mapDamage: testing for damage patterns in ancient DNA sequences
By Aurelien Ginolhac, M. Rasmussen, M. Gilbert, Eske Willerslev, Ludovic Antoine Alexandre Orlando. Bioinform., 2011
347 citations recorded by the source corpus.
Subfields: Ecology, Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/3ad4889aec89e0f806706f3c5a4944ddeb8a1fde
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Ecology
- Michael D. Martin
- Beth Shapiro
- M. Hofreiter
- Lars Fehren-Schmitz
- J. Krause
- Alan Cooper
- Eske Willerslev
- Wolfgang Haak
In Genetics
- Michael D. Martin
- M. Hofreiter
- Beth Shapiro
- Lars Fehren-Schmitz
- J. Krause
- Alan Cooper
- Wolfgang Haak
- Bastien Llamas
In Molecular Biology
- Beth Shapiro
- M. Hofreiter
- Thomas Sicheritz-Pontén
- Christian Carøe
- J. Krause
- Alexander Seitz
- Alan Cooper
- Shyam Gopalakrishnan
Citations in the corpus
- EAGER: efficient ancient genome reconstruction (2016, methodology): “The pipeline can authenticate aDNA samples based on DNA damage patterns with mapDamage [13] and includes methods that are offered by Preseq [14] to determine the complexity of sequencing libraries.”
- Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX (2014, methodology): “Evaluating the presence of postmortem DNA damage signatures from read alignments has now become part of a standard procedure to authenticate aDNA data sets 43,44 .”
- Single‐tube library preparation for degraded DNA (2017, background): “Although it is possible to remove uracil bases prior to library preparation (Briggs et al. 2010), paleogeneticists often choose to leave uracil damage patterns intact in order to authenticate the ancient origin of reads (e.g. Ginolhac et al. 2011; Meyer et al. 2016; Skoglund et al. 2014).”
- From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era (2017, positive): “…patterns are used to assess the authenticity of aDNA, and have been implemented in several recent bioinformatics programs (Helgason et al. 2007; Jónsson et al. 2013; Korneliussen, Albrechtsen, and Nielsen 2014; Skoglund et al. 2014; Renaud et al. 2015; Peltzer et al. 2016; Ginolhac et al. 2011).”
- Ancient DNA (2019, methodology): “Building upon previous guidelines [3, 38], nine criteria for authenticity were set out more than a decade ago by Cooper and Poinar [39], and additional criteria have been proposed since this time.”