Unlocking the vault: next-generation museum population genomics

Quantifying Population Genetic Differentiation from Next-Generation Sequencing Data

(2013) Matteo Fumagalli et al.   GENETICS

Comparative Population Genomics of the Ejaculate in Humans and the Great Apes

(2013) Jeffrey M. Good et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novotranscriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set

(2013) Sonal Singhal   Molecular Ecology Resources

Next-Generation Museomics Disentangles One of the Largest Primate Radiations

(2013) Katerina Guschanski et al.   SYSTEMATIC BIOLOGY

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Climate and refugial origin influence the mitochondrial lineage distribution of weasels (Mustela nivalis) in a phylogeographic suture zone

(2012) ALLAN D. MCDEVITT et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

(2012) Ke Bi et al.   BMC GENOMICS

A Low-Cost Exon Capture Method Suitable for Large-Scale Screening of Genetic Deafness by the Massively-Parallel Sequencing Approach

(2012) Wenxue Tang et al.   Genetic Testing and Molecular Biomarkers

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer 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

An Effort to Use Human-Based Exome Capture Methods to Analyze Chimpanzee and Macaque Exomes

(2012) Xin Jin et al.   PLoS One

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Climate-induced range contraction drives genetic erosion in an alpine mammal

(2012) Emily M. Rubidge et al.   Nature Climate Change

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

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

(2011) Ted Cosart et al.   BMC GENOMICS

Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

(2011) V. C. Mason et al.   GENOME RESEARCH

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

(2011) J. E. McCormack et al.   GENOME RESEARCH

Museum genomics: low-cost and high-accuracy genetic data from historical specimens

(2011) KEVIN C. ROWE et al.   Molecular Ecology Resources

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Phylogeny Estimation of the Radiation of Western North American Chipmunks (Tamias) in the Face of Introgression Using Reproductive Protein Genes

(2011) Noah Reid et al.   SYSTEMATIC BIOLOGY

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

(2011) María C. Ávila-Arcos et al.   Scientific Reports

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

The role of climate, habitat, and species co-occurrence as drivers of change in small mammal distributions over the past century

(2010) EMILY M. RUBIDGE et al.   GLOBAL CHANGE BIOLOGY

Genomic-scale capture and sequencing of endogenous DNA from feces

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

Road blocks on paleogenomes—polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA

(2010) Patricia Heyn et al.   NUCLEIC ACIDS RESEARCH

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

(2010) H. A. Burbano et al.   SCIENCE

De novo transcriptome assembly with ABySS

(2009) I. Birol et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing

(2009) Emily Hodges et al.   Nature Protocols

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

Birds track their Grinnellian niche through a century of climate change

(2009) M. W. Tingley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic analyses of historic and modern marbled murrelets suggest decoupling of migration and gene flow after habitat fragmentation

(2009) M. Z. Peery et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes

(2009) A. W. Briggs et al.   SCIENCE

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

(2008) I. Hellmann et al.   GENOME RESEARCH

The Effect of Ancient DNA Damage on Inferences of Demographic Histories

(2008) E. Axelsson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Estimation of Nucleotide Diversity, Disequilibrium Coefficients, and Mutation Rates from High-Coverage Genome-Sequencing Projects

(2008) M. Lynch   MOLECULAR BIOLOGY AND EVOLUTION

To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations?

(2008) ÜLO VÄLI et al.   MOLECULAR ECOLOGY

Ancient hybridization and mitochondrial capture between two species of chipmunks

(2008) JEFFREY M. GOOD et al.   MOLECULAR ECOLOGY

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

Historical DNA analysis reveals living descendants of an extinct species of Galapagos tortoise

(2008) N. Poulakakis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of a Century of Climate Change on Small-Mammal Communities in Yosemite National Park, USA

(2008) C. Moritz et al.   SCIENCE