Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens

Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)

(2020) Loïs Rancilhac et al.   JOURNAL OF NATURAL HISTORY

Present‐Day DNA Contamination in Ancient DNA Datasets

(2020) Stéphane Peyrégne et al.   BIOESSAYS

Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA

(2020) Marie-Theres Gansauge et al.   Nature Protocols

Ancestral mitogenome capture of the Southeast Asian banded linsang

(2020) Johanna L. A. Paijmans et al.   PLoS One

Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations

(2019) Gui-Lian Sheng et al.   CURRENT BIOLOGY

Whole-genome sequencing based on formalin-fixed paraffin-embedded endomyocardial biopsies for genetic studies on outcomes after heart transplantation

(2019) Gustav Zar et al.   PLoS One

Xenopus fraseri: Mr. Fraser, where did your frog come from?

(2019) Ben J. Evans et al.   PLoS One

Historical museum collections clarify the evolutionary history of cryptic species radiation in the world's largest amphibians

(2019) Samuel T. Turvey et al.   Ecology and Evolution

Increasing the utility of barcode databases through high-throughput sequencing of amplicons from dried museum specimens, an example on parasitic hymenoptera (Braconidae)

(2018) Julien Haran et al.   BIOLOGICAL CONTROL

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project

(2018) Pauline Robbe et al.   GENETICS IN MEDICINE

Collections-based science in the 21st Century

(2018) Vicki A. Funk   Journal of Systematics and Evolution

Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool

(2018) Ulrike Taron et al.   Genes

Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards

(2018) Jimmy A. McGuire et al.   PeerJ

Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences

(2018) Cesare de Filippo et al.   BMC BIOLOGY

Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens

(2017) Sara Ruane et al.   Molecular Ecology Resources

Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA

(2017) John S. Sproul et al.   Molecular Ecology Resources

Rapid recovery of nuclear and mitochondrial genes by genome skimming from Northern Hemisphere freshwater crayfish

(2017) Frederic Grandjean et al.   ZOOLOGICA SCRIPTA

A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica

(2017) Michael Westbury et al.   Nature Communications

Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct

(2017) Mary M. Peacock et al.   Royal Society Open Science

Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation

(2017) Naoki Einaga et al.   PLoS One

Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears

(2016) Gloria G. Fortes et al.   MOLECULAR ECOLOGY

Combining bleach and mild predigestion improves ancient DNA recovery from bones

(2016) Sanne Boessenkool et al.   Molecular Ecology Resources

Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA

(2016) Mathias Stiller et al.   Oncotarget

Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections

(2016) David K Yeates et al.   Current Opinion in Insect Science

Capturing protein-coding genes across highly divergent species

(2016) Chenhong Li et al.   BIOTECHNIQUES

The Utility of Genome Skimming for Phylogenomic Analyses as Demonstrated for Glycerid Relationships (Annelida, Glyceridae)

(2015) Sandy Richter et al.   Genome Biology and Evolution

Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes

(2015) Elizabeth A. Hoffman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The use of museum specimens with high-throughput DNA sequencers

(2015) Andrew S. Burrell et al.   JOURNAL OF HUMAN EVOLUTION

Impact of enrichment conditions on cross-species capture of fresh and degraded DNA

(2015) Johanna L. A. Paijmans et al.   Molecular Ecology Resources

Sequence capture of ultraconserved elements from bird museum specimens

(2015) John E. McCormack et al.   Molecular Ecology Resources

Interordinal gene capture, the phylogenetic position of Steller’s sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia

(2015) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Museums: The endangered dead

(2015) Christopher Kemp   NATURE

DNA capture reveals transoceanic gene flow in endangered river sharks

(2015) Chenhong Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Taxonomy 2.0: Sequencing of old type specimens supports the description of two new species of the Lasiocampa decolorata group from Morocco (Lepidoptera, Lasiocampidae)

(2015) WOLFGANG SPEIDEL et al.   ZOOTAXA

Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics

(2015) Sarah Munchel et al.   Oncotarget

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing

(2015) Sarah M. Hykin et al.   PLoS One

Ancient DNA and the tropics: a rodent's tale

(2014) T. A. Gutierrez-Garcia et al.   Biology Letters

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

(2014) Pontus Skoglund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specimen collection: An essential tool

(2014) L. A. Rocha et al.   SCIENCE

Comparison of protocols for DNA extraction from long-term preserved formalin fixed tissues

(2013) Stefan Paireder et al.   ANALYTICAL BIOCHEMISTRY

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

The relevance of time series in molecular ecology and conservation biology

(2013) Jan C. Habel et al.   BIOLOGICAL REVIEWS

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

(2013) Ludovic Orlando et al.   NATURE

The complete genome sequence of a Neanderthal from the Altai Mountains

(2013) Kay Prüfer et al.   NATURE

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

(2013) Marie-Theres Gansauge et al.   Nature Protocols

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

(2013) J. Dabney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

(2013) F. J. Vonk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ancient DNA Damage

(2013) J. Dabney et al.   Cold Spring Harbor Perspectives in Biology

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Contribution to the molecular phylogenetic analysis of extant holocephalan fishes (Holocephali, Chimaeriformes)

(2012) Martin Licht et al.   ORGANISMS DIVERSITY & EVOLUTION

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

(2012) M. E. Allentoft et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

(2012) M. Meyer et al.   SCIENCE

Molecular phylogeny and node time estimation of bioluminescent Lantern Sharks (Elasmobranchii: Etmopteridae)

(2010) Nicolas Straube et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Computational challenges in the analysis of ancient DNA

(2010) Kay Prüfer et al.   GENOME BIOLOGY

High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil

(2009) Jianghai Lin et al.   ANALYTICAL BIOCHEMISTRY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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