ArticleGenome biology2010
Computational challenges in the analysis of ancient DNA.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 1 of them a synthesis that pooled it.
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Who cites it
60 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Environmental palaeogenomic reconstruction of an Ice Age algal population.Communications biology · 2021Pooled it
- On the ancestry and evolution of the extinct dire wolf.Cell genomics · 2026Article
- CHARON: estimating the drift time and the number of individuals in environmental DNA with diploid individuals.G3 (Bethesda, Md.) · 2026Article
- A comparative analysis dataset for improving genuine SNP identification in ancient maize aDNA.Data in brief · 2026Article
- Genetic affinities between the ancient Greek colony of Amvrakia and its metropolis.Genome biology · 2026Article
- Introgressed mitochondrial fragments from archaic hominins alter nuclear genome function in modern humans.Science advances · 2026Article
- SAFARI: pangenome alignment of ancient DNA using purine/pyrimidine encodings.NAR genomics and bioinformatics · 2025Article
- Fifteenth century CE Bolivian maize reveals genetic affinities with ancient Peruvian maize.eLife · 2025Article
- CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.Genome biology · 2025Article
- clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples.Genomics, proteomics & bioinformatics · 2025Article
- The Genomic Signature of Demographic Decline in a Long-Distance Migrant in a Range-Extreme Population.Molecular ecology · 2025Article
- Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data.Genome biology · 2025Article
- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
- Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.Briefings in bioinformatics · 2024Article
- soibean: High-Resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs.Molecular biology and evolution · 2024Article
- Deep-time phylogenetic inference by paleoproteomic analysis of dental enamel.Nature protocols · 2024Article
- Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data.Microorganisms · 2023Article
- Challenges and Opportunities behind the Use ofPlants (Basel, Switzerland) · 2023Review
- Dynamic evolution of size and colour in the highly specializedProceedings. Biological sciences · 2023Article
- Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data.BMC genomics · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.
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Registered trials
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