Ancient DNA analysis

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works

Inference of Population Structure Using Multilocus Genotype Data

Pritchard, J. K., Stephens, M., & Donnelly, P. (2000) · Genetics · doi:10.1093/genetics/155.2.945 · Cited by 33,871 · see citing works

Biological identifications through DNA barcodes

Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003) · Proceedings of the Royal Society of London. Series B: Biological Sciences · doi:10.1098/rspb.2002.2218 · Cited by 13,376 · see citing works

Fast and accurate long-read alignment with Burrows-Wheeler transform.

Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063 · see citing works

Fast model-based estimation of ancestry in unrelated individuals

Alexander, D. H., Novembre, J., & Lange, K. (2009) · Genome Research · doi:10.1101/gr.094052.109 · Cited by 9,898 · see citing works

Population Structure and Eigenanalysis

Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280 · see citing works

Kraken: ultrafast metagenomic sequence classification using exact alignments

Wood, D. E., & Salzberg, S. L. (2014) · Genome Biology · doi:10.1186/gb-2014-15-3-r46 · Cited by 4,521 · see citing works

Coming of age: ten years of next-generation sequencing technologies

Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352 · see citing works

A draft sequence of the Neandertal genome

Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318 · see citing works

Accurate whole human genome sequencing using reversible terminator chemistry

Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684 · see citing works

Ancient Admixture in Human History

Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T., & Reich, D. (2012) · Genetics · doi:10.1534/genetics.112.145037 · Cited by 2,848 · see citing works

A reference panel of 64,976 haplotypes for genotype imputation

the Haplotype Reference Consortium (2016) · Nature Genetics · doi:10.1038/ng.3643 · Cited by 2,836 · see citing works

Inference of human population history from individual whole-genome sequences

Li, H., & Durbin, R. (2011) · Nature · doi:10.1038/nature10231 · Cited by 2,590 · see citing works

The complete genome sequence of a Neanderthal from the Altai Mountains

Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature12886 · Cited by 2,254 · see citing works

Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and SequencingPreprint

Meyer, M., & Kircher, M. (2010) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot5448 · Cited by 2,233 · see citing works

AdapterRemoval v2: rapid adapter trimming, identification, and read merging

Schubert, M., Lindgreen, S., & Orlando, L. (2016) · BMC Research Notes · doi:10.1186/s13104-016-1900-2 · Cited by 2,091 · see citing works

Genetic history of an archaic hominin group from Denisova Cave in Siberia

Reich, D., Green, R. E., Kircher, M., Krause, J., Patterson, N., Durand, E. Y., Viola, B., Briggs, A. W., Stenzel, U., Johnson, P. L. F., et al. (2010) · Nature · doi:10.1038/nature09710 · Cited by 1,991 · see citing works

A high-coverage genome sequence from an archaic denisovan individual

Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967 · see citing works

Massive migration from the steppe was a source for Indo-European languages in Europe

Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al. (2015) · Nature · doi:10.1038/nature14317 · Cited by 1,940 · see citing works

Bayesian community-wide culture-independent microbial source tracking

Knights, D., Kuczynski, J., Charlson, E. S., Zaneveld, J., Mozer, M. C., Collman, R. G., Bushman, F. D., Knight, R. D., & Kelley, S. T. (2011) · Nature Methods · doi:10.1038/nmeth.1650 · Cited by 1,839 · see citing works

Metagenomic microbial community profiling using unique clade-specific marker genes

Segata, N., Waldron, L., Ballarini, A., Narasimhan, V., Jousson, O., & Huttenhower, C. (2012) · Nature Methods · doi:10.1038/nmeth.2066 · Cited by 1,776 · see citing works

Reconstructing Indian population history

Reich, D., Thangaraj, K., Patterson, N., Price, A. L., & Singh, L. (2009) · Nature · doi:10.1038/nature08365 · Cited by 1,674 · see citing works

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F., & Orlando, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt193 · Cited by 1,669 · see citing works

Population genomics of Bronze Age Eurasia

Allentoft, M. E., Sikora, M., Sjögren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. B., Schroeder, H., Ahlström, T., Vinner, L., et al. (2015) · Nature · doi:10.1038/nature14507 · Cited by 1,550 · see citing works

The Missing Diversity in Human Genetic Studies

Sirugo, G., Williams, S. M., & Tishkoff, S. A. (2019) · Cell · doi:10.1016/j.cell.2019.02.048 · Cited by 1,516 · see citing works

Genome-wide patterns of selection in 230 ancient Eurasians

Mathieson, I., Lazaridis, I., Rohland, N., Mallick, S., Patterson, N., Roodenberg, S. A., Harney, E., Stewardson, K., Fernandes, D., Novak, M., et al. (2015) · Nature · doi:10.1038/nature16152 · Cited by 1,515 · see citing works

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314445110 · Cited by 1,443 · see citing works

Ancient human genomes suggest three ancestral populations for present-day Europeans

Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357 · see citing works

Genetic analyses from ancient DNA

Pääbo, S., Poinar, H., Serre, D., Jaenicke-Després, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L., & Hofreiter, M. (2004) · Annual Review of Genetics · doi:10.1146/annurev.genet.37.110801.143214 · Cited by 1,333 · see citing works

Neandertal DNA sequences and the origin of modern humans.

Krings, M., Stone, A., Schmitz, R., Krainitzki, H., Stoneking, M., & Pääbo, S. (1997) · Cell · doi:10.1016/s0092-8674(00)80310-4 · Cited by 1,274 · see citing works

Inference of Population Structure using Dense Haplotype Data

Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002453 · Cited by 1,188 · see citing works

The Third Revolution in Sequencing Technology

van Dijk, E., Jaszczyszyn, Y., Naquin, D., & Thermes, C. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.05.008 · Cited by 1,186 · see citing works

Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding

Taberlet, P., Coissac, É., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C., & Willerslev, E. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl938 · Cited by 1,184 · see citing works

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

Kircher, M., Sawyer, S., & Meyer, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr771 · Cited by 1,106 · see citing works

Characterization of the 1918 influenza virus polymerase genes

Taubenberger, J. K., Reid, A. H., Lourens, R. M., Wang, R., Jin, G., & Fanning, T. G. (2005) · Nature · doi:10.1038/nature04230 · Cited by 1,054 · see citing works

Inferring human population size and separation history from multiple genome sequences

Schiffels, S., & Durbin, R. M. (2014) · Nature Genetics · doi:10.1038/ng.3015 · Cited by 1,051 · see citing works

Genome sequence of a 45,000-year-old modern human from western Siberia

Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Aximu-Petri, A., Prüfer, K., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature13810 · Cited by 1,023 · see citing works

CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes

Komor, A. C., Badran, A. H., & Liu, D. R. (2016) · Cell · doi:10.1016/j.cell.2016.10.044 · Cited by 1,011 · see citing works

Patterns of damage in genomic DNA sequences from a neandertal

Briggs, A. W., Stenzel, U., Johnson, P. L. F., Green, R. E., Kelso, J., Prüfer, K., Meyer, M., Krause, J., Ronan, M. T., Lachmann, M., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704665104 · Cited by 981 · see citing works

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford Jr, T. W., Orlando, L., Metspalu, E., et al. (2014) · Nature · doi:10.1038/nature12736 · Cited by 963 · see citing works

Current perspectives and the future of domestication studies

Larson, G., Piperno, D. R., Allaby, R. G., Purugganan, M. D., Andersson, L., Arroyo‐Kalin, M., Barton, L., Vigueira, C. C., Denham, T. P., Dobney, K. M., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323964111 · Cited by 868 · see citing works

Ancient human genome sequence of an extinct Palaeo-Eskimo

Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., et al. (2010) · Nature · doi:10.1038/nature08835 · Cited by 849 · see citing works

Recalibrating equus evolution using the genome sequence of an early middle pleistocene horse

Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., et al. (2013) · Nature · doi:10.1038/nature12323 · Cited by 841 · see citing works

Variation graph toolkit improves read mapping by representing genetic variation in the reference

Garrison, E., Sirén, J., Novak, A. M., Hickey, G., Eizenga, J. M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M. F., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4227 · Cited by 821 · see citing works

A draft genome of Yersinia pestis from victims of the Black Death

Bos, K. I., Schuenemann, V. J., Golding, G. B., Burbano, H. A., Waglechner, N., Coombes, B. K., McPhee, J. B., DeWitte, S. N., Meyer, M., Schmedes, S. E., et al. (2011) · Nature · doi:10.1038/nature10549 · Cited by 808 · see citing works

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia

Krause, J., Fu, Q., Good, J. M., Viola, B., Shunkov, M. V., Derevianko, A. P., & Pääbo, S. (2010) · Nature · doi:10.1038/nature08976 · Cited by 792 · see citing works

DNA sequences from the quagga, an extinct member of the horse family

Higuchi, R., Bowman, B. H., Freiberger, M., Ryder, O. A., & Wilson, A. C. (1984) · Nature · doi:10.1038/312282a0 · Cited by 791 · see citing works

An aboriginal Australian genome reveals separate human dispersals into Asia

Rasmussen, M., Guo, X., Wang, Y., Lohmueller, K. E., Rasmussen, S., Albrechtsen, A., Skotte, L., Lindgreen, S., Metspalu, M., Jombart, T., et al. (2011) · Science · doi:10.1126/science.1211177 · Cited by 787 · see citing works

The formation of human populations in South and Central Asia

Narasimhan, V. M., Patterson, N. J., Moorjani, P., Rohland, N., Bernardos, R. L., Mallick, S., Lazaridis, I., Nakatsuka, N. J., Olalde, Í., Lipson, M., et al. (2019) · Science · doi:10.1126/science.aat7487 · Cited by 767 · see citing works

Organoid single-cell genomic atlas uncovers human-specific features of brain development

Kanton, S., Boyle, M. J., He, Z., Santel, M., Weigert, A., Sanchís-Calleja, F., Guijarro, P., Sidow, L., Fleck, J. S., Han, D., et al. (2019) · Nature · doi:10.1038/s41586-019-1654-9 · Cited by 761 · see citing works

Analysis of one million base pairs of Neanderthal DNA

Green, R. E., Krause, J., Ptak, S. E., Briggs, A. W., Ronan, M. T., Simons, J. F., Du, L., Egholm, M., Rothberg, J. M., Paunović, M., et al. (2006) · Nature · doi:10.1038/nature05336 · Cited by 758 · see citing works

The Beaker phenomenon and the genomic transformation of northwest Europe

Olalde, Í., Brace, S., Allentoft, M. E., Armit, I., Kristiansen, K., Booth, T. J., Rohland, N., Mallick, S., Szécsényi‐Nagy, A., Mittnik, A., et al. (2018) · Nature · doi:10.1038/nature25738 · Cited by 734 · see citing works

Tracing the peopling of the world through genomics

Nielsen, R., Akey, J. M., Jakobsson, M., Pritchard, J. K., Tishkoff, S., & Willerslev, E. (2017) · Nature · doi:10.1038/nature21347 · Cited by 728 · see citing works

A high-coverage Neandertal genome from Vindija Cave in Croatia

Prüfer, K., de Filippo, C., Grote, S., Mafessoni, F., Korlević, P., Hajdinjak, M., Vernot, B., Skov, L., Hsieh, P., Peyrégne, S., et al. (2017) · Science · doi:10.1126/science.aao1887 · Cited by 719 · see citing works

Estimating Individual Admixture Proportions from Next Generation Sequencing Data

Skotte, L., Korneliussen, T. S., & Albrechtsen, A. (2013) · Genetics · doi:10.1534/genetics.113.154138 · Cited by 703 · see citing works

Species-specific responses of Late Quaternary megafauna to climate and humans

Lorenzen, E. D., Nogués‐Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K. A., Ugan, A., Borregaard, M. K., Gilbert, M. T. P., Nielsen, R., et al. (2011) · Nature · doi:10.1038/nature10574 · Cited by 691 · see citing works

Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments

Willerslev, E., Hansen, A. J., Binladen, J., Brand, T. B., Gilbert, M. T. P., Shapiro, B., Bunce, M., Wiuf, C., Gilichinsky, D. A., & Cooper, A. (2003) · Science · doi:10.1126/science.1084114 · Cited by 687 · see citing works

Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data

Meisner, J., & Albrechtsen, A. (2018) · Genetics · doi:10.1534/genetics.118.301336 · Cited by 673 · see citing works

Genome flux and stasis in a five millennium transect of European prehistory

Gamba, C., Jones, E. R., Teasdale, M. D., McLaughlin, R. L., Gonzalez-Fortes, G., Mattiangeli, V., Domboróczki, L., Kővári, I., Pap, I., Anders, A., et al. (2014) · Nature Communications · doi:10.1038/ncomms6257 · Cited by 667 · see citing works

Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania

Reich, D., Patterson, N., Kircher, M., Delfin, F., Nandineni, M. R., Pugach, I., Ko, A. M.-S., Ko, Y.-C., Jinam, T. A., Phipps, M. E., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.09.005 · Cited by 656 · see citing works

Sequencing and analysis of Neanderthal genomic DNA

Noonan, J. P., Coop, G., Kudaravalli, S., Smith, D., Krause, J., Alessi, J., Chen, F., Platt, D., Pääbo, S., Pritchard, J. K., et al. (2006) · Science · doi:10.1126/science.1131412 · Cited by 629 · see citing works

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

Adler, C. J., Dobney, K., Weyrich, L. S., Kaidonis, J., Walker, A. W., Haak, W., Bradshaw, C. J. A., Townsend, G., Sołtysiak, A., Alt, K. W., et al. (2013) · Nature Genetics · doi:10.1038/ng.2536 · Cited by 621 · see citing works

Pathogens and host immunity in the ancient human oral cavity

Warinner, C., Rodrigues, J. F. M., Vyas, R., Trachsel, C., Shved, N., Grossmann, J., Radini, A., Hancock, Y., Tito, R. Y., Fiddyment, S., et al. (2014) · Nature Genetics · doi:10.1038/ng.2906 · Cited by 618 · see citing works

Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA

Poinar, H. N., Schwarz, C., Qi, J., Shapiro, B., MacPhee, R. D. E., Buigues, B., Tikhonov, A., Huson, D. H., Tomsho, L. P., Auch, A. F., et al. (2005) · Science · doi:10.1126/science.1123360 · Cited by 618 · see citing works

DNA analysis of an early modern human from Tianyuan Cave, China

Fu, Q., Meyer, M., Gao, X., Stenzel, U., Burbano, H. A., Kelso, J., & Pääbo, S. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1221359110 · Cited by 608 · see citing works

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

Bos, K. I., Harkins, K. M., Herbig, A., Coscollá, M., Weber, N., Comas, I., Forrest, S. A., Bryant, J. M., Harris, S. R., Schuenemann, V. J., et al. (2014) · Nature · doi:10.1038/nature13591 · Cited by 608 · see citing works

Assessing ancient DNA studies

Gilbert, M. T. P., Bandelt, H.-J., Hofreiter, M., & Barnes, I. (2005) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2005.07.005 · Cited by 602 · see citing works

Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe

Skoglund, P., Malmström, H., Raghavan, M., Storå, J., Hall, P. N., Willerslev, E., Gilbert, M. T. P., Götherström, A., & Jakobsson, M. (2012) · Science · doi:10.1126/science.1216304 · Cited by 593 · see citing works

Ancient DNA extraction from bones and teeth

Rohland, N., & Hofreiter, M. (2007) · Nature Protocols · doi:10.1038/nprot.2007.247 · Cited by 584 · see citing works

Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins

Meyer, M., Arsuaga, J.-L., de Filippo, C., Nagel, S., Aximu-Petri, A., Nickel, B., Martínez, I., Gracia, A., de Castro, J. M. B., Carbonell, E., et al. (2016) · Nature · doi:10.1038/nature17405 · Cited by 584 · see citing works

Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

Rohland, N., Harney, E., Mallick, S., Nordenfelt, S., & Reich, D. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2013.0624 · Cited by 572 · see citing works

Fifty thousand years of Arctic vegetation and megafaunal diet

Willerslev, E., Davison, J., Moora, M., Zobel, M., Coissac, É., Edwards, M. E., Lorenzen, E. D., Vestergård, M., Gussarova, G. L., Haile, J., et al. (2014) · Nature · doi:10.1038/nature12921 · Cited by 570 · see citing works

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

Maričić, T., Whitten, M., & Pääbo, S. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014004 · Cited by 566 · see citing works

A Genealogical Interpretation of Principal Components Analysis

McVean, G. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000686 · Cited by 566 · see citing works

The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals

Krause, J., Lalueza‐Fox, C., Orlando, L., Enard, W., Green, R. E., Burbano, H. A., Hublin, J., Hänni, C., Fortea, J., Vives, M. D. L. R., et al. (2007) · Current Biology · doi:10.1016/j.cub.2007.10.008 · Cited by 562 · see citing works

Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA

Gansauge, M.-T., & Meyer, M. (2013) · Nature Protocols · doi:10.1038/nprot.2013.038 · Cited by 541 · see citing works

A mitochondrial genome sequence of a hominin from Sima de los Huesos

Meyer, M., Fu, Q., Aximu-Petri, A., Glocke, I., Nickel, B., Arsuaga, J.-L., Martínez, I., Gracia, A., de Castro, J. M. B., Carbonell, E., et al. (2014) · Nature · doi:10.1038/nature12788 · Cited by 534 · see citing works

Ancient DNA DamagePreprint

Dabney, J., Meyer, M., & Pääbo, S. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012567 · Cited by 530 · see citing works

The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing

Binladen, J., Gilbert, M. T. P., Bollback, J. P., Panitz, F., Bendixen, C., Nielsen, R., & Willerslev, E. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000197 · Cited by 522 · see citing works

Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland

Willerslev, E., Cappellini, E., Boomsma, W., Nielsen, R., Hebsgaard, M. B., Brand, T. B., Hofreiter, M., Bunce, M., Poinar, H. N., Dahl‐Jensen, D., et al. (2007) · Science · doi:10.1126/science.1141758 · Cited by 521 · see citing works

The prehistoric peopling of Southeast Asia

McColl, H., Racimo, F., Vinner, L., Demeter, F., Gakuhari, T., Moreno-Mayar, J. V., van Driem, G., Gram Wilken, U., Seguin-Orlando, A., de la Fuente Castro, C., et al. (2018) · Science · doi:10.1126/science.aat3628 · Cited by 517 · see citing works

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX

Schubert, M., Ermini, L., Sarkissian, C. S. I. D., Jónsson, H., Ginolhac, A., Schaefer, R., Martin, M. D., Fernández, R., Kircher, M., McCue, M. E., et al. (2014) · Nature Protocols · doi:10.1038/nprot.2014.063 · Cited by 515 · see citing works

Accurate sex identification of ancient human remains using DNA shotgun sequencing

Skoglund, P., Storå, J., Götherström, A., & Jakobsson, M. (2013) · Journal of Archaeological Science · doi:10.1016/j.jas.2013.07.004 · Cited by 510 · see citing works

Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA

Renaud, G., Slon, V., Duggan, A. T., & Kelso, J. (2015) · Genome Biology · doi:10.1186/s13059-015-0776-0 · Cited by 509 · see citing works

EAGER: efficient ancient genome reconstruction

Peltzer, A., Jäger, G., Herbig, A., Seitz, A., Kniep, C., Krause, J., & Nieselt, K. (2016) · Genome Biology · doi:10.1186/s13059-016-0918-z · Cited by 509 · see citing works

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

Skoglund, P., Northoff, B. H., Shunkov, M. V., Derevianko, A. P., Pääbo, S., Krause, J., & Jakobsson, M. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1318934111 · Cited by 499 · see citing works

Molecular Coproscopy: Dung and Diet of the Extinct Ground Sloth Nothrotheriops shastensis

Poinar, H. N., Hofreiter, M., Spaulding, W. G., Martin, P. S., Stankiewicz, B. A., Bland, H. A., Evershed, R. P., Possnert, G., & Pääbo, S. (1998) · Science · doi:10.1126/science.281.5375.402 · Cited by 498 · see citing works

Mitochondrial DNA sequences from a 7000-year old brain

Pääbo, S., Gifford, J. A., & Wilson, A. C. (1988) · Nucleic Acids Research · doi:10.1093/nar/16.20.9775 · Cited by 493 · see citing works

A framework for enhancing ethical genomic research with Indigenous communities

Claw, K. G., Anderson, M. Z., Begay, R. L., Tsosie, K. S., Fox, K., Garrison, N. A., Bader, A. C., Bardill, J., Bolnick, D. A., Brooks, J. L., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05188-3 · Cited by 493 · see citing works

Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis

Wagner, D. M., Klunk, J., Harbeck, M., Devault, A. M., Waglechner, N., Sahl, J. W., Enk, J. M., Birdsell, D. N., Kuch, M., Lumibao, C. Y., et al. (2014) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(13)70323-2 · Cited by 493 · see citing works

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

Briggs, A. W., Stenzel, U., Meyer, M., Krause, J., Kircher, M., & Pääbo, S. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1163 · Cited by 491 · see citing works

DNA extraction from Pleistocene bones by a silica-based purification method

Höss, M., & Pääbo, S. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.16.3913 · Cited by 490 · see citing works

Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA

Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., & Pääbo, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034131 · Cited by 489 · see citing works

137 ancient human genomes from across the Eurasian steppes

Damgaard, P. D. B., Marchi, N., Rasmussen, S., Peyrot, M., Renaud, G., Korneliussen, T. S., Moreno-Mayar, J. V., Pedersen, M. W., Goldberg, A., Usmanova, E., et al. (2018) · Nature · doi:10.1038/s41586-018-0094-2 · Cited by 489 · see citing works

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

Jun, G., Flickinger, M., Hetrick, K. N., Romm, J. M., Doheny, K. F., Abecasis, G. R., Boehnke, M., & Kang, H. M. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.09.004 · Cited by 484 · see citing works

Skyline‐plot methods for estimating demographic history from nucleotide sequences

Ho, S. Y. W., & Shapiro, B. (2011) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2011.02988.x · Cited by 482 · see citing works

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476 · see citing works

Ancient DNA indicates human population shifts and admixture in northern and southern China

Yang, M. A., Fan, X., Sun, B., Chen, C., Lang, J., Ko, Y., Tsang, C.-H., Chiu, H.-L., Wang, T., Bao, Q., et al. (2020) · Science · doi:10.1126/science.aba0909 · Cited by 465 · see citing works

Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'

Thompson, J. R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.9.2083 · Cited by 452 · see citing works

Neandertal and Denisovan DNA from Pleistocene sediments

Slon, V., Hopfe, C., Weiß, C. L., Mafessoni, F., Vives, M. D. L. R., Lalueza‐Fox, C., Rosas, A., Soressi, M., Knul, M. V., Miller, R., et al. (2017) · Science · doi:10.1126/science.aam9695 · Cited by 451 · see citing works

Genomic and archaeological evidence suggest a dual origin of domestic dogs

Frantz, L., Mullin, V. E., Pionnier-Capitan, M., Lebrasseur, O., Ollivier, M., Perri, A. R., Linderholm, A. E., Mattiangeli, V., Teasdale, M. D., Dimopoulos, E. A., et al. (2016) · Science · doi:10.1126/science.aaf3161 · Cited by 449 · see citing works

Postglacial viability and colonization in North America’s ice-free corridor

Pedersen, M. W., Ruter, A., Schweger, C. E., Friebe, H., Staff, R. A., Kjeldsen, K. K., Mendoza, M. L. Z., Beaudoin, A. B., Zutter, C., Larsen, N. K., et al. (2016) · Nature · doi:10.1038/nature19085 · Cited by 445 · see citing works

No Evidence of Neandertal mtDNA Contribution to Early Modern Humans

Serre, D., Langaney, A., Chech, M., Teschler‐Nicola, M., Paunović, M., Mennecier, P., Hofreiter, M., Possnert, G., & Pääbo, S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020057 · Cited by 437 · see citing works

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

Keller, A., Graefen, A., Ball, M., Matzas, M., Boisguerin, V., Maixner, F., Leidinger, P., Backes, C., Khairat, R., Forster, M., et al. (2012) · Nature Communications · doi:10.1038/ncomms1701 · Cited by 437 · see citing works

Identification of Mycobacterium tuberculosis DNA in a pre-Columbian Peruvian mummy.

Salo, W. L., Aufderheide, A. C., Buikstra, J. E., et al. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.6.2091 · Cited by 436 · see citing works

The first horse herders and the impact of early Bronze Age steppe expansions into Asia

Damgaard, P. D. B., Martiniano, R., Kamm, J., Moreno-Mayar, J. V., Kroonen, G., Peyrot, M., Barjamovic, G., Rasmussen, S., Zacho, C. M., Baimukhanov, N., et al. (2018) · Science · doi:10.1126/science.aar7711 · Cited by 424 · see citing works

Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

Moreno-Mayar, J. V., Potter, B. A., Vinner, L., Steinrücken, M., Rasmussen, S., Terhorst, J., Kamm, J., Albrechtsen, A., Malaspinas, A., Sikora, M., et al. (2018) · Nature · doi:10.1038/nature25173 · Cited by 423 · see citing works

Ancient genomes document multiple waves of migration in Southeast Asian prehistory

Lipson, M., Cheronet, O., Mallick, S., Rohland, N., Oxenham, M. F., Pietrusewsky, M., Pryce, T. O., Willis, A., Matsumura, H., Buckley, H. R., et al. (2018) · Science · doi:10.1126/science.aat3188 · Cited by 420 · see citing works

DNA Damage and DNA Sequence Retrieval from Ancient Tissues

Höss, M., Jaruga, P., Zastawny, T. H., Dizdaroğlu, M., & Pääbo, S. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.7.1304 · Cited by 403 · see citing works

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

Lachance, J., & Tishkoff, S. A. (2013) · BioEssays · doi:10.1002/bies.201300014 · Cited by 402 · see citing works

Ancient and modern environmental DNA

Pedersen, M. W., Overballe‐Petersen, S., Ermini, L., Sarkissian, C. S. I. D., Haile, J., Hellström, M., Spens, J., Thomsen, P. F., Bohmann, K., Cappellini, E., et al. (2014) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0383 · Cited by 396 · see citing works

Parallel palaeogenomic transects reveal complex genetic history of early European farmers

Lipson, M., Szécsényi-Nagy, A., Mallick, S., Pósa, A., Stégmár, B., Keerl, V., Rohland, N., Stewardson, K., Ferry, M., Michel, M., et al. (2017) · Nature · doi:10.1038/nature24476 · Cited by 389 · see citing works

Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds

Skoglund, P., Ersmark, E., Palkopoulou, E., & Dalén, L. (2015) · Current Biology · doi:10.1016/j.cub.2015.04.019 · Cited by 380 · see citing works

Long livestock farming history and human landscape shaping revealed by lake sediment DNA

Giguet‐Covex, C., Pansu, J., Arnaud, F., Rey, P.-J., Griggo, C., Gielly, L., Domaizon, I., Coissac, É., David, F., Choler, P., et al. (2014) · Nature Communications · doi:10.1038/ncomms4211 · Cited by 371 · see citing works

Ancient bone DNA amplified

Hagelberg, E., Sykes, B. C., & Hedges, R. E. M. (1989) · Nature · doi:10.1038/342485a0 · Cited by 371 · see citing works

Ancient genomes revisit the ancestry of domestic and Przewalski’s horses

Gaunitz, C., Fages, A., Hanghøj, K., Albrechtsen, A., Khan, N., Schubert, M., Seguin‐Orlando, A., Owens, I. J., Felkel, S., Bignon‐Lau, O., et al. (2018) · Science · doi:10.1126/science.aao3297 · Cited by 371 · see citing works

Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth

Palkopoulou, E., Mallick, S., Skoglund, P., Enk, J. M., Rohland, N., Li, H., Omrak, A., Vartanyan, S., Poinar, H. N., Götherström, A., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.04.007 · Cited by 370 · see citing works

Early human dispersals within the Americas

Moreno-Mayar, J. V., Vinner, L., Damgaard, P. D. B., Castro, C. D. L. F., Chan, J., Spence, J. P., Allentoft, M. E., Vimala, T., Racimo, F., Pinotti, T., et al. (2018) · Science · doi:10.1126/science.aav2621 · Cited by 365 · see citing works

Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae

Schuenemann, V. J., Singh, P., Mendum, T. A., Krause‐Kyora, B., Jäger, G., Bos, K. I., Herbig, A., Economou, C., Benjak, A., Busso, P., et al. (2013) · Science · doi:10.1126/science.1238286 · Cited by 359 · see citing works

Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing

Rohland, N., Glocke, I., Aximu‐Petri, A., & Meyer, M. (2018) · Nature Protocols · doi:10.1038/s41596-018-0050-5 · Cited by 358 · see citing works

Glacial Survival of Boreal Trees in Northern Scandinavia

Parducci, L., Jørgensen, T., Tollefsrud, M. M., Elverland, E., Alm, T., Fontana, S. L., Bennett, K. D., Haile, J., Matetovici, I., Suyama, Y., et al. (2012) · Science · doi:10.1126/science.1216043 · Cited by 353 · see citing works

Sequencing the nuclear genome of the extinct woolly mammoth

Miller, W., Drautz, D. I., Ratan, A., Pusey, B. N., Qi, J., Lesk, A. M., Tomsho, L. P., Packard, M., Zhao, F., Sher, A. V., et al. (2008) · Nature · doi:10.1038/nature07446 · Cited by 345 · see citing works

A view of Neandertal genetic diversity

Krings, M., Capelli, C., Tschentscher, F., Geisert, H., Meyer, S., von Haeseler, A., Großschmidt, K., Possnert, G., Paunović, M., & Pääbo, S. (2000) · Nature Genetics · doi:10.1038/79855 · Cited by 339 · see citing works

Population genomics of the Viking world

Margaryan, A., Lawson, D. J., Sikora, M., Racimo, F., Rasmussen, S., Moltke, I., Cassidy, L. M., Jørsboe, E., Ingason, A., Pedersen, M. W., et al. (2020) · Nature · doi:10.1038/s41586-020-2688-8 · Cited by 336 · see citing works

Neanderthals in central Asia and Siberia

Krause, J., Orlando, L., Serre, D., Viola, B., Prüfer, K., Richards, M. P., Hublin, J.-J., Hänni, C., Derevianko, A. P., & Pääbo, S. (2007) · Nature · doi:10.1038/nature06193 · Cited by 333 · see citing works

Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

Sikora, M., Seguin‐Orlando, A., Sousa, V. C., Albrechtsen, A., Korneliussen, T. S., Ko, A., Rasmussen, S., Dupanloup, I., Nigst, P. R., Bosch, M. D., et al. (2017) · Science · doi:10.1126/science.aao1807 · Cited by 333 · see citing works

Single‐tube library preparation for degraded DNA

Carøe, C., Gopalakrishnan, S., Vinner, L., Mak, S. S. T., Sinding, M. S., Castruita, J. A. S., Wales, N., Sicheritz‐Pontén, T., & Gilbert, M. T. P. (2017) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12871 · Cited by 331 · see citing works

Estimating genetic kin relationships in prehistoric populations

Monroy Kuhn, J. M., Jakobsson, M., & Günther, T. (2018) · PLOS ONE · doi:10.1371/journal.pone.0195491 · Cited by 330 · see citing works

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Fages, A., Hanghøj, K., Khan, N., Gaunitz, C., Seguin‐Orlando, A., Leonardi, M., Constantz, C. M., Gamba, C., Al‐Rasheid, K. A. S., Albizuri, S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.049 · Cited by 328 · see citing works

Improving ancient DNA read mapping against modern reference genomes

Schubert, M., Ginolhac, A., Lindgreen, S., Thompson, J. F., AL-Rasheid, K. A., Willerslev, E., Krogh, A., & Orlando, L. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-178 · Cited by 325 · see citing works

Early Allelic Selection in Maize as Revealed by Ancient DNA

Jaenicke-Després, V., Buckler, E. S., Smith, B. D., Gilbert, M. T. P., Cooper, A., Doebley, J., & Pääbo, S. (2003) · Science · doi:10.1126/science.1089056 · Cited by 324 · see citing works

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

Carpenter, M. L., Buenrostro, J. D., Valdiosera, C. E., Schroeder, H., Allentoft, M. E., Sikora, M., Rasmussen, M. A., Gravel, S., Guillén, S. E., Nekhrizov, G., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.10.002 · Cited by 322 · see citing works

Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in Island Southeast Asia and Oceania

Larson, G., Cucchi, T., Fujita, M., Matisoo-Smith, E. A., Robins, J. H., Anderson, A., Rolett, B. V., Spriggs, M., Dolman, G., Kim, T.-H., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607753104 · Cited by 320 · see citing works

Taxonomic structure and functional association of foxtail millet root microbiome

Jin, T., Wang, Y., Huang, Y., Xu, J. H., Zhang, P., Wang, N., Liu, X., Chu, H., Liu, G., Jiang, H., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix089 · Cited by 317 · see citing works

Multiproxy evidence highlights a complex evolutionary legacy of maize in South America

Kistler, L., Maezumi, S. Y., de Souza, J. G., Przelomska, N. A. S., Costa, F. M., Smith, O., Loiselle, H., Ramos‐Madrigal, J., Wales, N., Ribeiro, E. R., et al. (2018) · Science · doi:10.1126/science.aav0207 · Cited by 317 · see citing works

Length and GC-Biases During Sequencing Library Amplification: A Comparison of Various Polymerase-Buffer Systems with Ancient and Modern DNA Sequencing Libraries

Dabney, J., & Meyer, M. (2012) · BioTechniques · doi:10.2144/000113809 · Cited by 316 · see citing works

Genomic structure in Europeans dating back at least 36,200 years

Seguin-Orlando, A., Korneliussen, T. S., Sikora, M., Malaspinas, A.-S., Manica, A., Moltke, I., Albrechtsen, A., Ko, A., Margaryan, A., Moiseyev, V., et al. (2014) · Science · doi:10.1126/science.aaa0114 · Cited by 315 · see citing works

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

Mak, S. S. T., Gopalakrishnan, S., Carøe, C., Geng, C., Liu, S., Sinding, M. S., Kuderna, L. F. K., Zhang, W., Fu, S., Vieira, F. G., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix049 · Cited by 314 · see citing works

Ancient DNA reveals late survival of mammoth and horse in interior Alaska

Haile, J., FROESE, D. G., MacPhee, R. D. E., Roberts, R. G., Arnold, L. J., Reyes, A. V., Rasmussen, M. A., Nielsen, R., Brook, B. W., Robinson, S., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0912510106 · Cited by 313 · see citing works

Ancient pathogen genomics as an emerging tool for infectious disease research

Spyrou, M. A., Bos, K. I., Herbig, A., & Krause, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0119-1 · Cited by 313 · see citing works

A high-coverage Neandertal genome from Chagyrskaya Cave

Mafessoni, F., Grote, S., de Filippo, C., Slon, V., Kolobova, K. A., Viola, B., Markin, S. V., Chintalapati, M., Peyrégne, S., Skov, L., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2004944117 · Cited by 309 · see citing works

Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico

Vågene‬, Å. J., Herbig, A., Campana, M. G., García, N. M. R., Warinner, C., Sabin, S. J., Spyrou, M. A., Valtueña, A. A., Huson, D. H., Tuross, N., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0446-6 · Cited by 307 · see citing works

Archaeogenomic evidence reveals prehistoric matrilineal dynasty

Kennett, D. J., Plog, S., George, R. J., Culleton, B. J., Watson, A. S., Skoglund, P., Rohland, N., Mallick, S., Stewardson, K., Kistler, L., et al. (2017) · Nature Communications · doi:10.1038/ncomms14115 · Cited by 301 · see citing works

Kinship-based social inequality in Bronze Age Europe

Mittnik, A., Massy, K., Knipper, C., Wittenborn, F., Friedrich, R., Pfrengle, S., Burri, M., Carlichi-Witjes, N., Deeg, H., Furtwängler, A., et al. (2019) · Science · doi:10.1126/science.aax6219 · Cited by 300 · see citing works

Ancient Rome: A genetic crossroads of Europe and the Mediterranean

Antonio, M. L., Gao, Z., Moots, H. M., Lucci, M., Candilio, F., Sawyer, S., Oberreiter, V., Calderon, D., Devitofranceschi, K., Aikens, R. C., et al. (2019) · Science · doi:10.1126/science.aay6826 · Cited by 294 · see citing works

A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia

Krause, J., Briggs, A. W., Kircher, M., Maričić, T., Zwyns, N., Derevianko, A. P., & Pääbo, S. (2010) · Current Biology · doi:10.1016/j.cub.2009.11.068 · Cited by 290 · see citing works

Animal domestication in the era of ancient genomics

Frantz, L., Bradley, D. G., Larson, G., & Orlando, L. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0225-0 · Cited by 290 · see citing works

Reconstructing ancient genomes and epigenomes

Orlando, L., Gilbert, M. T. P., & Willerslev, E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3935 · Cited by 279 · see citing works

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

Korneliussen, T. S., Moltke, I., Albrechtsen, A., & Nielsen, R. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-289 · Cited by 278 · see citing works

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

Costello, M., Fleharty, M., Abreu, J., Farjoun, Y., Ferriera, S., Holmes, L., Granger, B. R., Green, L., Howd, T., Mason, T., et al. (2018) · BMC Genomics · doi:10.1186/s12864-018-4703-0 · Cited by 276 · see citing works

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

Burbano, H. A., Hodges, E. C., Green, R. E., Briggs, A. W., Krause, J., Meyer, M., Good, J. M., Maričić, T., Johnson, P. L. F., Xuan, Z., et al. (2010) · Science · doi:10.1126/science.1188046 · Cited by 276 · see citing works

Improving access to endogenous DNA in ancient bones and teeth

Damgaard, P. D. B., Margaryan, A., Schroeder, H., Orlando, L., Willerslev, E., & Allentoft, M. E. (2015) · Scientific Reports · doi:10.1038/srep11184 · Cited by 275 · see citing works

Genetic origins of the Minoans and Mycenaeans

Lazaridis, I., Mittnik, A., Patterson, N. J., Mallick, S., Rohland, N., Pfrengle, S., Furtwängler, A., Peltzer, A., Posth, C., Vasilakis, A., et al. (2017) · Nature · doi:10.1038/nature23310 · Cited by 275 · see citing works

leeHom: adaptor trimming and merging for Illumina sequencing reads

Renaud, G., Stenzel, U., & Kelso, J. F. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku699 · Cited by 274 · see citing works

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

Kircher, M., Stenzel, U., & Kelso, J. F. (2009) · Genome biology · doi:10.1186/gb-2009-10-8-r83 · Cited by 271 · see citing works

Reducing Microbial and Human Contamination in DNA Extractions from Ancient Bones and Teeth

Korlević, P., Gerber, T., Gansauge, M.-T., Hajdinjak, M., Nagel, S., Aximu‐Petri, A., & Meyer, M. (2015) · BioTechniques · doi:10.2144/000114320 · Cited by 267 · see citing works

Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America

Flegontov, P., Altınışık, N. E., Changmai, P., Rohland, N., Mallick, S., Adamski, N., Bolnick, D. A., Broomandkhoshbacht, N., Candilio, F., Culleton, B. J., et al. (2019) · Nature · doi:10.1038/s41586-019-1251-y · Cited by 264 · see citing works

Genebank genomics bridges the gap between the conservation of crop diversity and plant breeding

Mascher, M., Schreiber, M., Scholz, U., Graner, A., Reif, J. C., & Stein, N. (2019) · Nature Genetics · doi:10.1038/s41588-019-0443-6 · Cited by 260 · see citing works

Quantifying Temporal Genomic Erosion in Endangered Species

Díez-del-Molino, D., Sánchez-Barreiro, F., Barnes, I., Gilbert, M. T. P., & Dalén, L. (2018) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2017.12.002 · Cited by 258 · see citing works

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

Warinner, C., Speller, C., & Collins, M. J. (2014) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0376 · Cited by 256 · see citing works

Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible and Is DNA Leaching a Factor?

Haile, J., Holdaway, R. N., Oliver, K. L., Bunce, M., Gilbert, M. T. P., Nielsen, R., Munch, K., Ho, S. Y. W., Shapiro, B., & Willerslev, E. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm016 · Cited by 255 · see citing works

Ancient genomes indicate population replacement in Early Neolithic Britain

Brace, S., Diekmann, Y., Booth, T. J., van Dorp, L., Faltyskova, Z., Rohland, N., Mallick, S., Olalde, Í., Ferry, M., Michel, M., et al. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0871-9 · Cited by 255 · see citing works

The genetic history of admixture across inner Eurasia

Jeong, C., Balanovsky, O. P., Lukianova, E., Kahbatkyzy, N., Flegontov, P., Владимирович, З. В., Immel, A., Wang, C., Iksan, O., Khussainova, E., et al. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0878-2 · Cited by 245 · see citing works

Genomic Sequencing of Pleistocene Cave Bears

Noonan, J. P., Hofreiter, M., Smith, D. R., Priest, J. R., Rohland, N., Rabeder, G., Krause, J., Detter, J. C., Pääbo, S., & Rubin, E. M. (2005) · Science · doi:10.1126/science.1113485 · Cited by 242 · see citing works

The 5300-year-old Helicobacter pylori genome of the Iceman

Maixner, F., Krause‐Kyora, B., Turaev, D., Herbig, A., Hoopmann, M. R., Hallows, J. L., Kusebauch, U., Vigl, E. E., Malfertheiner, P., Mégraud, F., et al. (2016) · Science · doi:10.1126/science.aad2545 · Cited by 238 · see citing works

40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia

Yang, M. A., Gao, X., Theunert, C., Tong, H., Aximu‐Petri, A., Nickel, B., Slatkin, M., Meyer, M., Pääbo, S., Kelso, J. F., et al. (2017) · Current Biology · doi:10.1016/j.cub.2017.09.030 · Cited by 237 · see citing works

Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase

Gansauge, M.-T., Gerber, T., Glocke, I., Korlević, P., Lippik, L., Nagel, S., Riehl, L. M., Schmidt, A., & Meyer, M. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx033 · Cited by 232 · see citing works

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Park, S. D. E., Magee, D. A., McGettigan, P., Teasdale, M. D., Edwards, C. J., Lohan, A. J., Murphy, A., Braud, M., Donoghue, M. T. A., Liu, Y., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0790-2 · Cited by 228 · see citing works

The presence and impact of reference bias on population genomic studies of prehistoric human populations

Günther, T., & Nettelblad, C. (2019) · PLOS Genetics · doi:10.1371/journal.pgen.1008302 · Cited by 228 · see citing works

Ancient Cattle Genomics, Origins, and Rapid Turnover in the Fertile Crescent

Verdugo, M. P., Mullin, V. E., Scheu, A., Mattiangeli, V., Daly, K. G., Maisano Delser, P., Hare, A. J., Burger, J., Collins, M. J., Kehati, R., et al. (2019) · Science · doi:10.1126/science.aav1002 · Cited by 227 · see citing works

The use and domestication of Theobroma cacao during the mid-Holocene in the upper Amazon

Zarrillo, S., Gaikwad, N. W., Lanaud, C., Powis, T. G., Viot, C. R., Lesur, I., Fouet, O., Argout, X., Guichoux, E., Salin, F., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0697-x · Cited by 225 · see citing works

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent

Daly, K. G., Delser, P. M., Mullin, V. E., Scheu, A., Mattiangeli, V., Teasdale, M. D., Hare, A. J., Bürger, J., Verdugo, M. P., Collins, M. J., et al. (2018) · Science · doi:10.1126/science.aas9411 · Cited by 223 · see citing works

Ancient genomic changes associated with domestication of the horse

Librado, P., Gamba, C., Gaunitz, C., Sarkissian, C. S. I. D., Pruvost, M., Albrechtsen, A., Fages, A., Khan, N., Schubert, M., Jagannathan, V., et al. (2017) · Science · doi:10.1126/science.aam5298 · Cited by 222 · see citing works

Manual and automated preparation of single-stranded DNA libraries for the sequencing of DNA from ancient biological remains and other sources of highly degraded DNA

Gansauge, M.-T., Aximu‐Petri, A., Nagel, S., & Meyer, M. (2020) · Nature Protocols · doi:10.1038/s41596-020-0338-0 · Cited by 222 · see citing works

The Neandertal type site revisited: Interdisciplinary investigations of skeletal remains from the Neander Valley, Germany

Schmitz, R. W., Serre, D., Bonani, G., Feine, S. C., Hillgruber, F., Krainitzki, H., Pääbo, S., & Smith, F. H. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.192464099 · Cited by 221 · see citing works

A Paleogenomic Perspective on Evolution and Gene Function: New Insights from Ancient DNA

Shapiro, B., & Hofreiter, M. (2014) · Science · doi:10.1126/science.1236573 · Cited by 220 · see citing works

Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan

Gokhman, D., Lavi, E., Prüfer, K., Fraga, M. F., Riancho, J. A., Kelso, J. F., Pääbo, S., Meshorer, E., & Carmel, L. (2014) · Science · doi:10.1126/science.1250368 · Cited by 219 · see citing works

A dynastic elite in monumental Neolithic society

Cassidy, L. M., Maoldúin, R. Ó., Kador, T., Lynch, A., Jones, C., Woodman, P. C., Murphy, E., Ramsey, G., Dowd, M., Noonan, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2378-6 · Cited by 219 · see citing works

Female exogamy and gene pool diversification at the transition from the Final Neolithic to the Early Bronze Age in central Europe

Knipper, C., Mittnik, A., Massy, K., Kociumaka, C., Küçükkalıpçı, İ., Maus, M., Wittenborn, F., Metz, S. E., Staskiewicz, A., Krause, J., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706355114 · Cited by 211 · see citing works

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America

Swarts, K., Gutaker, R. M., Benz, B. F., Blake, M., Bukowski, R., Holland, J. B., Kruse-Peeples, M., Lepak, N. K., Prim, L., Romay, M. C., et al. (2017) · Science · doi:10.1126/science.aam9425 · Cited by 207 · see citing works

Signatures of Archaic Adaptive Introgression in Present-Day Human Populations

Racimo, F., Marnetto, D., & Huerta-Sánchez, E. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw216 · Cited by 200 · see citing works

Evolutionary Genomics and Conservation of the Endangered Przewalski’s Horse

Sarkissian, C. S. I. D., Ermini, L., Schubert, M., Yang, M. A., Librado, P., Fumagalli, M., Jónsson, H., Bar‐Gal, G. K., Albrechtsen, A., Vieira, F. G., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.08.032 · Cited by 198 · see citing works

The evolutionary history of dogs in the Americas

Leathlobhair, M. N., Perri, A. R., Irving-Pease, E. K., Witt, K. E., Linderholm, A. E., Haile, J., Lebrasseur, O., Ameen, C., Blick, J. P., Boyko, A. R., et al. (2018) · Science · doi:10.1126/science.aao4776 · Cited by 197 · see citing works

A Robust Framework for Microbial Archaeology

Warinner, C., Herbig, A., Mann, A. E., Yates, J. A. F., Weiß, C. L., Burbano, H. A., Orlando, L., & Krause, J. (2017) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-091416-035526 · Cited by 194 · see citing works

The neandertal genome and ancient DNA authenticity

Green, R. E., Briggs, A. W., Krause, J., Prüfer, K., Burbano, H. A., Siebauer, M., Lachmann, M., & Pääbo, S. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.222 · Cited by 190 · see citing works

A Paleogenomic Reconstruction of the Deep Population History of the Andes

Nakatsuka, N. J., Lazaridis, I., Barbieri, C., Skoglund, P., Rohland, N., Mallick, S., Posth, C., Harkins, K. M., Ferry, M., Harney, É., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.015 · Cited by 190 · see citing works

Inconsistencies in Neanderthal Genomic DNA Sequences

Wall, J. D., & Kim, S. K. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030175 · Cited by 180 · see citing works

A Molecular Approach to the Sexing of the Triple Burial at the Upper Paleolithic Site of Dolní Věstonice

Mittnik, A., Wang, C., Svoboda, J. A., & Krause, J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0163019 · Cited by 179 · see citing works

Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes

Spyrou, M. A., Keller, M., Ильгизовна, Т. Р., Scheib, C. L., Nelson, E. A., Valtueña, A. A., Neumann, G. U., Walker, D., Alterauge, A., Carty, N., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12154-0 · Cited by 176 · see citing works

Comparing the performance of three ancient DNA extraction methods for high‐throughput sequencing

Gamba, C., Hanghøj, K., Gaunitz, C., Alfarhan, A., Alquraishi, S. A., Al‐Rasheid, K. A. S., Bradley, D. G., & Orlando, L. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12470 · Cited by 176 · see citing works

Extensive Human DNA Contamination in Extracts from Ancient Dog Bones and Teeth

Malmström, H., Storå, J., Dalén, L., Holmlund, G., & Götherström, A. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi195 · Cited by 175 · see citing works

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genomePreprint

Pedersen, J. S., Valen, E., Velazquez, A. M. V., Parker, B. J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D. J., Kelly, T. K., Vang, S., et al. (2013) · Genome Research · doi:10.1101/gr.163592.113 · Cited by 171 · see citing works

Population Turnover in Remote Oceania Shortly after Initial Settlement

Lipson, M., Skoglund, P., Spriggs, M., Valentin, F., Bedford, S., Shing, R., Buckley, H. R., Phillip, I., Ward, G. K., Mallick, S., et al. (2018) · Current Biology · doi:10.1016/j.cub.2018.02.051 · Cited by 171 · see citing works

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage

Velsko, I. M., Fellows Yates, J. A., Aron, F., Hagan, R. W., Frantz, L. A. F., Loe, L., Martinez, J. B. R., Chaves, E., Gosden, C., Larson, G., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0717-3 · Cited by 170 · see citing works

Relatively well preserved DNA is present in the crystal aggregates of fossil bones

Salamon, M., Tuross, N., Arensburg, B., & Weiner, S. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503718102 · Cited by 169 · see citing works

Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers

Sánchez‐Quinto, F., Schroeder, H., Ramírez, Ó., Ávila‐Arcos, M. C., Pybus, M., Olalde, Í., Velazquez, A. M. V., Marcos, M. E. P., Encinas, J. M. V., Bertranpetit, J., et al. (2012) · Current Biology · doi:10.1016/j.cub.2012.06.005 · Cited by 169 · see citing works

The origin and evolution of maize in the Southwestern United States

da Fonseca, R. R., Smith, B. D., Wales, N., Cappellini, E., Skoglund, P., Fumagalli, M., Castruita, J. A. S., Carøe, C., Ávila‐Arcos, M. C., Hufnagel, D. E., et al. (2015) · Nature Plants · doi:10.1038/nplants.2014.3 · Cited by 167 · see citing works

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

Ziesemer, K. A., Mann, A. E., Sankaranarayanan, K., Schroeder, H., Ozga, A. T., Brandt, B. W., Zaura, E., Waters‐Rist, A. L., Hoogland, M. L. P., Salazar‐García, D. C., et al. (2015) · Scientific Reports · doi:10.1038/srep16498 · Cited by 166 · see citing works

Partial genomic survival of cave bears in living brown bears

Barlow, A., Cahill, J. A., Hartmann, S. A., Theunert, C., Xenikoudakis, G., Fortes, G. G., Paijmans, J. L. A., Rabeder, G., Frischauf, C., Grandal‐d'Anglade, A., et al. (2018) · Nature Ecology & Evolution · doi:10.1038/s41559-018-0654-8 · Cited by 164 · see citing works

Unravelling reference bias in ancient DNA datasets

Dolenz, S., van der Valk, T., Jin, C., Oppenheimer, J., Sharif, M. B., Orlando, L., Shapiro, B., Dalén, L., & Heintzman, P. D. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae436 · Cited by 33 · see citing works

ИСПОЛЬЗОВAНИЕ ПОТЕНЦИAЛA СОЦИAЛЬНЫХ ПAРТНЕРОВ В ПОДГОТОВКЕ БУДУЩИХ ПЕДAГОГОВ

Атабекова, Б. Б. (2024) · Habaršy. Pedagogika ġylymdary seriâsy · doi:10.51889/2959-5762.2023.80.4.019

Cloning and Characterization of Rat BAT3 cDNA

Ozaki, T., Hanaoka, E., Naka, M., et al. (1999) · DNA and Cell Biology · doi:10.1089/104454999315222 · Cited by 22 · see citing works

EFFECT OF THE NEMATODE PHASMARHABDITIS HERMAPHRODITA ON YOUNG STAGES OF THE PEST SLUG ARION LUSITANICUS

Grimm, B. (2002) · Journal of Molluscan Studies · doi:10.1093/mollus/68.1.25 · Cited by 41 · see citing works

HLA-B-associated transcript 3 (Bat3)/Scythe is essential for p300-mediated acetylation of p53Preprint

Sasaki, T., Gan, E. C., Wakeham, A. C., Kornbluth, S. A., Mak, T. W., & Okada, H. (2007) · Genes & Development · doi:10.1101/gad.1534107 · Cited by 127 · see citing works

Anthoxanthum Mosaic Virus

Catherall, P. L. (1970) · Plant Pathology · doi:10.1111/j.1365-3059.1970.tb00999.x · Cited by 6 · see citing works