little-book-of-smiley-plots/CITATION.cff at main · SPAAM-community/little-book-of-smiley-plots · GitHub

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cff-version: 1.2.0
abstract: |
  A key part of any ancient DNA project is to show that the DNA is exactly that - that the DNA is ancient, rather than from modern contamination.
  A key authentication method is to show the presence of elevated C to T deamination patterns (and the complementary G to A) at the end of DNA molecules - known as damage patterns - originally reported by (Briggs et al. 2007).
  These patterns can be plotted in what have been colloquially known as ’Smiley Plots. However, there can be a wide range of smiley plots, some which show valid ancient DNA, and others that do not - either due to not actually having true ancient DNA but also from laboratory and/or bioinformatic artifacts.
  This book aims to act as a reference guide to interpreting ancient DNA damage plots, providing a wide range of example ‘smiley plots’, with descriptions of what the describe and what can cause them. As an added bit of fun, each type of smiley plot comes with a artistic interpretation of the line shape contributed by members of the ancient DNA community.
authors:
  - family-names: Fellows Yates
    given-names: James A.
    orcid: https://orcid.org/0000-0001-5585-6277
  - family-names: Zeibig
    given-names: Teresa
    orcid: https://orcid.org/0009-0000-2068-3505
  - family-names: Andrades Valtueña
    given-names: Aida
    orcid: https://orcid.org/0000-0002-1737-2228
  - family-names: Heintzmann
    given-names: Pete D.
    orcid: https://orcid.org/0000-0002-6449-0219
  - family-names: Guschanski
    given-names: Katerina
    orcid: https://orcid.org/0000-0002-8493-5457
  - family-names: Brealey
    given-names: Jaelle C.
    orcid: https://orcid.org/0000-0001-7068-2017
  - family-names: Dagtas
    given-names: Nihan D.
    orcid: https://orcid.org/0000-0003-2658-7295
  - family-names: Fagernäs
    given-names: Zandra
    orcid: https://orcid.org/0000-0003-2667-3556
  - family-names: Santos
    given-names: Patrícia
  - family-names: Hübner
    given-names: Alexander
    orcid: https://orcid.org/0000-0003-3572-9996
  - family-names: Wiborg Runge
    given-names: Anne Kathrine
    orcid: https://orcid.org/0000-0003-2421-4831
  - family-names: Korlević
    given-names: Petra
    orcid: https://orcid.org/0000-0002-5418-5587
  - family-names: Vukovikj
    given-names: Maja
  - family-names: Psonis
    given-names: Nikos
    orcid: https://orcid.org/0000-0002-2083-9001
  - family-names: Warinner
    given-names: Christina
    orcid: https://orcid.org/0000-0002-4528-5877
  - family-names: Wegner
    given-names: Carl-Eric
    orcid: https://orcid.org/0000-0002-4339-6602
title: "The Little Book of Smiley Plots: A collection of ancient DNA patterns and their causes"
keywords:
  - ancient DNA
  - aDNA
  - palaeogenetics
  - palaeogenomics
  - archaeogenetics
  - archaeogenomics
  - ancient metagenomics
  - microbiome
  - pathogen
  - bioinformatics
  - reference guide
  - damage patterns
  - misincorporation patterns
version: "1.0.0"
date-released: "2025-09-21"
license: CC0-1.0
license-url: https://github.com/SPAAM-community/little-book-of-smiley-plots/blob/main/LICENSE
repository-code: "https://github.com/SPAAM-community/little-book-of-smiley-plots/"
url: "https://www.spaam-community.org/little-book-of-smiley-plots/"
doi: 10.5281/zenodo.17170743
type: dataset