Reconstructing ancient genomes and epigenomes (Q35657312)

9 August 2017

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title

Reconstructing ancient genomes and epigenomes (English)

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9 August 2017

1

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Marcus Thomas Pius Gilbert

9 August 2017

series ordinal

2

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9 August 2017

3

Eske Willerslev

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publication date

9 June 2015

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9 August 2017

published in

Nature Reviews Genetics

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9 August 2017

volume

16

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9 August 2017

issue

7

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9 August 2017

page(s)

395-408

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DNA sequences from the quagga, an extinct member of the horse family

9 August 2017

cites work

1 reference

Ancient bone DNA amplified

21 January 2018

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Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification

21 January 2018

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Ancient human genome sequence of an extinct Palaeo-Eskimo

21 January 2018

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Sequencing the nuclear genome of the extinct woolly mammoth

21 January 2018

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A Draft Sequence of the Neandertal Genome

21 January 2018

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

21 January 2018

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Reconstructing genome evolution in historic samples of the Irish potato famine pathogen.

21 January 2018

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Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae

21 January 2018

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Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

21 January 2018

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Second-pandemic strain of Vibrio cholerae from the Philadelphia cholera outbreak of 1849.

21 January 2018

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Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array

21 January 2018

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Yersinia pestis and the plague of Justinian 541-543 AD: a genomic analysis.

21 January 2018

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An Aboriginal Australian genome reveals separate human dispersals into Asia

21 January 2018

1 reference

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

21 January 2018

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A high-coverage genome sequence from an archaic Denisovan individual

21 January 2018

1 reference

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

21 January 2018

1 reference

Genome flux and stasis in a five millennium transect of European prehistory

21 January 2018

1 reference

Speciation with gene flow in equids despite extensive chromosomal plasticity

21 January 2018

1 reference

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

21 January 2018

1 reference

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

21 January 2018

1 reference

The complete genome sequence of a Neanderthal from the Altai Mountains

21 January 2018

1 reference

The genetic prehistory of the New World Arctic

21 January 2018

1 reference

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

21 January 2018

1 reference

The genome of a Late Pleistocene human from a Clovis burial site in western Montana

21 January 2018

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Prehistoric genomes reveal the genetic foundation and cost of horse domestication

21 January 2018

1 reference

Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years

21 January 2018

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Genome data from a sixteenth century pig illuminate modern breed relationships

21 January 2018

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Reduced fitness in progeny from old parents in a natural population

21 January 2018

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Sequencing technologies - the next generation

21 January 2018

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

21 January 2018

1 reference

A mitochondrial genome sequence of a hominin from Sima de los Huesos

21 January 2018

1 reference

Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan

21 January 2018

1 reference

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

21 January 2018

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Major transitions in human evolution revisited: a tribute to ancient DNA.

21 January 2018

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A paleogenomic perspective on evolution and gene function: new insights from ancient DNA.

21 January 2018

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An epigenetic window into the past?

21 January 2018

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DNA damage and DNA sequence retrieval from ancient tissues

21 January 2018

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Statistical evidence for miscoding lesions in ancient DNA templates

21 January 2018

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DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA

21 January 2018

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Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA.

21 January 2018

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Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

21 January 2018

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Patterns of damage in genomic DNA sequences from a Neandertal

21 January 2018

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True single-molecule DNA sequencing of a pleistocene horse bone

21 January 2018

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Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA.

21 January 2018

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Next-generation sequencing offers new insights into DNA degradation

21 January 2018

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

21 January 2018

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Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments

21 January 2018

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

21 January 2018

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Nuclear gene sequences from a late pleistocene sloth coprolite

21 January 2018

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Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA

21 January 2018

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

21 January 2018

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The thermal history of human fossils and the likelihood of successful DNA amplification

21 January 2018

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New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains

21 January 2018

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Improving the performance of true single molecule sequencing for ancient DNA

21 January 2018

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Shotgun microbial profiling of fossil remains

21 January 2018

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Relatively well preserved DNA is present in the crystal aggregates of fossil bones

21 January 2018

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Survival and recovery of DNA from ancient teeth and bones

21 January 2018

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Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes

21 January 2018

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A new strategy for genome assembly using short sequence reads and reduced representation libraries

21 January 2018

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Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA.

21 January 2018

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

21 January 2018

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Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

21 January 2018

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Selective enrichment of damaged DNA molecules for ancient genome sequencing

21 January 2018

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Targeted retrieval and analysis of five Neandertal mtDNA genomes

21 January 2018

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Multiplexed DNA sequence capture of mitochondrial genomes using PCR products

21 January 2018

1 reference

Partial uracil-DNA-glycosylase treatment for screening of ancient DNA

21 January 2018

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Targeted investigation of the Neandertal genome by array-based sequence capture

21 January 2018

1 reference

A revised timescale for human evolution based on ancient mitochondrial genomes

21 January 2018

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Mitochondrial phylogenomics of modern and ancient equids

21 January 2018

1 reference

Patterns of coding variation in the complete exomes of three Neandertals.

21 January 2018

1 reference

DNA analysis of an early modern human from Tianyuan Cave, China

21 January 2018

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Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries

21 January 2018

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Ancient whole genome enrichment using baits built from modern DNA.

21 January 2018

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Tracking niche variation over millennial timescales in sympatric killer whale lineages

21 January 2018

1 reference

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

21 January 2018

1 reference

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

21 January 2018

1 reference

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

21 January 2018

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

21 January 2018

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Parallel detection of ancient pathogens via array-based DNA capture

21 January 2018

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Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX.

21 January 2018

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AdapterRemoval: easy cleaning of next-generation sequencing reads

21 January 2018

1 reference

Fast and accurate short read alignment with Burrows-Wheeler transform

21 January 2018

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Fast gapped-read alignment with Bowtie 2

21 January 2018

1 reference

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

21 January 2018

1 reference

Metagenomic microbial community profiling using unique clade-specific marker genes

21 January 2018

1 reference

Improving ancient DNA read mapping against modern reference genomes

21 January 2018

1 reference

Adaptable probabilistic mapping of short reads using position specific scoring matrices

21 January 2018

1 reference

mapDamage: testing for damage patterns in ancient DNA sequences

21 January 2018

1 reference

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

21 January 2018

1 reference

SNPest: a probabilistic graphical model for estimating genotypes

21 January 2018

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Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe

21 January 2018

1 reference

Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics

21 January 2018

1 reference

Genomic affinities of two 7,000-year-old Iberian hunter-gatherers

21 January 2018

1 reference

The Neandertal genome and ancient DNA authenticity

21 January 2018

1 reference

Genetic history of an archaic hominin group from Denisova Cave in Siberia

21 January 2018

1 reference

High-resolution analysis of cytosine methylation in ancient DNA

21 January 2018

1 reference

Molecular breeding of polymerases for amplification of ancient DNA

21 January 2018

1 reference

The origin and evolution of maize in the Southwestern United States

21 January 2018

1 reference

Toward a new history and geography of human genes informed by ancient DNA

21 January 2018

1 reference

Deep sequencing of RNA from ancient maize kernels

21 January 2018

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Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops

21 January 2018

1 reference

Biochemistry. Unlocking ancient protein palimpsests

21 January 2018

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Direct evidence of milk consumption from ancient human dental calculus

21 January 2018

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Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

21 January 2018

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Pathogens and host immunity in the ancient human oral cavity

21 January 2018

1 reference

Ancient human genomes suggest three ancestral populations for present-day Europeans

21 January 2018

1 reference

Genome sequence of a 45,000-year-old modern human from western Siberia

21 January 2018

1 reference

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia

21 January 2018

1 reference

A 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins: using the latest advances in ancient genomics, the mitochondrial genome sequence of a 400,000-year-old hominin has been deciphered

21 January 2018

1 reference

Revising the human mutation rate: implications for understanding human evolution

21 January 2018

1 reference

Fast model-based estimation of ancestry in unrelated individuals

21 January 2018

1 reference

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).

21 January 2018

1 reference

Investigating population history using temporal genetic differentiation

21 January 2018

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Testing for ancient admixture between closely related populations

21 January 2018

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Ancient admixture in human history

21 January 2018

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Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins

21 January 2018

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The date of interbreeding between Neandertals and modern humans

21 January 2018

1 reference

Using Ancient DNA to Understand Evolutionary and Ecological Processes

21 January 2018

1 reference

Improving access to endogenous DNA in ancient bones and teeth

31 March 2020

1 reference

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

31 March 2020

1 reference

Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns

31 March 2020

1 reference

Massive migration from the steppe was a source for Indo-European languages in Europe

31 March 2020

1 reference

Comparative performance of two whole-genome capture methodologies on ancient DNA Illumina libraries

31 March 2020

1 reference

Morphological and genetic evidence for early Holocene cattle management in northeastern China.

31 March 2020

1 reference

Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics

31 March 2020

1 reference

ExaML version 3: a tool for phylogenomic analyses on supercomputers

31 March 2020

1 reference

Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process

31 March 2020

1 reference

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26055157

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26055157

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Improving access to endogenous DNA in ancient bones and teeth

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26055157

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRG3935

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Dimensions Publication ID

9 August 2017

1028996959

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