Research graph
References from Comparing the Performance of Double‐Stranded and Single‐Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction. Local targets link to admitted publications; unresolved targets remain external evidence.
Dental Calculus: The Calcified Biofilm and Its Role in Disease Development
10.1111/prd.12151 · 2018 · External reference
Unresolved reference
2010 · External reference
A Neanderthal Deciduous Human Molar With Incipient Carious Infection From the Middle Palaeolithic de Nadale cave, Italy: Arnaud et al
10.1002/ajpa.23111 · 2017 · External reference
10.17504/protocols.io.bidyka7w
10.17504/protocols.io.bidyka7w · 2020 · External reference
10.17504/protocols.io.bqcsmswe
10.17504/protocols.io.bqcsmswe · External reference
Unresolved reference
External reference
Middle Paleolithic and Uluzzian Human Remains From Fumane Cave, Italy
10.1016/j.jhevol.2014.03.001 · 2014 · External reference
Library Construction for Ancient Genomics: Single Strand or Double Strand?
10.2144/000114176 · 2014 · External reference
Reconstructing Double‐Stranded DNA Fragments on a Single‐Molecule Level Reveals Patterns of Degradation in Ancient Samples
10.1101/gr.263863.120 · 2020 · External reference
Patterns of Damage in Genomic DNA Sequences From a Neandertal
10.1073/pnas.0704665104 · 2007 · External reference
Single‐Tube Library Preparation for Degraded DNA
10.1111/2041-210x.12871 · 2018 · External reference
Application of a Novel “Pan‐Genome”‐Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains
10.1371/journal.pone.0145861 · 2015 · External reference
Complete Mitochondrial Genome Sequence of a Middle Pleistocene Cave Bear Reconstructed From Ultrashort DNA Fragments
10.1073/pnas.1314445110 · 2013 · External reference
Ancient DNA Damage
10.1101/cshperspect.a012567 · 2013 · External reference
Partial Genetic Turnover in Neandertals: Continuity in the East and Population Replacement in the West
10.1093/molbev/mss074 · 2012 · External reference
Twelve Years of SAMtools and BCFtools
10.1093/gigascience/giab008 · 2021 · External reference
Simple Statistical Identification and Removal of Contaminant Sequences in Marker‐Gene and Metagenomics Data
10.1186/s40168-018-0605-2 · 2018 · External reference
DNA From Human Ancient Bacteria: A Novel Source of Genetic Evidence From Archaeological Dental Calculus
10.1111/j.1475-4754.2012.00707.x · 2013 · External reference
Unresolved reference
External reference
Assessing Alignment‐Based Taxonomic Classification of Ancient Microbial DNA
10.7717/peerj.6594 · 2019 · External reference
10.1128/msystems.00187‐18
10.1128/msystems.00187‐18 · External reference
A Unified Protocol for Simultaneous Extraction of DNA and Proteins From Archaeological Dental Calculus
10.1016/j.jas.2020.105135 · 2020 · External reference
Community‐Curated and Standardised Metadata of Published Ancient Metagenomic Samples With AncientMetagenomeDir
10.1038/s41597-021-00816-y · 2021 · External reference
Reproducible, Portable, and Efficient Ancient Genome Reconstruction With nf‐core/eager
10.7717/peerj.10947 · 2021 · External reference
The Evolution and Changing Ecology of the African Hominid Oral Microbiome
10.1073/pnas.2021655118 · 2021 · External reference
Genome Sequence of a 45,000‐Year‐Old Modern Human From Western Siberia
10.1038/nature13810 · 2014 · External reference
Ancient Species Diversity and Niche Adaptation in Tannerella and Porphyromonas Revealed Through Pangenomics
10.1093/gbe/evag136 · 2026 · External reference
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
10.1038/s41596-020-0338-0 · 2020 · External reference
Single‐Stranded DNA Library Preparation From Highly Degraded DNA Using T4 DNA Ligase
2017 · External reference
Single‐Stranded DNA Library Preparation for the Sequencing of Ancient or Damaged DNA
10.1038/nprot.2013.038 · 2013 · External reference
A Method for Single‐Stranded Ancient DNA Library Preparation
10.1007/978-1-4939-9176-1_9 · 2019 · External reference
ESR and U‐Series Analyses of Enamel and Dentine Fragments of the Banyoles Mandible
10.1016/j.jhevol.2005.10.001 · 2006 · External reference
DNA Sequences From Multiple Amplifications Reveal Artifacts Induced by Cytosine Deamination in Ancient DNA
10.1093/nar/29.23.4793 · 2001 · External reference
Structure, Function and Diversity of the Healthy Human Microbiome
10.1038/nature11234 · 2012 · External reference
Human Thanatomicrobiome Succession and Time Since Death
10.1038/srep29598 · 2016 · External reference
Bronze Age Population Dynamics and the Rise of Dairy Pastoralism on the Eastern Eurasian Steppe
2018 · External reference
mapDamage2.0: Fast Approximate Bayesian Estimates of Ancient DNA Damage Parameters
2013 · External reference
A Fast and Efficient Single‐Stranded Genomic Library Preparation Method Optimized for Ancient DNA
10.1093/jhered/esab012 · 2021 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
ggdist: Visualizations of Distributions and Uncertainty in the Grammar of Graphics
2024 · External reference
Unresolved reference
External reference
Double Indexing Overcomes Inaccuracies in Multiplex Sequencing on the Illumina Platform
10.1093/nar/gkr771 · 2012 · External reference
Natural Products From Reconstructed Bacterial Genomes of the Middle and Upper Paleolithic
10.1126/science.adf5300 · 2023 · External reference
Bayesian Community‐Wide Culture‐Independent Microbial Source Tracking
10.1038/nmeth.1650 · 2011 · External reference
Multilocus Sequence Analysis of Porphyromonas gingivalis Indicates Frequent Recombination
10.1099/mic.0.26267-0 · 2003 · External reference
The Consequences of Genetic Drift for Bacterial Genome Complexity
10.1101/gr.091785.109 · 2009 · External reference
Fast and Accurate Short Read Alignment With Burrows‐Wheeler Transform
2009 · External reference
The Sequence Alignment/Map Format and SAMtools
10.1093/bioinformatics/btp352 · 2009 · External reference
El Enterramiento Múltiple, Calcolítico, de Camino del Molino (Caravaca, Murcia). Metodología y Primeros Resultados de un Yacimiento Excepcional
10.3989/tp.2009.09025 · 2009 · External reference
A High‐Coverage Neandertal Genome From Chagyrskaya Cave
10.1073/pnas.2004944117 · 2020 · External reference
Hallstatt Miners Consumed Blue Cheese and Beer During the Iron Age and Retained a Non‐Westernized Gut Microbiome Until the Baroque Period
10.1016/j.cub.2021.09.031 · 2021 · External reference
Differential Preservation of Endogenous Human and Microbial DNA in Dental Calculus and Dentin
10.1038/s41598-018-28091-9 · 2018 · External reference
Cutadapt Removes Adapter Sequences From High‐Throughput Sequencing Reads
10.14806/ej.17.1.200 · 2011 · External reference
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
10.1371/journal.pone.0061217 · 2013 · External reference
The Middle to Upper Paleolithic Transition in La Güelga Cave (Asturias, Northern Spain)
10.1016/j.quaint.2017.08.061 · 2018 · External reference
Microbial Community Assembly and Metabolic Function During Mammalian Corpse Decomposition
10.1126/science.aad2646 · 2016 · External reference
Nuclear DNA Sequences From the Middle Pleistocene Sima de los Huesos Hominins
10.1038/nature17405 · 2016 · External reference
A Mitochondrial Genome Sequence of a Hominin From Sima de los Huesos
10.1038/nature12788 · 2014 · External reference
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing
10.1101/pdb.prot5448 · 2010 · External reference
A High‐Coverage Genome Sequence From an Archaic Denisovan Individual
10.1126/science.1224344 · 2012 · External reference
10.17504/protocols.io.q26g71w48gwz/v1
10.17504/protocols.io.q26g71w48gwz/v1 · External reference
10.17504/protocols.io.261ge1j6wv47/v1
10.17504/protocols.io.261ge1j6wv47/v1 · External reference
Subsistence Strategies in Traditional Societies Distinguish Gut Microbiomes
10.1038/ncomms7505 · 2015 · External reference
Temporal Stability of the Human Skin Microbiome
10.1016/j.cell.2016.04.008 · 2016 · External reference
Unresolved reference
External reference
dnaMATE: A Consensus Melting Temperature Prediction Server for Short DNA Sequences
10.1093/nar/gki379 · 2005 · External reference
ape 5.0: An Environment for Modern Phylogenetics and Evolutionary Analyses in R
10.1093/bioinformatics/bty633 · 2019 · External reference
A Complete Domain‐to‐Species Taxonomy for Bacteria and Archaea
10.1038/s41587-020-0501-8 · 2020 · External reference
GTDB: An Ongoing Census of Bacterial and Archaeal Diversity Through a Phylogenetically Consistent, Rank Normalized and Complete Genome‐Based Taxonomy
10.1093/nar/gkab776 · 2022 · External reference
Unresolved reference
External reference
A High‐Coverage Neandertal Genome From Vindija Cave in Croatia
10.1126/science.aao1887 · 2017 · External reference
The Complete Genome Sequence of a Neanderthal From the Altai Mountains
10.1038/nature12886 · 2014 · External reference
Unresolved reference
2023 · External reference
The First Neanderthal Specimen From Serbia: Maxillary First Molar From the Late Pleistocene of Pešturina Cave
10.1016/j.jhevol.2019.03.018 · 2019 · External reference
10.1128/msystems.00039‐18
10.1128/msystems.00039‐18 · External reference
Nonpareil: A Redundancy‐Based Approach to Assess the Level of Coverage in Metagenomic Datasets
2014 · External reference
mixOmics: An R Package for Omics Feature Selection and Multiple Data Integration
10.1371/journal.pcbi.1005752 · 2017 · External reference
Extraction of Highly Degraded DNA From Ancient Bones, Teeth and Sediments for High‐Throughput Sequencing
10.1038/s41596-018-0050-5 · 2018 · External reference
Ancient DNA Extraction From Bones and Teeth
10.1038/nprot.2007.247 · 2007 · External reference
Neandertal Cannibalism and Neandertal Bones Used as Tools in Northern Europe
10.1038/srep29005 · 2016 · External reference
Comparative Biometrical Study of the Mousterian Mandible From Cueva del Boquete de Zafarraya (Málaga, Spain)
10.1007/bf02436200 · 1999 · External reference
Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA
10.1371/journal.pone.0034131 · 2012 · External reference
AdapterRemoval v2: Rapid Adapter Trimming, Identification, and Read Merging
10.1186/s13104-016-1900-2 · 2016 · External reference
Theory of Prokaryotic Genome Evolution
10.1073/pnas.1614083113 · 2016 · External reference
SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing
10.1002/imt2.191 · 2024 · External reference
Neandertal and Denisovan DNA From Pleistocene Sediments
10.1126/science.aam9695 · 2017 · External reference
10.17504/protocols.io.4r3l287x3l1y/v3
10.17504/protocols.io.4r3l287x3l1y/v3 · External reference
Genome Analysis of Multiple Pathogenic Isolates of Streptococcus agalactiae : Implications for the Microbial ‘Pan‐Genome’
10.1073/pnas.0506758102 · 2005 · External reference
Unresolved reference
2017 · External reference
Exploring the Potential of Dental Calculus to Shed Light on Past Human Migrations in Oceania
10.1038/s41467-024-53920-z · 2024 · External reference
Microbial Differences Between Dental Plaque and Historic Dental Calculus Are Related to Oral Biofilm Maturation Stage
10.1186/s40168-019-0717-3 · 2019 · External reference
10.1128/msystems.00080‐18
10.1128/msystems.00080‐18 · External reference
High Conservation of the Dental Plaque Microbiome Across Populations With Differing Subsistence Strategies and Levels of Market Integration
10.1111/mec.16988 · 2023 · External reference
Global and Temporal Oral Microbial Catalog Expands Known Microbiome Diversity
2025 · External reference
10.1002/ajpa.70350
10.1002/ajpa.70350 · External reference
New Insights on Single‐Stranded Versus Double‐Stranded DNA Library Preparation for Ancient DNA
10.2144/000114364 · 2015 · External reference
Late Neandertals in Southeastern Iberia: Sima de las Palomas del Cabezo Gordo, Murcia, Spain
10.1073/pnas.0811213106 · 2008 · External reference
Neandertal Mandibles From the Sima de las Palomas del Cabezo Gordo, Murcia, Southeastern Spain
10.1002/ajpa.21223 · 2010 · External reference
A Robust Framework for Microbial Archaeology
10.1146/annurev-genom-091416-035526 · 2017 · External reference
Pathogens and Host Immunity in the Ancient Human Oral Cavity
10.1038/ng.2906 · 2014 · External reference
A New Era in Palaeomicrobiology: Prospects for Ancient Dental Calculus as a Long‐Term Record of the Human Oral Microbiome
10.1098/rstb.2013.0376 · 2015 · External reference
Neanderthal Behaviour, Diet, and Disease Inferred From Ancient DNA in Dental Calculus
10.1038/nature21674 · 2017 · External reference
Reconstruction of Ancient Microbial Genomes From the Human Gut
10.1038/s41586-021-03532-0 · 2021 · External reference
10.1007/978-3-319-24277-4
10.1007/978-3-319-24277-4 · 2016 · External reference
Improved Metagenomic Analysis With Kraken 2
10.1186/s13059-019-1891-0 · 2019 · External reference
Radiocarbon Dating Casts Doubt on the Late Chronology of the Middle to Upper Palaeolithic Transition in Southern Iberia
10.1073/pnas.1207656110 · 2013 · External reference
10.1099/mgen.0.000949
10.1099/mgen.0.000949 · External reference
Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery
10.1111/1755-0998.70054 · 2025 · External reference
Struo2: Efficient Metagenome Profiling Database Construction for Ever‐Expanding Microbial Genome Datasets
10.7717/peerj.12198 · 2021 · External reference
Intrinsic Challenges in Ancient Microbiome Reconstruction Using 16S rRNA Gene Amplification
10.1038/srep16498 · 2015 · External reference
