@article{TaronLellBarlowetal.2018,
  author    = {Taron, Ulrike H. and Lell, Moritz and Barlow, Axel and Paijmans, Johanna L. A.},
  title     = {Testing of Alignment Parameters for Ancient Samples},
  series = {Genese},
  volume    = {9},
  journal   = {Genese},
  number    = {3},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4425},
  doi       = {10.3390/genes9030157},
  pages     = {12},
  year      = {2018},
  abstract  = {High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present 'TAPAS', (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.},
  language  = {en}
}
@article{HofreiterHartmann2020,
  author    = {Hofreiter, Michael and Hartmann, Stefanie},
  title     = {Reconstructing protein-coding sequences from ancient DNA},
  series = {Odorant binding and chemosensory proteins},
  volume    = {642},
  journal   = {Odorant binding and chemosensory proteins},
  publisher = {Academic Press, an imprint of Elsevier},
  address   = {Cambridge, MA.},
  isbn      = {978-0-12-821157-1},
  issn      = {0076-6879},
  doi       = {10.1016/bs.mie.2020.05.008},
  pages     = {21 -- 33},
  year      = {2020},
  abstract  = {Obtaining information about functional details of proteins of extinct species is of critical importance for a better understanding of the real-life appearance, behavior and ecology of these lost entries in the book of life. In this chapter, we discuss the possibilities to retrieve the necessary DNA sequence information from paleogenomic data obtained from fossil specimens, which can then be used to express and subsequently analyze the protein of interest. We discuss the problems specific to ancient DNA, including mis-coding lesions, short read length and incomplete paleogenome assemblies. Finally, we discuss an alternative, but currently rarely used approach, direct PCR amplification, which is especially useful for comparatively short proteins.},
  language  = {en}
}
@article{PalkopoulouLipsonMallicketal.2018,
  author    = {Palkopoulou, Eleftheria and Lipson, Mark and Mallick, Swapan and Nielsen, Svend and Rohland, Nadin and Baleka, Sina Isabelle and Karpinski, Emil and Ivancevici, Atma M. and Thu-Hien To, and Kortschak, Daniel and Raison, Joy M. and Qu, Zhipeng and Chin, Tat-Jun and Alt, Kurt W. and Claesson, Stefan and Dalen, Love and MacPhee, Ross D. E. and Meller, Harald and Rocar, Alfred L. and Ryder, Oliver A. and Heiman, David and Young, Sarah and Breen, Matthew and Williams, Christina and Aken, Bronwen L. and Ruffier, Magali and Karlsson, Elinor and Johnson, Jeremy and Di Palma, Federica and Alfoldi, Jessica and Adelsoni, David L. and Mailund, Thomas and Munch, Kasper and Lindblad-Toh, Kerstin and Hofreiter, Michael and Poinar, Hendrik and Reich, David},
  title     = {A comprehensive genomic history of extinct and living elephants},
  series = {Proceedings of the National Academy of Sciences of the United States of America},
  volume    = {115},
  journal   = {Proceedings of the National Academy of Sciences of the United States of America},
  number    = {11},
  publisher = {National Acad. of Sciences},
  address   = {Washington},
  issn      = {0027-8424},
  doi       = {10.1073/pnas.1720554115},
  pages     = {E2566 -- E2574},
  year      = {2018},
  language  = {en}
}