Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries

(2012) Jesse Dabney et al.   BIOTECHNIQUES

Chimera-Free Library Prep for NGS Platforms

(2012) Michael Lodes   Genetic Engineering & Biotechnology News

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Mitogenomic sequences better resolve stock structure of southern Greater Caribbean green turtle rookeries

(2012) BRIAN M. SHAMBLIN et al.   MOLECULAR ECOLOGY

Marine turtle mitogenome phylogenetics and evolution

(2012) Sebastián Duchene et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility

(2012) Anton Nekrutenko et al.   NATURE REVIEWS GENETICS

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

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population

(2012) Rory Bowden et al.   PLoS Genetics

Empirical comparison of single nucleotide polymorphisms and microsatellites for population and demographic analyses of bowhead whales

(2012) PA Morin et al.   Endangered Species Research

Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae

(2011) Julia T Vilstrup et al.   BMC EVOLUTIONARY BIOLOGY

Unraveling the rapid radiation of crested newts (Triturus cristatus superspecies) using complete mitogenomic sequences

(2011) Ben Wielstra et al.   BMC EVOLUTIONARY BIOLOGY

Application of a method for estimating effective population size and admixture using diagnostic single nucleotide polymorphisms (SNPs): implications for conservation of threatened Paiute cutthroat trout (Oncorhynchus clarkii seleniris) in Silver King Creek, California

(2011) Amanda J. Finger et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

The genetic population structure of lacustrine sockeye salmon, Oncorhynchus nerka, in Japan as the endangered species

(2011) Yuichiro Kogura et al.   ENVIRONMENTAL BIOLOGY OF FISHES

Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation

(2011) Li Yu et al.   MITOCHONDRION

Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders

(2011) M. A. Pacheco et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA

(2011) SARAH L. MESNICK et al.   Molecular Ecology Resources

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Multiple Invasions into Freshwater by Pufferfishes (Teleostei: Tetraodontidae): A Mitogenomic Perspective

(2011) Yusuke Yamanoue et al.   PLoS One

Mitochondrial Genomes Reveal Slow Rates of Molecular Evolution and the Timing of Speciation in Beavers (Castor), One of the Largest Rodent Species

(2011) Susanne Horn et al.   PLoS One

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Mitogenome Phylogenetics: The Impact of Using Single Regions and Partitioning Schemes on Topology, Substitution Rate and Divergence Time Estimation

(2011) Sebastián Duchêne et al.   PLoS One

Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths

(2011) Jacob Enk et al.   GENOME BIOLOGY

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

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

(2011) Brian J Knaus et al.   BMC ECOLOGY

Positive selection on the killer whale mitogenome

(2010) A. D. Foote et al.   Biology Letters

Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

(2010) P. A. Morin et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Evolutionary Origin and Phylogeny of the Modern Holocephalans (Chondrichthyes: Chimaeriformes): A Mitogenomic Perspective

(2010) J. G. Inoue et al.   MOLECULAR BIOLOGY AND EVOLUTION

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons

(2010) Yi-Chiao Chan et al.   PLoS One

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence

(2010) S. Lavoue et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny

(2009) Tiratha Singh et al.   BMC GENOMICS

Big and Slow: Phylogenetic Estimates of Molecular Evolution in Baleen Whales (Suborder Mysticeti)

(2009) J. A. Jackson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Characterization of single nucleotide polymorphism markers for the green sea turtle (Chelonia mydas)

(2009) SUZANNE E. RODEN et al.   Molecular Ecology Resources

Assessing statistical power of SNPs for population structure and conservation studies

(2009) PHILLIP A. MORIN et al.   Molecular Ecology Resources

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

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

(2009) Emily Hodges et al.   Nature Protocols

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

(2008) M. T. P. Gilbert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Number of Alleles as a Predictor of the Relative Assignment Accuracy of Short Tandem Repeat (STR) and Single-Nucleotide-Polymorphism (SNP) Baselines for Chum Salmon

(2008) Christian T. Smith et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY