Improving the performance of true single molecule sequencing for ancient DNA View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-12

AUTHORS

Aurelien Ginolhac, Julia Vilstrup, Jesper Stenderup, Morten Rasmussen, Mathias Stiller, Beth Shapiro, Grant Zazula, Duane Froese, Kathleen E Steinmann, John F Thompson, Khaled AS AL-Rasheid, Thomas MP Gilbert, Eske Willerslev, Ludovic Orlando

ABSTRACT

BACKGROUND: Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase. RESULTS: We found that a significantly larger fraction of the horse genome could be covered following oligonucleotide spiking however not reproducibly and at the cost of extra post-sequencing filtering procedures and skewed %GC content. In contrast, we showed that treating ancient DNA extracts with DNA phosphatase improved the amount of endogenous sequence information recovered per sequencing channel by up to 3.3-fold, while still providing molecular signatures of endogenous ancient DNA damage, including cytosine deamination and fragmentation by depurination. Additionally, we confirmed the existence of molecular preservation niches in large bone crystals from which DNA could be preferentially extracted. CONCLUSIONS: We propose DNA phosphatase treatment as a mechanism to increase sequence coverage of ancient genomes when using Helicos tSMS as a sequencing platform. Together with mild denaturation temperatures that favor access to endogenous ancient templates over modern DNA contaminants, this simple preparation procedure can improve overall Helicos tSMS performance when damaged DNA templates are targeted. More... »

PAGES

177

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-13-177

DOI

http://dx.doi.org/10.1186/1471-2164-13-177

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1032076652

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22574620


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Animals", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Composition", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Mitochondrial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Fossils", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Horses", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nucleotidases", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Nucleotides", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Phylogeny", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5-7 \u00d8ster Voldgade, 1350, K\u00f8benhavn, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ginolhac", 
        "givenName": "Aurelien", 
        "id": "sg:person.01050333103.98", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050333103.98"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5-7 \u00d8ster Voldgade, 1350, K\u00f8benhavn, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Vilstrup", 
        "givenName": "Julia", 
        "id": "sg:person.01342327146.25", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01342327146.25"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5-7 \u00d8ster Voldgade, 1350, K\u00f8benhavn, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stenderup", 
        "givenName": "Jesper", 
        "id": "sg:person.01164561503.97", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01164561503.97"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5-7 \u00d8ster Voldgade, 1350, K\u00f8benhavn, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Rasmussen", 
        "givenName": "Morten", 
        "id": "sg:person.01013242545.03", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01013242545.03"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Pennsylvania State University", 
          "id": "https://www.grid.ac/institutes/grid.29857.31", 
          "name": [
            "Department of Biology, The Pennsylvania State University, 326 Mueller Lab, 16802, University Park, PA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Stiller", 
        "givenName": "Mathias", 
        "id": "sg:person.01365624305.68", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01365624305.68"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Pennsylvania State University", 
          "id": "https://www.grid.ac/institutes/grid.29857.31", 
          "name": [
            "Department of Biology, The Pennsylvania State University, 326 Mueller Lab, 16802, University Park, PA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Shapiro", 
        "givenName": "Beth", 
        "id": "sg:person.01241444046.39", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01241444046.39"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Department of Tourism and Culture, Government of Yukon, Yukon, Palaeontology Program, PO Box 2703 L2A, 2C6, Whitehorse, Yukon Territory Y1A, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Zazula", 
        "givenName": "Grant", 
        "id": "sg:person.07732654527.21", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07732654527.21"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Alberta", 
          "id": "https://www.grid.ac/institutes/grid.17089.37", 
          "name": [
            "Department of Earth and Atmospheric Sciences, University of Alberta, T6G 2E3, Edmonton, Alberta, Canada"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Froese", 
        "givenName": "Duane", 
        "id": "sg:person.01132401575.22", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01132401575.22"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Applications, Methods and Collaborations, Helicos BioSciences, One Kendall Square Bldg 200LL, 02139, Cambridge, MA, USA", 
            "Broad Institute of Massachusetts Institute of Technology and Harvard, 021423, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Steinmann", 
        "givenName": "Kathleen E", 
        "id": "sg:person.01253440745.00", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01253440745.00"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Helicos Biosciences (United States)", 
          "id": "https://www.grid.ac/institutes/grid.418487.6", 
          "name": [
            "Applications, Methods and Collaborations, Helicos BioSciences, One Kendall Square Bldg 200LL, 02139, Cambridge, MA, USA", 
            "NABsys Inc, 60 Clifford Street, 0290, Providence, RI, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Thompson", 
        "givenName": "John F", 
        "id": "sg:person.014051114644.24", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014051114644.24"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "King Saud University", 
          "id": "https://www.grid.ac/institutes/grid.56302.32", 
          "name": [
            "Zoology Department, College of Science King Saud University, P.O. Box, 2455, 11451, Riyadh, Saudi Arabia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "AL-Rasheid", 
        "givenName": "Khaled AS", 
        "id": "sg:person.01352355663.28", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01352355663.28"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5-7 \u00d8ster Voldgade, 1350, K\u00f8benhavn, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gilbert", 
        "givenName": "Thomas MP", 
        "id": "sg:person.01111262507.70", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01111262507.70"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5-7 \u00d8ster Voldgade, 1350, K\u00f8benhavn, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Willerslev", 
        "givenName": "Eske", 
        "id": "sg:person.0714231071.76", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714231071.76"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5-7 \u00d8ster Voldgade, 1350, K\u00f8benhavn, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Orlando", 
        "givenName": "Ludovic", 
        "id": "sg:person.01201152047.48", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01201152047.48"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1126/science.1188021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002597304"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1188021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002597304"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature07446", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003406391", 
          "https://doi.org/10.1038/nature07446"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1098/rsbl.2006.0515", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004740948"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf02337515", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006563380", 
          "https://doi.org/10.1007/bf02337515"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf02337515", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006563380", 
          "https://doi.org/10.1007/bf02337515"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/0471142727.mb0710s92", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007096038"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/0471142727.mb0710s92", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007096038"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.genet.37.110801.143214", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014567048"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0503718102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017795199"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0503718102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017795199"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/362709a0", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019428971", 
          "https://doi.org/10.1038/362709a0"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.122747.111", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020096058"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cub.2003.12.012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020335334"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1188046", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020995997"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1188046", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020995997"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature08835", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021776500", 
          "https://doi.org/10.1038/nature08835"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature08835", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021776500", 
          "https://doi.org/10.1038/nature08835"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05336", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022286131", 
          "https://doi.org/10.1038/nature05336"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05336", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022286131", 
          "https://doi.org/10.1038/nature05336"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05336", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022286131", 
          "https://doi.org/10.1038/nature05336"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0378-1119(94)90713-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023535700"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0378-1119(94)90713-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023535700"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1673-8527(07)60081-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023665888"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.mrfmmm.2004.06.060", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024985289"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0076-6879(10)72002-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027045392"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cub.2009.11.068", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028054623"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1354", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028638279", 
          "https://doi.org/10.1038/nmeth.1354"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btr347", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030568980"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2148-9-95", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035465276", 
          "https://doi.org/10.1186/1471-2148-9-95"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkp1163", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036956881"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/1475-4754.00064", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036961816"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.aanat.2011.07.003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037337752"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btp324", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038266369"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.1551", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039844797", 
          "https://doi.org/10.1038/nbt.1551"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/gbe/evr067", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040095022"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.106.057349", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041192332"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1534/genetics.106.057349", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041192332"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/1475-4754.t01-1-00071", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044532565"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0704665104", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045401726"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/sysbio/syq010", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046004748"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/25.17.3389", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047265454"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1146971", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047897915"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msn083", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048530400"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkq572", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049568274"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1105107108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049707959"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09710", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050205294", 
          "https://doi.org/10.1038/nature09710"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09710", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050205294", 
          "https://doi.org/10.1038/nature09710"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s11033-010-0145-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050621236", 
          "https://doi.org/10.1007/s11033-010-0145-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s11033-010-0145-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050621236", 
          "https://doi.org/10.1007/s11033-010-0145-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.281.5375.402", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051953666"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm588", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053124372"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1086/345379", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1058641019"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1086/345379", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1058641019"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1113485", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062452286"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1123360", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062453436"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1131412", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062454636"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1141758", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062455979"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1174462", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062460190"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2144/000113721", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1069096345"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1082939807", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2012-12", 
    "datePublishedReg": "2012-12-01", 
    "description": "BACKGROUND: Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase.\nRESULTS: We found that a significantly larger fraction of the horse genome could be covered following oligonucleotide spiking however not reproducibly and at the cost of extra post-sequencing filtering procedures and skewed %GC content. In contrast, we showed that treating ancient DNA extracts with DNA phosphatase improved the amount of endogenous sequence information recovered per sequencing channel by up to 3.3-fold, while still providing molecular signatures of endogenous ancient DNA damage, including cytosine deamination and fragmentation by depurination. Additionally, we confirmed the existence of molecular preservation niches in large bone crystals from which DNA could be preferentially extracted.\nCONCLUSIONS: We propose DNA phosphatase treatment as a mechanism to increase sequence coverage of ancient genomes when using Helicos tSMS as a sequencing platform. Together with mild denaturation temperatures that favor access to endogenous ancient templates over modern DNA contaminants, this simple preparation procedure can improve overall Helicos tSMS performance when damaged DNA templates are targeted.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2164-13-177", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.3784511", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.3100987", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2669364", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023790", 
        "issn": [
          "1471-2164"
        ], 
        "name": "BMC Genomics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "13"
      }
    ], 
    "name": "Improving the performance of true single molecule sequencing for ancient DNA", 
    "pagination": "177", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "98ce7027d7c290122247e61b02841cdc2827647a4d64c9fe32e038f141114efc"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "22574620"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965258"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2164-13-177"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1032076652"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2164-13-177", 
      "https://app.dimensions.ai/details/publication/pub.1032076652"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T19:07", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8678_00000506.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1471-2164-13-177"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-13-177'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-13-177'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-13-177'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-13-177'


 

This table displays all metadata directly associated to this object as RDF triples.

385 TRIPLES      21 PREDICATES      89 URIs      33 LITERALS      21 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2164-13-177 schema:about N28ed74756dd5492bbc0209e7ea1479cb
2 N2d13944b044c41e29e6ca6415b581061
3 N43f09923f20c4801a5f2d6f66a8225cf
4 N5665092875a643899893d25d774c76d8
5 N5dec0f5aea864b279c602c737756b063
6 N71841759f697405fa7c5640fd3b39f36
7 N91da9dca5519487c9ffd3f3e1b5741ba
8 N943ff23a8a09473598eef157269b8ccd
9 Nb5f36a762299472ebdf4a8c1c0e0632b
10 Nc7630c6df2f7456eac52b82dfe819465
11 Ncbde219dd6aa476da4c1a647405fdd68
12 Ne604a62ce2ed4c9cb66835f23929bd5c
13 anzsrc-for:06
14 anzsrc-for:0604
15 schema:author Nf23fec99c0474efc955bbbca2d177505
16 schema:citation sg:pub.10.1007/bf02337515
17 sg:pub.10.1007/s11033-010-0145-8
18 sg:pub.10.1038/362709a0
19 sg:pub.10.1038/nature05336
20 sg:pub.10.1038/nature07446
21 sg:pub.10.1038/nature08835
22 sg:pub.10.1038/nature09710
23 sg:pub.10.1038/nbt.1551
24 sg:pub.10.1038/nmeth.1354
25 sg:pub.10.1186/1471-2148-9-95
26 https://app.dimensions.ai/details/publication/pub.1082939807
27 https://doi.org/10.1002/0471142727.mb0710s92
28 https://doi.org/10.1016/0378-1119(94)90713-7
29 https://doi.org/10.1016/j.aanat.2011.07.003
30 https://doi.org/10.1016/j.cub.2003.12.012
31 https://doi.org/10.1016/j.cub.2009.11.068
32 https://doi.org/10.1016/j.mrfmmm.2004.06.060
33 https://doi.org/10.1016/s0076-6879(10)72002-4
34 https://doi.org/10.1016/s1673-8527(07)60081-2
35 https://doi.org/10.1073/pnas.0503718102
36 https://doi.org/10.1073/pnas.0704665104
37 https://doi.org/10.1073/pnas.1105107108
38 https://doi.org/10.1086/345379
39 https://doi.org/10.1093/bioinformatics/btp324
40 https://doi.org/10.1093/bioinformatics/btr347
41 https://doi.org/10.1093/gbe/evr067
42 https://doi.org/10.1093/molbev/msn083
43 https://doi.org/10.1093/nar/25.17.3389
44 https://doi.org/10.1093/nar/gkm588
45 https://doi.org/10.1093/nar/gkp1163
46 https://doi.org/10.1093/nar/gkq572
47 https://doi.org/10.1093/sysbio/syq010
48 https://doi.org/10.1098/rsbl.2006.0515
49 https://doi.org/10.1101/gr.122747.111
50 https://doi.org/10.1111/1475-4754.00064
51 https://doi.org/10.1111/1475-4754.t01-1-00071
52 https://doi.org/10.1126/science.1113485
53 https://doi.org/10.1126/science.1123360
54 https://doi.org/10.1126/science.1131412
55 https://doi.org/10.1126/science.1141758
56 https://doi.org/10.1126/science.1146971
57 https://doi.org/10.1126/science.1174462
58 https://doi.org/10.1126/science.1188021
59 https://doi.org/10.1126/science.1188046
60 https://doi.org/10.1126/science.281.5375.402
61 https://doi.org/10.1146/annurev.genet.37.110801.143214
62 https://doi.org/10.1534/genetics.106.057349
63 https://doi.org/10.2144/000113721
64 schema:datePublished 2012-12
65 schema:datePublishedReg 2012-12-01
66 schema:description BACKGROUND: Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Molecule DNA Sequencing (tSMS), have shown great potential for sequencing DNA molecules from Pleistocene fossils. Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase. RESULTS: We found that a significantly larger fraction of the horse genome could be covered following oligonucleotide spiking however not reproducibly and at the cost of extra post-sequencing filtering procedures and skewed %GC content. In contrast, we showed that treating ancient DNA extracts with DNA phosphatase improved the amount of endogenous sequence information recovered per sequencing channel by up to 3.3-fold, while still providing molecular signatures of endogenous ancient DNA damage, including cytosine deamination and fragmentation by depurination. Additionally, we confirmed the existence of molecular preservation niches in large bone crystals from which DNA could be preferentially extracted. CONCLUSIONS: We propose DNA phosphatase treatment as a mechanism to increase sequence coverage of ancient genomes when using Helicos tSMS as a sequencing platform. Together with mild denaturation temperatures that favor access to endogenous ancient templates over modern DNA contaminants, this simple preparation procedure can improve overall Helicos tSMS performance when damaged DNA templates are targeted.
67 schema:genre research_article
68 schema:inLanguage en
69 schema:isAccessibleForFree true
70 schema:isPartOf N468544e7863345fb876e69c1bff62813
71 Nf1e818a001b245a5af94d36152697fa3
72 sg:journal.1023790
73 schema:name Improving the performance of true single molecule sequencing for ancient DNA
74 schema:pagination 177
75 schema:productId N21d72da365684b51b80c1400fe508fb8
76 N5f9f6f8d4e2347fab7f7de4f4e1c5204
77 Nbd6ee3a552614979958054b45467554f
78 Nc2736f8b7f884c41ac4fa5a0d3d4dec8
79 Nc8bdd18af4fd4a6faff7431ff5362174
80 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032076652
81 https://doi.org/10.1186/1471-2164-13-177
82 schema:sdDatePublished 2019-04-10T19:07
83 schema:sdLicense https://scigraph.springernature.com/explorer/license/
84 schema:sdPublisher N25fc2ee758a545f0b64b7aefadf5b9d8
85 schema:url http://link.springer.com/10.1186%2F1471-2164-13-177
86 sgo:license sg:explorer/license/
87 sgo:sdDataset articles
88 rdf:type schema:ScholarlyArticle
89 N1b2ce3b0369e499ab8d36d861783b5fc rdf:first sg:person.01132401575.22
90 rdf:rest N6ed8d0002cd84c54a7cf8da277eb008b
91 N21d72da365684b51b80c1400fe508fb8 schema:name readcube_id
92 schema:value 98ce7027d7c290122247e61b02841cdc2827647a4d64c9fe32e038f141114efc
93 rdf:type schema:PropertyValue
94 N25fc2ee758a545f0b64b7aefadf5b9d8 schema:name Springer Nature - SN SciGraph project
95 rdf:type schema:Organization
96 N28ed74756dd5492bbc0209e7ea1479cb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
97 schema:name Horses
98 rdf:type schema:DefinedTerm
99 N2d13944b044c41e29e6ca6415b581061 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
100 schema:name Nucleotidases
101 rdf:type schema:DefinedTerm
102 N34d1dcc2d1ad4ccc9556e8ae7609e67a rdf:first sg:person.01365624305.68
103 rdf:rest N373205c080464ad89b07a7dfd649e390
104 N373205c080464ad89b07a7dfd649e390 rdf:first sg:person.01241444046.39
105 rdf:rest Naa97428859b64c72b5b8056bece12211
106 N43f09923f20c4801a5f2d6f66a8225cf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
107 schema:name Sequence Analysis, DNA
108 rdf:type schema:DefinedTerm
109 N468544e7863345fb876e69c1bff62813 schema:issueNumber 1
110 rdf:type schema:PublicationIssue
111 N4c4b6743563d4a5e8f00f10d7fe934f0 rdf:first sg:person.01111262507.70
112 rdf:rest N77bafb90977d49f2a2eb3ac0d46f20b9
113 N5665092875a643899893d25d774c76d8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
114 schema:name Phylogeny
115 rdf:type schema:DefinedTerm
116 N5dec0f5aea864b279c602c737756b063 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
117 schema:name Nucleotides
118 rdf:type schema:DefinedTerm
119 N5f9f6f8d4e2347fab7f7de4f4e1c5204 schema:name dimensions_id
120 schema:value pub.1032076652
121 rdf:type schema:PropertyValue
122 N66b0bcb073654a02be2451669f7f0a67 rdf:first sg:person.01201152047.48
123 rdf:rest rdf:nil
124 N6ed8d0002cd84c54a7cf8da277eb008b rdf:first sg:person.01253440745.00
125 rdf:rest N7599429ce56a4421a845e67c53c24e00
126 N71841759f697405fa7c5640fd3b39f36 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
127 schema:name Base Sequence
128 rdf:type schema:DefinedTerm
129 N7599429ce56a4421a845e67c53c24e00 rdf:first sg:person.014051114644.24
130 rdf:rest Nbd0dba0766444ad9b5851088b69ee5ed
131 N77bafb90977d49f2a2eb3ac0d46f20b9 rdf:first sg:person.0714231071.76
132 rdf:rest N66b0bcb073654a02be2451669f7f0a67
133 N7f491fa0796c45bca408b458082d7279 rdf:first sg:person.01342327146.25
134 rdf:rest Ncd6b201ed377473887b741e9335692ba
135 N91da9dca5519487c9ffd3f3e1b5741ba schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name DNA
137 rdf:type schema:DefinedTerm
138 N943ff23a8a09473598eef157269b8ccd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
139 schema:name Base Composition
140 rdf:type schema:DefinedTerm
141 Naa97428859b64c72b5b8056bece12211 rdf:first sg:person.07732654527.21
142 rdf:rest N1b2ce3b0369e499ab8d36d861783b5fc
143 Nb5f36a762299472ebdf4a8c1c0e0632b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
144 schema:name Animals
145 rdf:type schema:DefinedTerm
146 Nbd0dba0766444ad9b5851088b69ee5ed rdf:first sg:person.01352355663.28
147 rdf:rest N4c4b6743563d4a5e8f00f10d7fe934f0
148 Nbd6ee3a552614979958054b45467554f schema:name nlm_unique_id
149 schema:value 100965258
150 rdf:type schema:PropertyValue
151 Nc2736f8b7f884c41ac4fa5a0d3d4dec8 schema:name doi
152 schema:value 10.1186/1471-2164-13-177
153 rdf:type schema:PropertyValue
154 Nc7630c6df2f7456eac52b82dfe819465 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
155 schema:name DNA, Mitochondrial
156 rdf:type schema:DefinedTerm
157 Nc8bdd18af4fd4a6faff7431ff5362174 schema:name pubmed_id
158 schema:value 22574620
159 rdf:type schema:PropertyValue
160 Ncbde219dd6aa476da4c1a647405fdd68 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
161 schema:name Fossils
162 rdf:type schema:DefinedTerm
163 Ncd6b201ed377473887b741e9335692ba rdf:first sg:person.01164561503.97
164 rdf:rest Ne28afd4020294b4aa4b37784deda74d9
165 Ne28afd4020294b4aa4b37784deda74d9 rdf:first sg:person.01013242545.03
166 rdf:rest N34d1dcc2d1ad4ccc9556e8ae7609e67a
167 Ne604a62ce2ed4c9cb66835f23929bd5c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
168 schema:name Genome
169 rdf:type schema:DefinedTerm
170 Nf1e818a001b245a5af94d36152697fa3 schema:volumeNumber 13
171 rdf:type schema:PublicationVolume
172 Nf23fec99c0474efc955bbbca2d177505 rdf:first sg:person.01050333103.98
173 rdf:rest N7f491fa0796c45bca408b458082d7279
174 Nf783c6db5b06413688228efc1a8aaf1c schema:name Department of Tourism and Culture, Government of Yukon, Yukon, Palaeontology Program, PO Box 2703 L2A, 2C6, Whitehorse, Yukon Territory Y1A, Canada
175 rdf:type schema:Organization
176 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
177 schema:name Biological Sciences
178 rdf:type schema:DefinedTerm
179 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
180 schema:name Genetics
181 rdf:type schema:DefinedTerm
182 sg:grant.2669364 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-13-177
183 rdf:type schema:MonetaryGrant
184 sg:grant.3100987 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-13-177
185 rdf:type schema:MonetaryGrant
186 sg:grant.3784511 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-13-177
187 rdf:type schema:MonetaryGrant
188 sg:journal.1023790 schema:issn 1471-2164
189 schema:name BMC Genomics
190 rdf:type schema:Periodical
191 sg:person.01013242545.03 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
192 schema:familyName Rasmussen
193 schema:givenName Morten
194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01013242545.03
195 rdf:type schema:Person
196 sg:person.01050333103.98 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
197 schema:familyName Ginolhac
198 schema:givenName Aurelien
199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050333103.98
200 rdf:type schema:Person
201 sg:person.01111262507.70 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
202 schema:familyName Gilbert
203 schema:givenName Thomas MP
204 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01111262507.70
205 rdf:type schema:Person
206 sg:person.01132401575.22 schema:affiliation https://www.grid.ac/institutes/grid.17089.37
207 schema:familyName Froese
208 schema:givenName Duane
209 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01132401575.22
210 rdf:type schema:Person
211 sg:person.01164561503.97 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
212 schema:familyName Stenderup
213 schema:givenName Jesper
214 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01164561503.97
215 rdf:type schema:Person
216 sg:person.01201152047.48 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
217 schema:familyName Orlando
218 schema:givenName Ludovic
219 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01201152047.48
220 rdf:type schema:Person
221 sg:person.01241444046.39 schema:affiliation https://www.grid.ac/institutes/grid.29857.31
222 schema:familyName Shapiro
223 schema:givenName Beth
224 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01241444046.39
225 rdf:type schema:Person
226 sg:person.01253440745.00 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
227 schema:familyName Steinmann
228 schema:givenName Kathleen E
229 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01253440745.00
230 rdf:type schema:Person
231 sg:person.01342327146.25 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
232 schema:familyName Vilstrup
233 schema:givenName Julia
234 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01342327146.25
235 rdf:type schema:Person
236 sg:person.01352355663.28 schema:affiliation https://www.grid.ac/institutes/grid.56302.32
237 schema:familyName AL-Rasheid
238 schema:givenName Khaled AS
239 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01352355663.28
240 rdf:type schema:Person
241 sg:person.01365624305.68 schema:affiliation https://www.grid.ac/institutes/grid.29857.31
242 schema:familyName Stiller
243 schema:givenName Mathias
244 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01365624305.68
245 rdf:type schema:Person
246 sg:person.014051114644.24 schema:affiliation https://www.grid.ac/institutes/grid.418487.6
247 schema:familyName Thompson
248 schema:givenName John F
249 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014051114644.24
250 rdf:type schema:Person
251 sg:person.0714231071.76 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
252 schema:familyName Willerslev
253 schema:givenName Eske
254 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714231071.76
255 rdf:type schema:Person
256 sg:person.07732654527.21 schema:affiliation Nf783c6db5b06413688228efc1a8aaf1c
257 schema:familyName Zazula
258 schema:givenName Grant
259 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.07732654527.21
260 rdf:type schema:Person
261 sg:pub.10.1007/bf02337515 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006563380
262 https://doi.org/10.1007/bf02337515
263 rdf:type schema:CreativeWork
264 sg:pub.10.1007/s11033-010-0145-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050621236
265 https://doi.org/10.1007/s11033-010-0145-8
266 rdf:type schema:CreativeWork
267 sg:pub.10.1038/362709a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019428971
268 https://doi.org/10.1038/362709a0
269 rdf:type schema:CreativeWork
270 sg:pub.10.1038/nature05336 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022286131
271 https://doi.org/10.1038/nature05336
272 rdf:type schema:CreativeWork
273 sg:pub.10.1038/nature07446 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003406391
274 https://doi.org/10.1038/nature07446
275 rdf:type schema:CreativeWork
276 sg:pub.10.1038/nature08835 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021776500
277 https://doi.org/10.1038/nature08835
278 rdf:type schema:CreativeWork
279 sg:pub.10.1038/nature09710 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050205294
280 https://doi.org/10.1038/nature09710
281 rdf:type schema:CreativeWork
282 sg:pub.10.1038/nbt.1551 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039844797
283 https://doi.org/10.1038/nbt.1551
284 rdf:type schema:CreativeWork
285 sg:pub.10.1038/nmeth.1354 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028638279
286 https://doi.org/10.1038/nmeth.1354
287 rdf:type schema:CreativeWork
288 sg:pub.10.1186/1471-2148-9-95 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035465276
289 https://doi.org/10.1186/1471-2148-9-95
290 rdf:type schema:CreativeWork
291 https://app.dimensions.ai/details/publication/pub.1082939807 schema:CreativeWork
292 https://doi.org/10.1002/0471142727.mb0710s92 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007096038
293 rdf:type schema:CreativeWork
294 https://doi.org/10.1016/0378-1119(94)90713-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023535700
295 rdf:type schema:CreativeWork
296 https://doi.org/10.1016/j.aanat.2011.07.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037337752
297 rdf:type schema:CreativeWork
298 https://doi.org/10.1016/j.cub.2003.12.012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020335334
299 rdf:type schema:CreativeWork
300 https://doi.org/10.1016/j.cub.2009.11.068 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028054623
301 rdf:type schema:CreativeWork
302 https://doi.org/10.1016/j.mrfmmm.2004.06.060 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024985289
303 rdf:type schema:CreativeWork
304 https://doi.org/10.1016/s0076-6879(10)72002-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027045392
305 rdf:type schema:CreativeWork
306 https://doi.org/10.1016/s1673-8527(07)60081-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023665888
307 rdf:type schema:CreativeWork
308 https://doi.org/10.1073/pnas.0503718102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017795199
309 rdf:type schema:CreativeWork
310 https://doi.org/10.1073/pnas.0704665104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045401726
311 rdf:type schema:CreativeWork
312 https://doi.org/10.1073/pnas.1105107108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049707959
313 rdf:type schema:CreativeWork
314 https://doi.org/10.1086/345379 schema:sameAs https://app.dimensions.ai/details/publication/pub.1058641019
315 rdf:type schema:CreativeWork
316 https://doi.org/10.1093/bioinformatics/btp324 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038266369
317 rdf:type schema:CreativeWork
318 https://doi.org/10.1093/bioinformatics/btr347 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030568980
319 rdf:type schema:CreativeWork
320 https://doi.org/10.1093/gbe/evr067 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040095022
321 rdf:type schema:CreativeWork
322 https://doi.org/10.1093/molbev/msn083 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048530400
323 rdf:type schema:CreativeWork
324 https://doi.org/10.1093/nar/25.17.3389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047265454
325 rdf:type schema:CreativeWork
326 https://doi.org/10.1093/nar/gkm588 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053124372
327 rdf:type schema:CreativeWork
328 https://doi.org/10.1093/nar/gkp1163 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036956881
329 rdf:type schema:CreativeWork
330 https://doi.org/10.1093/nar/gkq572 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049568274
331 rdf:type schema:CreativeWork
332 https://doi.org/10.1093/sysbio/syq010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046004748
333 rdf:type schema:CreativeWork
334 https://doi.org/10.1098/rsbl.2006.0515 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004740948
335 rdf:type schema:CreativeWork
336 https://doi.org/10.1101/gr.122747.111 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020096058
337 rdf:type schema:CreativeWork
338 https://doi.org/10.1111/1475-4754.00064 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036961816
339 rdf:type schema:CreativeWork
340 https://doi.org/10.1111/1475-4754.t01-1-00071 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044532565
341 rdf:type schema:CreativeWork
342 https://doi.org/10.1126/science.1113485 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062452286
343 rdf:type schema:CreativeWork
344 https://doi.org/10.1126/science.1123360 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062453436
345 rdf:type schema:CreativeWork
346 https://doi.org/10.1126/science.1131412 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062454636
347 rdf:type schema:CreativeWork
348 https://doi.org/10.1126/science.1141758 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062455979
349 rdf:type schema:CreativeWork
350 https://doi.org/10.1126/science.1146971 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047897915
351 rdf:type schema:CreativeWork
352 https://doi.org/10.1126/science.1174462 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062460190
353 rdf:type schema:CreativeWork
354 https://doi.org/10.1126/science.1188021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002597304
355 rdf:type schema:CreativeWork
356 https://doi.org/10.1126/science.1188046 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020995997
357 rdf:type schema:CreativeWork
358 https://doi.org/10.1126/science.281.5375.402 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051953666
359 rdf:type schema:CreativeWork
360 https://doi.org/10.1146/annurev.genet.37.110801.143214 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014567048
361 rdf:type schema:CreativeWork
362 https://doi.org/10.1534/genetics.106.057349 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041192332
363 rdf:type schema:CreativeWork
364 https://doi.org/10.2144/000113721 schema:sameAs https://app.dimensions.ai/details/publication/pub.1069096345
365 rdf:type schema:CreativeWork
366 https://www.grid.ac/institutes/grid.17089.37 schema:alternateName University of Alberta
367 schema:name Department of Earth and Atmospheric Sciences, University of Alberta, T6G 2E3, Edmonton, Alberta, Canada
368 rdf:type schema:Organization
369 https://www.grid.ac/institutes/grid.29857.31 schema:alternateName Pennsylvania State University
370 schema:name Department of Biology, The Pennsylvania State University, 326 Mueller Lab, 16802, University Park, PA, USA
371 rdf:type schema:Organization
372 https://www.grid.ac/institutes/grid.418487.6 schema:alternateName Helicos Biosciences (United States)
373 schema:name Applications, Methods and Collaborations, Helicos BioSciences, One Kendall Square Bldg 200LL, 02139, Cambridge, MA, USA
374 NABsys Inc, 60 Clifford Street, 0290, Providence, RI, USA
375 rdf:type schema:Organization
376 https://www.grid.ac/institutes/grid.5254.6 schema:alternateName University of Copenhagen
377 schema:name Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5-7 Øster Voldgade, 1350, København, Denmark
378 rdf:type schema:Organization
379 https://www.grid.ac/institutes/grid.56302.32 schema:alternateName King Saud University
380 schema:name Zoology Department, College of Science King Saud University, P.O. Box, 2455, 11451, Riyadh, Saudi Arabia
381 rdf:type schema:Organization
382 https://www.grid.ac/institutes/grid.66859.34 schema:alternateName Broad Institute
383 schema:name Applications, Methods and Collaborations, Helicos BioSciences, One Kendall Square Bldg 200LL, 02139, Cambridge, MA, USA
384 Broad Institute of Massachusetts Institute of Technology and Harvard, 021423, Cambridge, MA, USA
385 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...