Rasmus Nielsen et al.   PLoS One

Harnessing genomics for delineating conservation units

(2012) W. Chris Funk et al.   TRENDS IN ECOLOGY & EVOLUTION

Exome-wide DNA capture and next generation sequencing in domestic and wild species

(2011) Ted Cosart et al.   BMC GENOMICS

Expanding whole exome resequencing into non-human primates

(2011) Eric J Vallender   GENOME BIOLOGY

Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

(2011) Brian J Knaus et al.   BMC ECOLOGY

Expression of interest: transcriptomics and the designation of conservation units

(2010) MICHAEL M. HANSEN   MOLECULAR ECOLOGY

Genomic-scale capture and sequencing of endogenous DNA from feces

(2010) GEORGE H. PERRY et al.   MOLECULAR ECOLOGY

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Genome-wide scans for footprints of natural selection

(2009) T. K. Oleksyk et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

ldne: a program for estimating effective population size from data on linkage disequilibrium

(2008) ROBIN S. WAPLES et al.   Molecular Ecology Resources

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One