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Castellano, S., G. Parra, F.A. Sánchez-Quinto, F. Racimo, M. Kuhlwilm, M. Kircher, S. Sawyer, Q. Fu, A. Heinze, B. Nickel, J. Dabney, M. Siebauer, L. White, H.A. Burbano, G. Renaud, U. Stenzel, C. Lalueza-Fox, M. de la Rasilla, A. Rosas, P.Rudan, D. Brajković, Ž. Kucan, I. Gušic, M.V. Shunkov, A.P. Derevianko, B. Viola, M. Meyer, J. Kelso, A. Andrés and S. Pääbo: Patterns of coding variation in the complete exomes of three Neandertals. PNAS 111, 6666-71 (2014).

Gansauge, M.-T. and M. Meyer: Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Research, doi: 10.1101/gr.174201.114 (2014).

Meyer, M., Q. Fu, A. Aximu-Petri, I. Glocke, B. Nickel, J.-L. Arsuaga, I. Martínez, A. Gracia, J.M. Bermúdez de Castro, E. Carbonell and S. Pääbo: A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505, 403-406 (2014).

Prüfer, K., F. Racimo, N. Patterson, F. Jay, S. Sankararaman, S. Sawyer, A. Heinze, G. Renaud, P.H. Sudmant, C. de Filippo, H. Li, S. Mallick, M. Dannemann, Q. Fu, M. Kircher, M. Kuhlwilm, M. Lachmann, M. Meyer, M. Ongyerth, M. Siebauer, C. Theunert, A. Tandon, P. Moorjani, J. Pickrell, J.C. Mullikin, S.H. Vohr, R.E. Green, I. Hellmann, P.L.F. Johnson, H. Blanche, H. Cann, J.O. Kitzman, J. Shendure, E.E. Eichler, E.S. Lein, T.E. Bakken, L.V. Golovanova, V.B. Doronichev, M.V. Shunkov, A.P. Derevianko, B. Viola, M. Slatkin, D. Reich, J. Kelso and S. Pääbo: The complete genome sequence of a Neandertal from the Altai Mountains. Nature 505, 43-49 (2014).

Weigert, A., C. Helm, M. Meyer, B. Nickel, D. Arendt, B. Hausdorf, S.R. Santos, K.M. Halanych, G. Purschke, C. Bleidorn and T.H. Struck: Illuminating the base of the annelid tree using transcriptomics. Molecular Biology and Evolution 31, 1391-1401 (2014).

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Dabney, J., M. Meyer and S. Pääbo: Ancient DNA damage. In: DNA repair, mutagenesis, and other responses to DNA damage. (Eds.) E.C. Friedberg et al. Cold Spring Harbor Perspectives in biology 5(7): a012567 (2013).

Dabney, J., M. Knapp, I. Glocke, M.-T. Gansauge, A. Weihmann, B. Nickel, C. Valdiosera, N. Garcia, S. Pääbo, J.-L. Arsuaga and M. Meyer: Complete mitochondrial genome sequence of a Middle Pleistocene cave bear recontructed from ultrashort DNA fragments. PNAS 110, 15758-63(2013).

Fu, Qiaomei, M. Meyer, G. Xing, U. Stenzel, H.A. Burbano, J. Kelso and S. Pääbo: DNA analysis of an early modern human from Tianyuan Cave, China. PNAS 10, 2223-27 (2013).

Gansauge, M.-T. and M. Meyer: Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nature Protocols 8, 737-748 (2013).

Maricic, T., V. Günther, O. Georgiev, S. Gehre, M. Ćurlin, C. Schreiweis, R. Naumann, H.A. Burbano, M. Meyer, C. Lalueza-Fox, M. de la Rasilla, A. Rosas, S. Gajović, J. Kelso, W. Enard, W. Schaffner and S. Pääbo: A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Molecular Biology and Evolution 30(4), 844-852 (2013).

Thalmann, O., B. Shapiro, P. Cui, V.J. Schuenemann, S.K. Sawyer, D.L. Greenfield, M.B. Germonpré, M.V. Sablin, F. López-Giráldez, X. Domingo-Roura, H. Napierala, H.-P. Uerpmann, D.M. Laponte, A.A. Acosta, L. Giemsch, R.W. Schmitz, B. Worthington, J.E. Buikstra, A. Druzhkova, A.S. Graphodatsky, N.D. Ovodov, N. Wahlberg, A.H. Freedman, R.M. Schweizer, K.-P. Koepfli, J.A. Leonard, M. Meyer, J. Krause, S. Pääbo, R.E. Green and R.K. Wayne: Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science 342, 871-874 (2013).

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Dabney, J. and M. Meyer: Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. BioTechniques 52, 87-94 (2012).

Gravlund, P., K. Aaris-Sørensen, M. Hofreiter, M. Meyer, J.P. Bollback and N. Noe-Nygaard: Ancient DNA extracted from Danish auroch (Bos primigenius): Genetic diversity and preservation. Annals of Anatomy 194, 103-11 (2012).

Hartmann, S., C. Helm, B. Nickel, M. Meyer, T.H. Struck, R. Tiedemann, J. Selbig and C. Bleidorn: Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data. PLoS ONE 7, e29843 (2012).

Hering, L, M.J. Henze, M. Kohler, A. Kelber, C. Bleidorn, M. Leschke, B. Nickel, M. Meyer, M. Kircher, P. Sunnucks and G. Mayer: Opsins in onychophora (velvet worms) suggest a single origin and subsequent diversification of visual pigments in arthropods. Mol. Biol. Evol. 29, 3451-8 (2012).

Kircher, M., S. Sawyer, M. Meyer: Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Research 40(1) e3 (2012).

Knapp, M., M. Stiller and M. Meyer: Generating barcoded libraries for multiplex high-throughput sequencing. In: Ancient DNA: Methods and protocols, Methods in Molecular Biology, vol. 840, Springer Science+Business Media, (Eds.) B. Shapiro and M. Hofreiter, pp. 155-170 (2012).

Meyer, M., M. Kircher, M.-T. Gansauge, H. Li, F. Racimo, S. Mallick, J.G. Schraiber, F. Jay, K. Prüfer, C. de Filippo, P.H. Sudmant, C. Alkan, Q. Fu, R. Do, N. Rohland, A. Tandon, M. Siebauer, R.E. Green, K. Bryc, A.W. Briggs, U. Stenzel, J. Dabney, J. Shendure, J. Kitzman, M.F. Hammer, M.V. Shunkov, A.P. Derevianko, N. Patterson, A.M. Andrés, E.E. Eichler, M. Slatkin, D. Reich, J. Kelso and S. Pääbo: A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222-226, doi: 10.1126/science.1224344 (2012).

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Bos, K.I., V.J. Schuenemann, G.B. Golding, H.A. Burbano, N. Waglechner, B.K. Coombes, J.B. McPhee, S.N. DeWitte, M. Meyer, S. Schmedes, J. Wood, D.J.D. Earn, D.A. Herring, P. Bauer, H.N. Poinar and J. Krause: A draft genome of Yersinia pestis from victims of the Black Death. Nature 478, 506-510 (2011).Lerner, H.R.L., M. Meyer, H.F. James, M. Hofreiter and R.C. Fleischer: Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeydreepers. Current Biology 8, 1838-44 (2011).

Stewart, J.R., S. Aspinall, M. Beech, P. Fenberg, P. Hellyer, N. Larkin, S.W. Lokier, F.G. Marx, M. Meyer, R. Miller, P.S. Rainbow, J.D. Taylor, J.E. Whittaker, K. Al-Mehsin, C.J. Strohmenger: Biotically constrained palaeoenvironmental conditions of a mid-Holocene intertidal lagoon on the southern shore of the Arabian Gulf: evidence associated with a whale skeleton at Musaffah, Abu Dhabi, UAE. Quaternary Science Reviews 30, 3675-90 (2011).

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Briggs, A.W., U. Stenzel, M. Meyer, J. Krause, M. Kircher and S. Pääbo: Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Research 38 (6), e87 (2010).

Burbano, H.A., E. Hodges, R.E. Green, A.W. Briggs, J. Krause, M. Meyer, J.M. Good, T. Maricic, P.L.F. Johnson, Z. Xuan, M. Rooks, A. Bhattacharjee, L. Brizuela, F.W. Albert, M. de la Rasilla, J. Fortea, A. Rosas, M. Lachmann, G.J. Hannon and S. Pääbo: Targeted investigaton of the Neandertal genome by array-based sequence capture. Science 328, 723-725 (2010).

Green, R.E., J. Krause, A.W. Briggs, T. Maricic, U. Stenzel, M. Kircher, N. Patterson, H. Li, W. Zhai, M.H.-Y. Fritz, N.F. Hansen, E.Y. Durand, A.-S. Malaspinas, J.D. Jensen, T. Marques-Bonet, C. Alkan, K. Prüfer, M. Meyer, H.A. Burbano, J.M. Good, R. Schultz, A. Aximu-Petri, A. Butthof, B. Höber, B. Höffner, M. Siegemund, A. Weihmann, C. Nusbaum, E.S. Lander, C. Russ, N. Novod, J. Affourtit, M. Egholm, C. Verna, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, V.B. Doronichev, L.V. Golovanova, C. Lalueza-Fox, M. de la Rasilla, J. Fortea, A. Rosas, R.W. Schmitz, P.L.F. Johnson, E.E. Eichler, D. Falush, E. Birney, J.C. Mullikin, M. Slatkin, R. Nielsen, J. Kelso, M. Lachmann, D. Reich and S. Pääbo: A draft sequence of the Neandertal genome. Science 328, 710-722 (2010).

Heyn, P., U. Stenzel, A.W. Briggs, M. Kircher, M. Hofreiter and M. Meyer: Road blocks on paleogenomes – polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA. Nucleic Acids Research 38, e161, doi:10.1093/nar/gkq572 (2010).

Meyer, M., and M. Kircher: Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harbor Protocols doi:10.1101/pdb.prot5448 (2010).

Reich, D., R.E. Green, M. Kircher, J. Krause, N. Patterson, E.Y. Durand, B. Viola, A.W. Briggs, U. Stenzel, P.L.F. Johnson, T. Maricic, J.M. Good, T. Marques-Bonet, C. Alkan, Q. Fu, S. Mallick, H. Li, M. Meyer, E.E. Eichler, M. Stoneking, M. Richards, S. Talamo, M.V. Shunkov, A.P. Derevianko, J.-J. Hublin, J. Kelso, M. Slatkin and S. Pääbo: Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468, 1053-60 (2010).

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Stiller, M., M. Knapp, U. Stenzel, M. Hofreiter and M. Meyer: Direct multiplex sequencing (DMPS) - a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Research 19, 1843-1848 (2009).

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Green, R.E., A.-S. Malaspinas, J. Krause, A.W. Briggs, P.L.F. Johnson, C. Uhler, M. Meyer, J.M. Good, T. Maricic, U. Stenzel, K. Prüfer, M. Siebauer, H.A. Burbano, M. Ronan, J.M. Rothberg, M. Egholm, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, M. Wikström, L. Laakkonen, J. Kelso, M. Slatkin and S. Pääbo: A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134, 416-426 (2008).

Meyer, M., U. Stenzel and M. Hofreiter: Parallel tagged sequencing on the 454 platform. Nature Protocols 3, 267-278 (2008).

Meyer, M., A. W. Briggs, T. Maricic, B. Höber, B. Höffner, J. Krause, A. Weihmann, , S. Pääbo and M. Hofreiter: From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Research doi:10.1093/nar/gkm1095, 36, e5 (2008).

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Briggs, A.W., U. Stenzel, P.L.F. Johnson, R.E. Green, J. Kelso, K. Prüfer, M. Meyer, J. Krause, M.T. Ronan, M. Lachmann and S. Pääbo: Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl. Acad. Sci. USA 104, 14616-21 (2007).

Meyer, M., U. Stenzel, S. Myles, K. Prüfer and M. Hofreiter: Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Research 35, e97 (2007).

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Römpler, H., P.H. Dear, J. Krause, M. Meyer, N. Rohland, T. Schöneberg, H. Spriggs, M. Stiller and M. Hofreiter: Multiplex amplification of ancient DNA. Nature Protocols 1, 720-728 (2006).

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Ebersberger, I. and M. Meyer: A genomic region evolving toward different GC contents in humans and chimpanzees indicates a recent and regionally limited shift in the mutation pattern. Molecular Biology and Evolution 22, 1240-1245 (2005).

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