Orlando, L., Gilbert, M. T. & Willerslev, E. Reconstructing ancient genomes and epigenomes. Nat. Rev. Genet. 16, 395–408 (2015).
Google Scholar
Smith, Z. D. & Meissner, A. DNA methylation: Roles in mammalian development. Nat. Rev. Genet. 14, 204–220 (2013).
Google Scholar
Schmidt, M., Maie, T., Dahl, E., Costa, I. G. & Wagner, W. Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites. BMC Biol. 18, 178 (2020).
Google Scholar
Moss, J. et al. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat. Commun. 9, 5068 (2018).
Google Scholar
Shen, H. & Laird, P. W. Interplay between the cancer genome and epigenome. Cell 153, 38–55 (2013).
Google Scholar
Koch, C. M. & Wagner, W. Epigenetic-aging-signature to determine age in different tissues. Aging (Albany N.Y.) 3, 1018–1027 (2011).
Google Scholar
Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol. 14, R115 (2013).
Google Scholar
Weidner, C. I. et al. Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol. 15, R24 (2014).
Google Scholar
Dabney, J., Meyer, M. & Paabo, S. Ancient DNA damage. Cold Spring Harb. Perspect Biol. 5, a012567 (2013).
Google Scholar
Gokhman, D. et al. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science 344, 523–527 (2014).
Google Scholar
Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).
Google Scholar
Bibikova, M. et al. High density DNA methylation array with single CpG site resolution. Genomics 98, 288–295 (2011).
Google Scholar
Pap, I., Susa, E. & Joszsa, L. Mummies from the 18–19th century Domanical Church of Vác, Hungary. Acta Biol. Szegediensis 42, 107–112 (1997).
Donoghue, H. D., Pap, I., Szikossy, I. & Spigelman, M. The Vác Mummy Project: Investigation of 265 eighteenth-century mummified remains from the TB pandemic era. In The Handbook of Mummy Studies (eds Shin, D. H. & Bianucci, R.) 1–30 (Springer, 2021).
Hotz, G. et al. Der rätselhafte Mumienfund aus der Barfüsserkirche in Basel. Ein aussergewöhnliches Beispiel interdisziplinärer Familienforschung. Jahrbuch der Schweizerischen Gesellschaft für Familienforschung 2018, 1–30 (2018).
Hotz, G. Das Rätsel der Anna Catharina Bischoff. Spektrum der Wissenschaft 3, 76–81 (2018).
Zhou, W., Triche, T. J. Jr., Laird, P. W. & Shen, H. SeSAMe: Reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. Nucleic Acids Res. 46, e123 (2018).
Google Scholar
Triche, T. J., Weisenberger, D. J., Van Den Berg, D., Laird, P. W. & Siegmund, K. D. low-level processing of illumina infinium DNA methylation beadarrays. Nucleic Acids Res. 41, e90 (2013).
Google Scholar
Ruiz-Hernandez, A. et al. Environmental chemicals and DNA methylation in adults: A systematic review of the epidemiologic evidence. Clin. Epigenet. 7, 55 (2015).
Google Scholar
Pedersen, J. S. et al. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. 24, 454–466 (2014).
Google Scholar
Gaudin, M. & Desnues, C. Hybrid capture-based next generation sequencing and its application to human infectious diseases. Front. Microbiol. 9, 2924 (2018).
Google Scholar
Knapp, M. & Hofreiter, M. Next generation sequencing of ancient DNA: Requirements, strategies and perspectives. Genes (Basel) 1, 227–243 (2010).
Google Scholar
Koop, B. E. et al. Postmortem age estimation via DNA methylation analysis in buccal swabs from corpses in different stages of decomposition—A “proof of principle” study. Int. J. Legal Med. 135, 167–173 (2021).
Google Scholar
Joehanes, R. et al. Epigenetic signatures of cigarette smoking. Circ. Cardiovasc. Genet. 9, 436–447 (2016).
Google Scholar
Bozic, T. et al. Investigation of measurable residual disease in acute myeloid leukemia by DNA methylation patterns. Leukemia https://doi.org/10.1038/s41375-021-01316-z (2021).
Google Scholar
Pap, I. et al. 18–19th century tuberculosis in naturally mummified individuals (Vác, Hungary). In Tuberculosis Past and Present (eds Pálfi, G. et al.) 421–428 (Golden Books/Tuberculosis Foundation, 1999).
Kreissl Lonfat, B. M., Kaufmann, I. M. & Ruhli, F. A code of ethics for evidence-based research with ancient human remains. Anat. Rec. (Hoboken) 298, 1175–1181 (2015).
Google Scholar
Maixner, F. et al. The Iceman’s last meal consisted of fat, wild meat, and cereals. Curr. Biol. 28, 2348–2355 (2018).
Google Scholar
Tang, J. N. et al. An effective method for isolation of DNA from pig faeces and comparison of five different methods. J. Microbiol. Methods 75, 432–436 (2008).
Google Scholar
Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).
Google Scholar
Meyer, M. & Kircher, M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, 5448 (2010).
Google Scholar
Rosenbloom, K. R. et al. The UCSC genome browser database: 2015 update. Nucleic Acids Res. 43, D670–D681 (2015).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357 (2012).
Google Scholar
Peltzer, A. et al. EAGER: Efficient ancient genome reconstruction. Genome Biol. 17, 60 (2016).
Google Scholar
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. & Orlando, L. mapDamage2.0: Fast approximate Bayesian estimates of ancient DNA damage parameters. Bioinformatics 29, 1682–1684 (2013).
Google Scholar
Buchfink, B., Reuter, K. & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).
Google Scholar
Huson, D. H. et al. MEGAN Community edition—Interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12, e1004957 (2016).
Google Scholar
Ondov, B. D., Bergman, N. H. & Phillippy, A. M. Interactive metagenomic visualization in a Web browser. BMC Bioinform. 12, 385 (2011).
Google Scholar
Xu, Z., Langie, S. A., De Boever, P., Taylor, J. A. & Niu, L. RELIC: A novel dye-bias correction method for illumina methylation beadchip. BMC Genomics 18, 4 (2017).
Google Scholar
Lee, D. D. & Seung, H. S. Algorithms for non-negative matrix factorization. Adv. Neural. Inf. Process. Syst. 13(13), 556–562 (2001).
Schmidt, M., Maié, T., Dahl, E., Costa, I. G. & Wagner, W. Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites. BMC Biol. 34, 1969 (2020).
Frobel, J. et al. Leukocyte counts based on DNA methylation at individual cytosines. Clin. Chem. 64, 566–575 (2018).
Google Scholar
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