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Mining ancient microbiomes using selective enrichment of damaged DNA molecules
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/978-1-61779-516-9_23openalex-snapshot
Analysis of High-Throughput Ancient DNA Sequencing Data
inferredcites →https://doi.org/10.1016/j.cub.2009.11.068openalex-snapshot
A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia
inferredcites →https://doi.org/10.1016/j.jbiotec.2014.11.031openalex-snapshot
Complete genome sequence of Pseudomonas rhizosphaerae IH5T (=DSM 16299T), a phosphate-solubilizing rhizobacterium for bacterial biofertilizer
inferredcites →https://doi.org/10.1016/j.pbi.2017.01.002openalex-snapshot
Reinforcing plant evolutionary genomics using ancient DNA
inferredcites →https://doi.org/10.1038/35048692openalex-snapshot
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
inferredcites →https://doi.org/10.1038/nature10158openalex-snapshot
Genome sequence and analysis of the tuber crop potato
inferredcites →https://doi.org/10.1038/nature10549openalex-snapshot
A draft genome of Yersinia pestis from victims of the Black Death
inferredcites →https://doi.org/10.1038/nature11119openalex-snapshot
The tomato genome sequence provides insights into fleshy fruit evolution
inferredcites →https://doi.org/10.1038/nature12788openalex-snapshot
A mitochondrial genome sequence of a hominin from Sima de los Huesos
inferredcites →https://doi.org/10.1038/nature21674openalex-snapshot
Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus
inferredcites →https://doi.org/10.1038/ng.2536openalex-snapshot
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions
inferredcites →https://doi.org/10.1038/ng.2906openalex-snapshot
Pathogens and host immunity in the ancient human oral cavity
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nprot.2013.038openalex-snapshot
Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA
inferredcites →https://doi.org/10.1038/nrg3935openalex-snapshot
Reconstructing ancient genomes and epigenomes
inferredcites →https://doi.org/10.1073/pnas.0504930102openalex-snapshot
Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000
inferredcites →https://doi.org/10.1073/pnas.0704665104openalex-snapshot
Patterns of damage in genomic DNA sequences from a Neandertal
inferredcites →https://doi.org/10.1073/pnas.1712337115openalex-snapshot
Coprolites reveal ecological interactions lost with the extinction of New Zealand birds
inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btr509openalex-snapshot
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btr521openalex-snapshot
adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data
inferredcites →https://doi.org/10.1093/bioinformatics/btt193openalex-snapshot
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
inferredcites →https://doi.org/10.1093/bioinformatics/btu393openalex-snapshot
circlize implements and enhances circular visualization in R
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/nar/gkm965openalex-snapshot
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
inferredcites →https://doi.org/10.1093/nar/gkp1163openalex-snapshot
Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
inferredcites →https://doi.org/10.1093/nar/gkr771openalex-snapshot
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
inferredcites →https://doi.org/10.1093/nar/gku699openalex-snapshot
leeHom: adaptor trimming and merging for Illumina sequencing reads
inferredcites →https://doi.org/10.1093/nar/gkx033openalex-snapshot
Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase
inferredcites →https://doi.org/10.1098/rsos.160239openalex-snapshot
Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens
inferredcites →https://doi.org/10.1101/050559openalex-snapshot
MALT: Fast alignment and analysis of metagenomic DNA sequence data applied to the Tyrolean Iceman
inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot
Circos: An information aesthetic for comparative genomics
inferredcites →https://doi.org/10.1101/gr.174201.114openalex-snapshot
Selective enrichment of damaged DNA molecules for ancient genome sequencing
inferredcites →https://doi.org/10.1101/gr.5969107openalex-snapshot
MEGAN analysis of metagenomic data
inferredcites →https://doi.org/10.1101/pdb.prot5448openalex-snapshot
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing
inferredcites →https://doi.org/10.1111/1755-0998.12549openalex-snapshot
vcfr : a package to manipulate and visualize variant call format data in R
inferredcites →https://doi.org/10.1126/science.1123360openalex-snapshot
Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA
inferredcites →https://doi.org/10.1126/science.1178534openalex-snapshot
The B73 Maize Genome: Complexity, Diversity, and Dynamics
inferredcites →https://doi.org/10.1126/science.1216304openalex-snapshot
Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe
inferredcites →https://doi.org/10.1126/science.1260617openalex-snapshot
Comment on “Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans”
inferredcites →https://doi.org/10.1126/science.aam9425openalex-snapshot
Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America
inferredcites →https://doi.org/10.1128/jb.01122-10openalex-snapshot
Genome Sequence of the Biocontrol Agent Pantoea vagans Strain C9-1
inferredcites →https://doi.org/10.1146/annurev-genom-091416-035526openalex-snapshot
A Robust Framework for Microbial Archaeology
inferredcites →https://doi.org/10.1371/journal.pgen.1007155openalex-snapshot
The rate and potential relevance of new mutations in a colonizing plant lineage
inferredcites →https://doi.org/10.1371/journal.pone.0062799openalex-snapshot
No Ancient DNA Damage in Actinobacteria from the Neanderthal Bone
inferredcites →https://doi.org/10.2307/280894openalex-snapshot
Basketmaker II Subsistence: Carbon Isotopes and Other Dietary Indicators from Cedar Mesa, Utah
inferredcites →https://doi.org/10.4056/sigs.631049openalex-snapshot
Complete genome sequence of Streptosporangium roseum type strain (NI 9100T)
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
inferredcites →https://doi.org/10.7554/elife.00731openalex-snapshot
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine
inferredcites →https://doi.org/10.7554/elife.10005openalex-snapshot
Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1099/mgen.0.000384openalex-snapshot
The past, present and future of ancient bacterial DNA
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