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Recent Department Publications

Last update: July 31st, 2015

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2015

Alter, S. E., Meyer, M., Post, K., Czechowski, P., Gravlund, P., Gaines, C., Rosenbaum, H. C., Kaschner, K., Turvey, S. T., van der Plicht, J., Shapiro, B., & Hofreiter, M. (2015). Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100. Molecular Ecology, 24(7), 1510-1522.
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Benazzi, S., Slon, V., Talamo, S., Negrino, F., Peresani, M., Bailey, S. E., Sawyer, S., Panetta, D., Vicino, G., Starnini, E., Mannino, M. A., Salvadori, P. A., Meyer, M., Pääbo, S., & Hublin, J.-J. (2015). The makers of the Protoaurignacian and implications for Neandertal extinction. Science, 348(6236), 793-796.
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Bozek, K., Wei, Y., Yan, Z., Liu, X., Xiong, J., Sugimoto, M., Tomita, M., Pääbo, S., Sherwood, C. C., Hof, P. R., Ely, J. J., Li, Y., Steinhauser, D., Willmitzer, L., Giavalisco, P., & Khaitovich, P. (2015). Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque, and mouse tissues. Neuron, 85(4), 695-702.
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Cahill, J. A., Stirling, I., Kistler, L., Salamzade, R., Ersmark, E., Fulton, T. L., Stiller, M., Green, R. E., & Shapiro, B. (2015). Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Molecular Ecology, 24(6), 1205-1217.
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Cao, Q., Didelot, X., Wu, Z., Li, Z., He, L., Li, Y., Ni, M., You, Y., Lin, X., Li, Z., Gong, Y., Zheng, M., Zhang, M., Liu, J., Wang, W., Bo, X., Falush, D., Wang, S., & Zhang, J. (2015). Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis. Gut, 64(4), 554-561.
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Florio, M., Albert, M., Taverna, E., Namba, T., Brandl, H., Lewitus, E., Haffner, C., Sykes, A., Wong, F. K., Peters, J., Guhr, E., Klemroth, S., Prüfer, K., Kelso, J. F., Naumann, R., Nüsslein, I., Dahl, A., Lachmann, R., Pääbo, S., & Huttner, W. B. (2015). Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion. Science, 347(6229), 1465-1470.
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Fu, Q., Hajdinjak, M., Moldovan, O., Constantin, S., Mallick, S., Skoglund, P., Patterson, N., Rohland, N., Lazaridis, I., Nickel, B., Viola, B., Prüfer, K., Meyer, M., Kelso, J. F., Reich, D., & Pääbo, S. (2015). An early modern human from Romania with a recent Neanderthal ancestor (advance online). Nature.
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Germonpré, M., Sablin, M. V., Lázničková-Galetová, M., Després, V., Stevens, R. E., Stiller, M., & Hofreiter, M. (2015). Palaeolithic dogs and Pleistocene wolves revisited: A reply to Morey (2014). Journal of Archaeological Science, 54, 210-216.
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Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., Fu, Q., Mittnik, A., Bánffy, E., Economou, C., Francken, M., Friederich, S., Pena, R. G., Hallgren, F., Khartanovich, V., Khokhlov, A., Kunst, M., Kuznetsov, P., Meller, H., Mochalov, O., Moiseyev, V., Nicklisch, N., Pichler, S. L., Risch, R., Guerra, M. A. R., Roth, C., Szécsényi-Nagy, A., Wahl, J., Meyer, M., Krause, J., Brown, D., Anthony, D., Cooper, A., Alt, K. W., & Reich, D. (2015). Massive migration from the steppe was a source for Indo-European languages in Europe (advance online). Nature.
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Hughes, D. A., Kircher, M., He, Z., Guo, S., Fairbrother, G. L., Moreno, C. S., Khaitovich, P., & Stoneking, M. (2015). Evaluating intra- and inter-individual variation in the human placental transcriptome. Genome Biology, 16: 54.
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Li, M., Schröder, R., Ni, S., Madea, B., & Stoneking, M. (2015). Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations. Proceedings of the National Academy of Sciences of the United States of America, 112(8), 2491-2496.
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Macholdt, E., Slatkin, M., Pakendorf, B., & Stoneking, M. (2015). New insights into the history of the C-14010 lactase persistence variant in Eastern and Southern Africa. American Journal of Physical Anthropology, 156(4), 661-664.
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Nogueiro, I., Teixeira, J. C., Amorim, A., Gusmão, L., & Alvarez, L. (2015). Portuguese crypto-Jews: The genetic heritage of a complex history. Frontiers in Genetics, 6: 12.
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Nogueiro, I., Teixeira, J., Amorim, A., Gusmão, L., & Alvarez, L. (2015). Echoes from Sepharad: Signatures on the maternal gene pool of crypto-Jewish descendants. European Journal of Human Genetics, 23, 693-699.
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Pääbo, S. (2015). The diverse origins of the human gene pool (Commentary). Nature Reviews Genetics, 16, 313-314.
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Prüfer, K., & Meyer, M. (2015). Comment on “Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans”. Science, 347(6224), 835.
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Pugach, I., & Stoneking, M. (2015). Genome-wide insights into the genetic history of human populations. Investigative Genetics, 6: 6.
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Renaud, G., Stenzel, U., Maricic, T., Wiebe, V., & Kelso, J. F. (2015). deML: Robust demultiplexing of Illumina sequences using a likelihood-based approach. Bioinformatics, 31(5), 770-772.
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Slon, V., Glocke, I., Barkai, R., Gopher, A., Hershkovitz, I., & Meyer, M. (2015). Mammalian mitochondrial capture, a tool for rapid screening of DNA preservation in faunal and undiagnostic remains, and its application to Middle Pleistocene specimens from Qesem Cave (Israel) (advance online). Quaternary International.
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Teixeira, J. C., de Filippo, C., Weihmann, A., Meneu, J. R., Racimo, F., Dannemann, M., Nickel, B., Fischer, A., Halbwax, M., Andre, C., Atencia, R., Meyer, M., Parra, G., Pääbo, S., & Andrés, A. M. (2015). Long-term balancing selection in LAD1 maintains a missense trans-species polymorphism in humans, chimpanzees and bonobos. Molecular Biology and Evolution, 32(5), 1186-1196.
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Valverde, G., Zhou, H., Lippold, S., de Filippo, C., Tang, K., Herráez, D. L., Li, J., & Stoneking, M. (2015). A novel candidate region for genetic adaptation to high altitude in Andean populations. PLoS One, 10(5): e0125444.
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van Leeuwen, E. M., Karssen, L. C., Deelen, J., Isaacs, A., Medina-Gomez, C., Mbarek, H., Kanterakis, A., Trompet, S., Postmus, I., Verweij, N., van Enckevort, D. J., Huffman, J. E., White, C. C., Feitosa, M. F., Bartz, T. M., Manichaikul, A., Joshi, P. K., Peloso, G. M., Deelen, P., van Dijk, F., Willemsen, G., de Geus, E. J., Milaneschi, Y., Penninx, B. W., Francioli, L. C., Menelaou, A., Pulit, S. L., Rivadeneira, F., Hofman, A., Oostra, B. A., Franco, O. H., Leach, I. M., Beekman, M., de Craen, A. J., Uh, H.-W., Trochet, H., Hocking, L. J., Porteous, D. J., Sattar, N., Packard, C. J., Buckley, B. M., Brody, J. A., Bis, J. C., Rotter, J. I., Mychaleckyj, J. C., Campbell, H., Duan, Q., Lange, L. A., Wilson, J. F., Hayward, C., Polasek, O., Vitart, V., Rudan, I., Wright, A. F., Rich, S. S., Psaty, B. M., Borecki, I. B., Kearney, P. M., Stott, D. J., Cupples, L. A., Jukema, J. W., van der Harst, P., Sijbrands, E. J., Hottenga, J.-J., Uitterlinden, A. G., Swertz, M. A., van Ommen, G.-J.-B., de Bakker, P. I., Slagboom, P. E., Boomsma, D. I., Wijmenga, C., van Duijn, C. M., The Genome of the Netherlands Consortium, Stoneking, M., & Li, M. (2015). Genome of the Netherlands population - specific imputations identify an ​ABCA6 variant associated with cholesterol levels. Nature Communications, 6: 6065.
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Vaughan, A. E., Brumwell, A. N., Xi, Y., Gotts, J. E., Brownfield, D. G., Treutlein, B., Tan, K., Tan, V., Liu, F. C., Looney, M. R., Matthay, M. A., Rock, J. R., & Chapman, H. A. (2015). Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury. Nature, 517(7536), 621-625.
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Wei, Y.-N., Hu, H.-Y., Xie, G.-C., Fu, N., Ning, Z.-B., Zeng, R., & Khaitovich, P. (2015). Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. Genome Biology, 16: 41.
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White, L., Romagné, F., Müller, E., Erlebach, E., Weihmann, A., Parra, G., Andrés, A. M., & Castellano, S. (2015). Genetic adaptation to levels of dietary selenium in recent human history. Molecular Biology and Evolution, 32(6), 1507-1518.
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2014

Andrés, A. M., & Nowick, K. (Eds.). (2014). Genetics of human evolution [Special Issue]. Current Opinion in Genetics & Development, 29.
      
Andrés, A. M., & Nowick, K. (2014). Editorial overview: Genetics of human evolution: The genetics of human origins. Current Opinion in Genetics & Development, 29, v-vii.
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Barbieri, C., Güldemann, T., Naumann, C., Gerlach, L., Berthold, F., Nakagawa, H., Mpoloka, S. W., Stoneking, M., & Pakendorf, B. (2014). Unraveling the complex maternal history of Southern African Khoisan populations. American Journal of Physical Anthropology, 153(3), 435-448.
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Barbieri, C., Vicente, M., Oliveira, S., Bostoen, K., Rocha, J., Stoneking, M., & Pakendorf, B. (2014). Migration and interaction in a contact zone: mtDNA variation among Bantu-speakers in southern Africa. PLoS One, 9(6): e9911.
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Benazzi, S., Peresani, M., Talamo, S., Fu, Q., Mannino, M. A., Richards, M. P., & Hublin, J.-J. (2014). A reassessment of the presumed Neandertal remains from San Bernardino Cave, Italy. Journal of Human Evolution, 66(1), 89-94.
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Bozek, K., Wei, Y., Yan, Z., Liu, X., Xiong, J., Sugimoto, M., Tomita, M., Pääbo, S., Pieszek, R., Sherwood, C. C., Hof, P. R., Ely, J. J., Steinhauser, D., Bangsbo, J., Willmitzer, L., Hansson, O., Call, J., Giavalisco, P., & Khaitovich, P. (2014). Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS Biology, 12(5): e1001871.
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Carneiro, M., Albert, F. W., Afonso, S., Pereira, R. J., Burbano, H. A., Campos, R., Melo-Ferreira, J., Blanco-Aguiar, J. A., Villafuerte, R., Nachman, M. W., Good, J. M., & Ferrand, N. (2014). The genomic architecture of population divergence between subspecies of the European rabbit. PLoS Genetics, 10(8): e1003519.
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Carneiro, M., Rubin, C.-J., Palma, F. D., Albert, F. W., Alföldi, J., Barrio, A. M., Pielberg, G., Rafati, N., Sayyab, S., Turner-Maier, J., Younis, S., Afonso, S., Aken, B., Alves, J. M., Barrell, D., Bolet, G., Boucher, S., Burbano, H. A., Campos, R., Chang, J. L., Duranthon, V., Fontanesi, L., Garreau, H., Heiman, D., Johnson, J., Mage, R. G., Peng, Z., Queney, G., Rogel-Gaillard, C., Ruffier, M., Searle, S., Villafuerte, R., Xiong, A., Young, S., Forsberg-Nilsson, K., Good, J. M., Lander, E. S., Ferrand, N., Lindblad-Toh, K., & Andersson, L. (2014). Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science, 345(6200), 1074-1079.
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Castellano, S., Parra, G., Sánchez-Quinto, F. A., Racimo, F., Kuhlwilm, M., Kircher, M., Sawyer, S., Fu, Q., Heinze, A., Nickel, B., Dabney, J., Siebauer, M. F., White, L., Burbano, H. A., Renaud, G., Stenzel, U., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Rudan, P., Brajković, D., Kucan, Ž., Gušic, I., Shunkov, M. V., Derevianko, A. P., Viola, B., Meyer, M., Kelso, J. F., Andrés, A. M., & Pääbo, S. (2014). Patterns of coding variation in the complete exomes of three Neandertals. Proceedings of the National Academy of Sciences of the United States of America, 111(18), 6666-6671.
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Dabney, J., Meyer, M., & Pääbo, S. (2014). Ancient DNA damage. In E. C. Friedberg, S. J. Elledge, A. R. Lehmann, T. Lindahl, & M. Muzi-Falconi (Eds.), DNA Repair, Mutagenesis, and Other Responses to DNA Damage: A subject collection from Cold Spring Harbor Perspectives in Biology (pp. 19-26). New York: Cold Spring Harbor Laboratory Pr.
      
Deelen, P., Menelaou, A., van Leeuwen, E. M., Kanterakis, A., van Dijk, F., Medina-Gomez, C., Francioli, L. C., Hottenga, J. J., Karssen, L. C., Estrada, K., Kreiner-Møller, E., Rivadeneira, F., van Setten, J., Gutierrez-Achury, J., Westra, H.-J., Franke, L., van Enckevort, D., Dijkstra, M., Byelas, H., van Duijn, C. M., Genome of the Netherlands Consortium, de Bakker, P. I. W., Wijmenga, C., Swertz, M. A., Stoneking, M., & Li, M. (2014). Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'. European Journal of Human Genetics, 22(11), 1321-1326.
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Delfin, F. S., Ko, A.-M.-S., Li, M., Gunnarsdóttir, E. D., Tabbada, K. A., Salvador, J. M., Calacal, G. C., Sagum, M. S., Datar, F. A., Padilla, S. G., Ungria, M. C. A. D., & Stoneking, M. (2014). Complete mtDNA genomes of Filipino ethnolinguistic groups: A melting pot of recent and ancient lineages in the Asia-Pacific region. European journal of human genetics, 22(2), 228-237.
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Duggan, A. T. (2014). Investigations of the settlement and demographic history of Oceania through whole mitochondrial genome sequence analysis. PhD Thesis, Univ., Leipzig.
      
Duggan, A. T., & Stoneking, M. (2014). Recent developments in the genetic history of East Asia and Oceania. Current Opinion in Genetics & Development, 29, 9-14.
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Duggan, A. T., Evans, B., Friedlaender, F. R., Friedlaender, J. S., Koki, G., Merriwether, D. A., Kayser, M., & Stoneking, M. (2014). Maternal history of Oceania from complete mtDNA genomes: Contrasting ancient diversity with recent homogenization due to the Austronesian expansion. The American Journal of Human Genetics, 94(5), 721-733.
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Engelken, J., Carnero-Montoro, E., Pybus, M., Andrews, G. K., Lalueza-Fox, C., Comas, D., Sekler, I., de la Rasilla, M., Rosas, A., Stoneking, M., Valverde, M. A., Vicente, R., & Bosch, E. (2014). Extreme population differences in the human zinc transporter ZIP4 (SLC39A4) are explained by positive selection in Sub-Saharan Africa. PLoS Genetics, 10(2): e1004128.
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Ferreira, Z., Hurle, B., Andrés, A. M., Kretzschmar, W. W., Mullikin, J. C., Cherukuri, P. F., Cruz, P., Gonder, M. K., Stone, A. C., Tishkoff, S., Swanson, W. J., NISC Comparative Sequencing Program, Green, E. D., Clark, A. G., & Seixas, S. (2014). Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biology and Evolution, 5(12), 2512-2523.
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Francioli, L. C., Menelaou, A., Pulit, S. L., van Dijk, F., Palamara, P. F., Elbers, C. C., Neerincx, P. B. T., Ye, K., Guryev, V., Kloosterman, W. P., Deelen, P., Abdellaoui, A., van Leeuwen, E. M., van Oven, M., Vermaat, M., Li, M., Laros, J. F. J., Karssen, L. C., Kanterakis, A., Amin, N., Hottenga, J. J., Lameijer, E.-W., Kattenberg, M., Dijkstra, M., Byelas, H., van Setten, J., van Schaik, B. D. C., Bot, J., Nijman, I. J., Renkens, I., Marschall, T., Schönhuth, A., Hehir-Kwa, J. Y., Handsaker, R. E., Polak, P., Sohail, M., Vuzman, D., Hormozdiari, F., van Enckevort, D., Mei, H., Koval, V., Moed, M. H., van der Velde, K. J., Rivadeneira, F., Estrada, K., Medina-Gomez, C., Isaacs, A., McCarroll, S. A., Beekman, M., de Craen, A. J. M., Suchiman, H. E. D., Hofman, A., Oostra, B., Uitterlinden, A. G., Willemsen, G., Study, L. C., Platteel, M., Veldink, J. H., van den Berg, L. H., Pitts, S. J., Potluri, S., Sundar, P., Cox, D. R., Sunyaev, S. R., den Dunnen, J. T., Stoneking, M., de Knijff, P., Kayser, M., Li, Q., Li, Y., Du, Y., Chen, R., Cao, H., Li, N., Cao, S., Wang, J., Bovenberg, J. A., Pe'er, I., Slagboom, P. E., van Duijn, C. M., Boomsma, D. I., van Ommen, G.-J.-B., de Bakker, P. I. W., Swertz, M. A., Wijmenga, C., & Genome of the Netherlands Consortium, The (2014). Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nature Genetics, 46(8), 818-825.
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Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Ayinuer-Petri, A., Prüfer, K., de Filippo, C., Meyer, M., Zwyns, N., Salazar García, D. C., Kuzmin, Y. V., Keates, S. G., Kosintsev, P. A., Razhev, D. I., Richards, M. P., Peristov, N. V., Lachmann, M., Douka, K., Higham, T. F. G., Slatkin, M., Hublin, J.-J., Reich, D., Kelso, J. F., Viola, B., & Pääbo, S. (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 514(7523), 445-449.
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Gansauge, M.-T., & Meyer, M. (2014). Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Research, 24(9), 1543-1549.
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Gerth, M., Gansauge, M.-T., Weigert, A., & Bleidorn, C. (2014). Phylogenomic analyses uncover origin and spread of the Wolbachia pandemic. Nature Communications, 5: 5117.
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Giuliani, C., Barbieri, C., Li, M., Bucci, L., Monti, D., Passarino, G., Luiselli, D., Franceschi, C., Stoneking, M., & Garagnani, P. (2014). Transmission from centenarians to their offspring of mtDNA heteroplasmy revealed by ultra-deep sequencing. Aging, 6(6), 454-467. Retrieved from http://www.impactaging.com/papers/v6/n6/full/100661.html.
      

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Gokhman, D., Lavi, E., Prüfer, K., Fraga, M. F., Riancho, J. A., Kelso, J. F., Pääbo, S., Meshorer, E., & Carmel, L. (2014). Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science, 344(6183), 523-527.
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Guo, J., Tan, J., Yang, Y., Zhou, H., Hu, S., Hashan, A., Bahaxar, N., Xu, S., Weaver, T. D., Jin, L., Stoneking, M., & Tang, K. (2014). Variation and signatures of selection on the human face. Journal of Human Evolution, 75, 143-152.
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He, Z., Bammann, H., Han, D., Xie, G., & Khaitovich, P. (2014). Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation. RNA, 20(7), 1103-1111.
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Hellenthal, G., Busby, G. B. J., Band, G., Wilson, J. F., Capelli, C., Falush, D., & Myers, S. (2014). A genetic atlas of human admixture history. Science, 373(6172), 747-751.
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Henne, K., Li, J., Stoneking, M., Kessler, O., Schilling, H., Sonanini, A., Conrads, G., & Horz, H.-P. (2014). Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies. BMC Evolutionary Biology, 14: 190.
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Heyn, P., Kircher, M., Dahl, A., Kelso, J. F., Tomancak, P., Kalinka, A. T., & Neugebauer, K. M. (2014). The earliest transcribed zygotic genes are short, newly evolved and different across species. Cell Reports, 6(2), 285-292.
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Heyne, H. O., Lautenschläger, S., Nelson, R., Besnier, F., Rotival, M., Cagan, A., Kozhemyakina, R., Plyusnina, I. Z., Trut, L., Carlborg, Ö., Petretto, E., Kruglyak, L., Pääbo, S., Schöneberg, T., & Albert, F. W. (2014). Genetic influences on brain gene expression in rats selected for tameness and aggression. Genetics, 198(3), 1277-1290.
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Horn, S. (2014). TERT-Promoter-Mutationen im familiären und sporadischen Melanom. In Lebendige Wissenschaft: Spitzenforschung in der Dermatologie - Innovationen und Auszeichnungen 2014 (pp. 52-57). Lampertheim: Alpha-Informations-GmbH.
      
Horn, S., Prost, S., Stiller, M., Makowiecki, D., Kuznetsova, T., Benecke, N., Pucher, E., Hufthammer, A. K., Schouwenburg, C., Shapiro, B., & Hofreiter, M. (2014). Ancient mitochondrial DNA and the genetic history of Eurasian beaver (Castor fiber) in Europe. Molecular Ecology, 23(7), 1717-1729.
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Hu, H. Y., He, L., & Khaitovich, P. (2014). Deep sequencing reveals a novel class of bidirectional promoters associated with neuronal genes. BMC Genomics, 15: 457.
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Kelso, J. F., & Prüfer, K. (2014). Ancient humans and the origin of modern humans. Current Opinion in Genetics & Development, 29, 133-138.
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Key, F. M., Teixeira, J. C., de Filippo, C., & Andrés, A. M. (2014). Advantageous diversity maintained by balancing selection in humans. Current Opinion in Genetics & Development, 29, 45-51.
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Key, F.-M., Peter, B., Dennis, M. Y., Huerta-Sanchez, E., Tang, W., Prokunina-Olsson, L., Nielsen, R., & Andrés, A. M. (2014). Selection on a variant associated with improved viral clearance drives local, adaptive pseudogenization of Interferon Lambda 4 (IFNL 4). PLoS Genetics, 10(10): e1004681.
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Khrameeva, E. E., Bozek, K., He, L., Yan, Z., Jiang, X., Wei, Y., Tang, K., Gelfand, M. S., Prüfer, K., Kelso, J. F., Pääbo, S., Giavalisco, P., Lachmann, M., & Khaitovich, P. (2014). Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nature Communications, 5: 3584.
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Ko, A.-M.-S., Chen, C.-Y., Fu, Q., Delfin, F. S., Li, M., Chiu, H.-L., Stoneking, M., & Ko, Y.-C. (2014). Early Austronesians: Into and out of Taiwan. The American Journal of Human Genetics, 94(3), 426-436.
DOI          
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Lee, C.-H., Chiang, S.-L., Ko, A.-M.-S., Hua, C.-H., Tsai, M.-H., Warnakulasuriya, S., Ibrahim, S. O., Sunarjo,.-., Zain, R. B., Ling, T.-Y., Huang, C.-L., Lane, H.-Y., Lin, C.-C., & Ko, Y.-C. (2014). Betel-quid dependence domains and syndrome associated with betel-quid ingredients among chewers: An Asian multi-country evidence. Addiction, 109(7), 1194-1204.
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Li, J., Quinque, D., Horz, H.-P., Li, M., Rzhetskaya, M., Raff, J. A., Hayes, M. G., & Stoneking, M. (2014). Comparative analysis of the human saliva microbiome from different climate zones: Alaska, Germany, and Africa. BMC Microbiology, 14: 316.
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Lindskog, C., Kuhlwilm, M., Davierwala, A., Fu, N., Hegde, G., Uhlén, M., Navani, S., Pääbo, S., & Pontén, a. F. (2014). Analysis of candidate genes for lineage-specific expression changes in humans and primates. Journal of Proteome Research, 13(8), 3596-3606.
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Lippold, S., Xu, H., Ko, A., Li, M., Renaud, G., Butthoff, A., Schröder, R., & Stoneking, M. (2014). Human paternal and maternal demographic histories: Insights from high-resolution Y chromosome and mtDNA sequences. Investigative Genetics, 5: 13.
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Lipson, M., Loh, P.-R., Patterson, N., Moorjani, P., Ko, Y.-C., Stoneking, M., Berger, B., & Reich, D. (2014). Reconstructing Austronesian population history in Island Southeast Asia. Nature Communications, 5: 4689.
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Macholdt, E., Lede, V., Barbieri, C., Mpoloka, S. W., Chen, H., Slatkin, M., Pakendorf, B., & Stoneking, M. (2014). Tracing pastoralist migrations to Southern Africa with lactase persistence alleles. Current Biology, 24(8), 875-879.
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Meyer, M., Fu, Q., Ayinuer-Petri, A., Glocke, I., Nickel, B., Arsuaga, J.-L., Martínez, I., Gracia, A., de Castro, J. M. B., Carbonell, E., & Pääbo, S. (2014). A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature, 505(7483), 403-406.
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Mitchell, K. J., Pratt, R. C., Watson, L. N., Gibb, G. C., Llamas, B., Kasper, M., Edson, J., Hopwood, B., Male, D., Armstrong, K. N., Meyer, M., Hofreiter, M., Austin, J., Donnellan, S. C., Lee, M. S. Y., Phillips, M. J., & Cooper, A. (2014). Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular Biology and Evolution, 31(9), 2322-2330.
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Pääbo, S. (2014). Neanderthal man: In search of lost genomes. New York: Basic Books.
      
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Prüfer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P. H., de Filippo, C., Li, H., Mallick, S., Dannemann, M., Fu, Q., Kircher, M., Kuhlwilm, M., Lachmann, M., Meyer, M., Ongyerth, M., Siebauer, M. F., Theunert, C., Tandon, A., Moorjani, P., Pickrell, J., Mullikin, J. C., Vohr, S. H., Green, R. E., Hellmann, I., Johnson, P. L. F., Blanche, H., Cann, H., Kitzman, J. O., Shendure, J., Eichler, E. E., Lein, E. S., Bakken, T. E., Golovanova, L. V., Doronichev, V. B., Shunkov, M. V., Derevianko, A. P., Viola, B., Slatkin, M., Reich, D., Kelso, J. F., & Pääbo, S. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505(7481), 43-49.
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Pybus, M., Dall'Olio, G. M., Luisi, P., Uzkudun, M., Carreño-Torres, A., Pavlidis, P., Laayouni, H., Bertranpetit, J., & Engelken, J. (2014). 1000 genomes selection browser 1.0: A genome browser dedicated to signatures of natural selection in modern humans. Nucleic Acids Research, 42(D1), D903-D909.
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The SIGMA Type 2 Diabetes Consortium, Prüfer, K., Sawyer, S., Stenzel, U., Kelso, J., & Pääbo, S. (2014). Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature, 506, 97-101.
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2013

Barbieri, C., Butthoff, A., Bostoen, K., & Pakendorf, B. (2013). Genetic perspectives on the origin of clicks in Bantu languages from southwestern Zambia. European journal of human genetics: EJHG; the official journal of the European Society of Human Genetics, 21, 430-436.
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Barbieri, C., Vicente, M., Rocha, J., Mpoloka, S. W., Stoneking, M., & Pakendorf, B. (2013). Ancient substructure in early mtDNA lineages of southern Africa. American Journal of Human Genetics, 92, 285-292.
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Bedaso, Z. K., Wynna, J. G., Alemseged, Z., & Geraads, D. (2013). Dietary and paleoenvironmental reconstruction using stable isotopes of herbivore tooth enamel from middle Pliocene Dikika, Ethiopia: Implication for Australopithecus afarensis habitat and food resources. Journal of Human Evolution, 64(1), 21-38.
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Brandariz-Fontes, C., Leonard, J. A., Vega-Pla, J. L., Backström, N., Lindgren, G., Lippold, S., & Rico, C. (2013). Y-Chromosome Analysis in Retuertas Horses. PLoS One, 8(5): e64985.
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Brown, S., Savage, P. E., Ko, A.-M.-S., Stoneking, M., Ko, Y.-C., Loo, J.-H., & Trejaut, J. A. (2013). Correlations in the population structure of music, genes and language. Proceedings of the Royal Society of London. Series B: Biological Sciences, 281(1774): 20132072.
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Bruche, S., Gusset, M., Lippold, S., Barnett, R., Eulenberger, K., Junhold, J., Driscoll, C. A., & Hofreiter, M. (2013). A genetically distinct lion (Panthera leo) population from Ethiopia. European Journal of Wildlife Research, 59(2), 215-225.
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Dabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., & Meyer, M. (2013). Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proceedings of the National Academy of Sciences of the United States of America, 110(39), 15758-15763.
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Duggan, A. T., & Stoneking, M. (2013). A highly unstable recent mutation in human mtDNA. American Journal of Human Genetics, 92(2), 279-284.
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Ferreira, Z., Seixas, S., Andrés, A. M., Kretzschmar, W. W., Mullikin, J. C., Cherukuri, P. F., Cruz, P., Swanson, W. J., Clark, A. G., Green, E. D., & Hurle, B. (2013). Reproduction and immunity-driven natural selection in the human WFDC locus. Molecular Biology and Evolution, 30(4), 938-950.
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Fu, Q. (2013). Tracing human prehistory with genetic data of ancient and modern humans. PhD Thesis, Univ., Leipzig.
      
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Fu, Q., Mittnik, A., Johnson, P. L., Bos, K., Lari, M., Bollongino, R., Sun, C., Giemsch, L., Schmitz, R., Burger, J., Ronchitelli, A. M., Martini, F., Cremonesi, R. G., Svoboda, J., Bauer, P., Caramelli, D., Castellano, S., Reich, D., Pääbo, S., & Krause, J. (2013). A revised timescale for human evolution based on ancient mitochondrial genomes. Current Biology, 23(7), 553-559.
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Gansauge, M.-T., & Meyer, M. (2013). Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nature Protocols, 8(4), 737-748.
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Good, J. M., Wiebe, V., Albert, F., Burbano, H. A., Kircher, M., Green, R. E., Halbwax, M., André, C., Atencia, R., Fischer, A., & Pääbo, S. (2013). Comparative population genomics of the ejaculate in humans and the great apes. Molecular Biology and Evolution, 30(4), 964-976.
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Grossmann, T., Vaish, A., Franz, J., Schroeder, R., Stoneking, M., & Friederici, A. D. (2013). Emotional voice processing: Investigating the role of genetic variation in the serotonin transporter across development. PLoS One, 8(7): e68377.
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Guschanski, K., Krause, J., Sawyer, S., Valente, L. M., Bailey, S., Finstermeier, K., Sabin, R., Gilissen, E., Sonet, G., Nagy, Z. T., Lenglet, G., Mayer, F., & Savolainen, V. (2013). Next-generation museomics disentangles one of the largest primate radiations. Systematic Biology, 62(4), 539-554.
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Ka, S., Markljung, E., Ring, H., Albert, F. W., Harun-Or-Rashid, M., Wahlberg, P., Garcia-Roves, P. M., Zierath, J. R., Denbow, D. M., Pääbo, S., Siegel, P. B., Andersson, L., & Hallbook, F. (2013). Expression of carnitine palmitoyl-CoA transferase-1B is influenced by a cis-acting eQTL in two chicken lines selected for high and low body weight. Physiological Genomics, 45(9), 367-376.
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Kuhlwilm, M., Davierwala, A., & Pääbo, S. (2013). Identification of putative target genes of the transcription factor RUNX2. PLoS One, 8(12): e83218.
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Mazin, P., Xiong, J., Liu, X., Yan, Z., Zhang, X., Li, M., He, L., Somel, M., Yuan, Y., Chen, Y.-P.-P., Li, N., Hu, Y., Fu, N., Ning, Z., Zeng, R., Yang, H., Chen, W., Gelfand, M., & Khaitovich, P. (2013). Widespread splicing changes in human brain development and aging. Molecular Systems Biology, 9: 663.
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Prüfer, K., Langergraber, K. E., Pääbo, S., & Vigilant, L. (2013). Reply to Gibb and Hills: Divergence times, generation lengths and mutation rates in great apes and humans. Proceedings of the National Academy of Sciences of the United States of America, 110(8): E612.
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Pugach, I., & Stoneking, M. (2013). Reply to Price and Bird: No inconsistency between the date of gene flow from India and the Australian archaeological record. Proceedings of the National Academy of Sciences of the United States of America, 110(32): E2949.
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Pugach, I., Delfin, F., Gunnarsdóttir, E., Kayser, M., & Stoneking, M. (2013). Genome-wide data substantiate Holocene gene flow from India to Australia. Proceedings of the National Academy of Sciences of the United States of America, 110(5), 1803-1808.
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Renaud, G., Kircher, M., Stenzel, U., & Kelso, J. F. (2013). freeIbis: An efficient basecaller with calibrated quality scores for Illumina sequencers. Bioinformatics, 29(9), 1208-1209.
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Sheppard, S. K., Didelot, X., Meric, G., Torralbo, A., Jolley, K. A., Kelly, D. J., Bentley, S. D., Maiden, M. C. J., Parkhill, J., & Falush, D. (2013). Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proceedings of the National Academy of Sciences of the United States of America, 110(29), 11923-11927.
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Somel, M., Liu, X., & Khaitovich, P. (2013). Human brain evolution: transcripts, metabolites and their regulators. Nature Reviews Neuroscience, 14(2), 112-127.
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2012

Albert, F. W., Somel, M., Carneiro, M., Aximu-Petri, A., Halbwax, M., Thalmann, O., Blanco-Aguiar, J. A., Plyusnina, I. Z., Trut, L., Villafuerte, R., Ferrand, N., Kaiser, S., Jensen, P., & Pääbo, S. (2012). A comparison of brain gene expression levels in domesticated and wild animals. PLoS Genetics, 8(9): e1002962.
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Ballantyne, K. N., van Oven, M., Ralf, A., Stoneking, M., Mitchell, R. J., van Oorschot, R. A., & Kayser, M. (2012). MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania. Forensic Science International: Genetics, 6(4), 425-436.
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Barbieri, C., Whitten, M., Beyer, K., Schreiber, H., Li, M., & Pakendorf, B. (2012). Contrasting Maternal and Paternal Histories in the Linguistic Context of Burkina Faso. Molecular Biology and Evolution, 29(4), 1213 -1223.
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Burbano, H. A., Green, R. E., Maricic, T., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Kelso, J., Pollard, K. S., Lachmann, M., & Pääbo, S. (2012). Analysis of human accelerated DNA regions using archaic hominin genomes. PLoS One, 7(3): e32877.
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Clovis, Y. M., Enard, W., Marinaro, F., Huttner, W. B., & Tonelli, D. D. P. (2012). Convergent repression of Foxp2 3'UTR by miR-9 and miR-132 in embryonic mouse neocortex: implications for radial migration of neurons. Development, 139(18), 3332-3342.
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Dannemann, M., Nickel, B., Lizano, E., Burbano, H., & Kelso, J. F. (2012). Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. BMC Genomics, 13(Suppl. 3): 116.
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Dannemann, M., Prüfer, K., Lizano, E., Nickel, B., Burbano, H. A., & Kelso, J. (2012). Transcription factors are targeted by differentially expressed miRNAs in primates. Genome biology and evolution, 4(4), 552-564.
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de Filippo, C., Bostoen, K., Stoneking, M., & Pakendorf, B. (2012). Bringing together linguistic and genetic evidence to test the Bantu expansion. Proceedings of the Royal Society B: Biological Sciences, 279(1741), 3256-3263.
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Delfin, F., Myles, S., Choi, Y., Hughes, D., Illek, R., van Oven, M., Pakendorf, B., Kayser, M., & Stoneking, M. (2012). Bridging Near and Remote Oceania: mtDNA and NRY Variation in the Solomon Islands. Molecular Biology and Evolution, 29(2), 545-564.
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Duggan, A. T., Whitten, C. M., Wiebe, V., Crawford, M., Butthoff, A., Spitsyn, V., Makarov, S., Novgorodov, I., Osakovsky, V., & Pakendorf, B. (2012). Investigating the prehistory of Tungusic peoples of Siberia and the Amur-Ussuri region with complete mtDNA genome sequences and Y-chromosomal markers. PLoS One, 8(12): e83570.
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Enard, W. (2012). Functional primate genomics - leveraging the medical potential. Journal of Molecular Medicine, 90(5), 471-480.
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Fietz, S. A., Lachmann, R., Brandl, H., Kircher, M., Samusik, N., Schröder, R., Lakshmanaperumal, N., Henry, I., Vogt, J., Riehn, A., Distler, W., Nitsch, R., Enard, W., Pääbo, S., & Huttner, W. B. (2012). Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proceedings of the National Academy of Sciences of the United States of America, 109(29), 11836-11841.
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Fu, Q., Rudan, P., Pääbo, S., & Krause, J. (2012). Complete mitochondrial genomes reveal neolithic expansion into Europe. PLoS One, 7(3): e32473.
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Gravlund, P., Aaris-Sørensen, K., Hofreiter, M., Meyer, M., Bollback, J. P., & Noe-Nygaar, N. (2012). Ancient DNA extracted from Danish aurochs (Bos primigenius): Genetic diversity and preservation. Annals of Anatomy - Anatomischer Anzeiger, 194(1), 103-111.
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Kenny, E. E., Timpson, N. J., Sikora, M., Yee, M.-C., Moreno-Estrada, A., Eng, C., Huntsman, S., Burchard, E. G., Stoneking, M., Bustamante, C. D., & Myles, S. (2012). Melanesian blond hair is caused by an amino acid change in TYRP1. Science, 336(6081), 554-554.
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Khrameeva, E. E., Mironov, A. A., Fedonin, G. G., Khaitovich, P., & Gelfand, M. S. (2012). Spatial proximity and similarity of the epigenetic state of genome domains. PLoS One, 7(4): e33947.
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Kircher, M. (2012). Analysis of high-throughput ancient DNA sequencing data. In B. Shapiro, & M. Hofreiter (Eds.), Ancient DNA (pp. 197-228). New York: Humana Press.
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Knapp, M., Stiller, M., & Meyer, M. (2012). Generating barcoded libraries for multiplex high-throughput sequencing. In B. Shapiro, & M. Hofreiter (Eds.), Ancient DNA (pp. 155-170). New York: Humana Pr.
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Langergraber, K., Pruefer, K., Rowney, C., Boesch, C., Crockford, C., Fawcett, K., Inoue, E., Inoue-Muruyama, M., Mitani, J. C., Muller, M. N., Robbins, M. M., Schubert, G., Stoinski, T. S., Viola, B., Watts, D., Wittig, R., Wrangham, R. W., Zuberbühler, K., Pääbo, S., & Vigilant, L. (2012). Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proceedings of the National Academy of Sciences of the United States of America, 109(39), 15716-15721.
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Lawson, D. J., & Falush, D. (2012). Population identification using genetic data. Annual Review of Genomics and Human Genetics, 13, 337-361.
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Lawson, D. J., Hellenthal, G., Myers, S., & Falush, D. (2012). Inference of Population Structure using Dense Haplotype Data. PLoS Genetics, 8(1): e1002453.
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Lee, C.-H., Ko, A.-M.-S., Yen, C.-F., Chu, K.-S., Gao, Y.-J., Warnakulasuriya, S., Sunarjo,.-., Ibrahim, S. O., Zain, R. B., Patrick, W. K., & Ko, Y.-C. (2012). Betel-quid dependence and oral potentially malignant disorders in six Asian countries. British Journal of Psychiatry, 201(5), 383-391.
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Li, J., Menard, V., Benish, R. L., Jurevic, R. J., Guillemette, C., Stoneking, M., Zimmerman, P. A., & Mehlotra, R. K. (2012). Worldwide variation in human drug-metabolism enzyme genes CYP2B6 and UGT2B7: implications for HIV/AIDS treatment. Pharmacogenomics, 13(5), 555-570.
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Li, M., & Stoneking, M. (2012). A new approach for detecting low-level mutations in next-generation sequence data. Genome Biology, 13(5): R34.
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Li, M., Schröder, R., Ko, A.-M.-S., & Stoneking, M. (2012). Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs. Nucleic Acids Research, 40(18): e137.
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Liu, X., Somel, M., Tang, L., Yan, Z., Jiang, X., Guo, S., Yuan, Y., He, L., Oleksiak, A., Zhang, Y., Li, N., Hu, Y., Chen, W., Qiu, Z., Pääbo, S., & Khaitovich, P. (2012). Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques. Genome Research, 22(4), 611-622.
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Mailund, T., Halager, A. E., Westergaard, M., Dutheil, J. Y., Munch, K., Andersen, L. N., Lunter, G., Pruefer, K., Scally, A., Hobolth, A., & Schierup, M. H. (2012). A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genetics, 8(12): e1003125.
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Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., Filippo, C. d., Sudmant, P. H., Alkan, C., Fu, Q., Do, R., Rohland, N., Tandon, A., Siebauer, M., Green, R. E., Bryc, K., Briggs, A. W., Stenzel, U., Dabney, J., Shendure, J., Kitzman, J., Hammer, M. F., Shunkov, M. V., Derevianko, A. P., Patterson, N., Andrés, A. M., Eichler, E. E., Slatkin, M., Reich, D., Kelso, J., & Pääbo, S. (2012). A high-coverage genome sequence from an archaic Denisovan individual. Science, 338(6104), 222-226.
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Pickrell, J. K., Patterson, N., Berthold, F., Barbieri, C., Gerlach, L., Gueldemann, T., Kure, B., Mpoloka, S. W., Nakagawa, H., Naumann, C., Lipson, M., Loh, P.-R., Lachance, J., Mountain, J., Bustamante, C. D., Berger, B., Tishkoff, S. A., Henn, B. M., Stoneking, M., Reich, D., & Pakendorf, B. (2012). The genetic prehistory of southern Africa. Nature Communications, 3: 1143.
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Prüfer, K., Munch, K., Hellmann, I., Akagi, K., Miller, J. R., Walenz, B., Koren, S., Sutton, G., Kodira, C., Winer, R., Knight, J. R., Mullikin, J. C., Meader, S. J., Ponting, C. P., Lunter, G., Higashino, S., Hobolth, A., Dutheil, J., Karakoç, E., Alkan, C., Sajjadian, S., Catacchio, C. R., Ventura, M., Marques-Bonet, T., Eichler, E. E., André, C., Atencia, R., Mugisha, L., Junhold, J., Patterson, N., Siebauer, M., Good, J. M., Fischer, A., Ptak, S. E., Lachmann, M., Symer, D. E., Mailund, T., Schierup, M. H., Andrés, A. M., Kelso, J., & Pääbo, S. (2012). The bonobo genome compared with the chimpanzee and human genomes. Nature, 486(7404), 527-531.
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Quillen, E. E., Bauchet, M., Bigham, A. W., Delgado-Burbano, M. E., Faust, F. X., Klimentidis, Y. C., Mao, X., Stoneking, M., & Shriver, M. D. (2012). OPRM1 and EGFR contribute to skin pigmentation differences between Indigenous Americans and Europeans. Human Genetics, 131(7), 1073-1080.
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Ratikainen, I. I., Sødal, L. R. H., Kazem, A., & Wright, J. (2012). Private and public information use strategies by foraging groups of wild Siberian jays. Animal Behaviour, 83(5), 1243-1251.
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Rost, B., Gaasterland, T., Lengauer, T., Linial, M., Markel, S., McKay, B. M., Schneider, R., Horton, P., & Kelso, J. F. (2012). Paving the future: finding suitable ISMB venues. Bioinformatics, 28(19), 2556-2559.
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Sankararaman, S., Patterson, N., Li, H., Pääbo, S., & Reich, D. (2012). The date of interbreeding between Neandertals and modern humans. PLoS Genetics, 8(10): e1002947.
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Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., & Pääbo, S. (2012). Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS One, 7(3): e34131.
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Schmidt, M., Horn, S., Flieger, K., Ehlers, K., Wilhelm, C., & Schnetter, R. (2012). Synchroma pusillum sp. nov. and other New Algal Isolates with Chloroplast Complexes Confirm the Synchromophyceae (Ochrophyta) as a Widely Distributed Group of Amoeboid Algae. Protist, 163(4), 544-559.
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Stoneking, M. (2012). Genetic evidence concerning the origins and dispersals of modern humans. In M. H. Crawford, & B. C. Campbell (Eds.), Causes and Consequences of Human Migration: An Evolutionary Perspective (pp. 11-20). Cambridge: Cambridge Univ. Pr.
      
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Weng, K., Hu, H., Xu, G. A., Khaitovich, P., & Somel, M. (2012). Mechanisms of Dietary Response in Mice and Primates: A Role for EGR1 in Regulating the Reaction to Human-Specific Nutritional Content. PLoS One, 7(8): e43915.
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White, L., & Castellano, S. (2012). Evolutionary basis for the use of selenocysteine. In D. L. Hatfield, M. J. Berry, & V. N. Gladyshev (Eds.), Selenium: Its Molecular Biology and Role in Human Health (3, pp. 85-93). New York [u.a.]: Springer.
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Xu, S., & Stoneking, M. (2012). Reply to Denham and Donohue: Asian-Papuan genetic admixture is in excellent agreement with Austronesian dispersal in eastern Indonesia. Proceedings of the National Academy of Sciences of the United States of America, 109(39): E2578.
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Xu, S., Pugach, I., Stoneking, M., Kayser, M., Jina, L., & The HUGO Pan-Asian SNP Consortium (2012). Genetic dating indicates that the Asian–Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion. Proceedings of the National Academy of Sciences of the United States of America, 109(12), 4574-4579.
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Yuan, Y., Chen, Y.-P.-P., Boyd-Kirkup, J., Khaitovich, P., & Somel, M. (2012). Accelerated aging-related transcriptome changes in the female prefrontal cortex. Aging Cell, 11(5), 894-901.
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Abramson, G., Trejo Soto, C. A., & Oña Bubach, L. (2011). The role of asymmetric interactions on the effect of habitat destruction in mutualistic networks. PLoS ONE, 6(6): e21028.
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Benazzi, S., Viola, B., Kullmer, O., Fiorenza, L., Harvati, K., Paul, T., Gruppioni, G., Weber, G. W., & Mallegni, F. (2011). A reassessment of the Neanderthal teeth from Taddeo cave (southern Italy). Journal of Human Evolution, 61(4), 377-387.
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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., Wood, J., Earn, D. J. D., Herring, D. A., Bauer, P., Poinar, H. N., & Krause, J. (2011). A draft genome of Yersinia pestis from victims of the Black Death. Nature, 478(7370), 506-510.
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Brawand, D., Soumillon, M., Necsulea, A., Julien, P., Csárdi, G., Harrigan, P., Weier, M., Liechti, A., Aximu-Petri, A., Kircher, M., Albert, F. W., Zeller, U., Khaitovich, P., Grützner, F., Bergmann, S., Nielsen, R., Pääbo, S., & Kaessmann, H. (2011). The evolution of gene expression levels in mammalian organs. Nature, 478(7369), 343-348.
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Gralle, M., & Pääbo, S. (2011). A comprehensive functional analysis of ancestral human signal peptides. Molecular Biology and Evolution, 28(1), 25-28.
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Gross, A., Tönjes, A., Kovacs, P., Veeramah, K. R., Ahnert, P., Roshyara, N. R., Gieger, C., Rueckert, I.-M., Loeffler, M., Stoneking, M., Wichmann, H.-E., Novembre, J., Stumvoll, M., & Scholz, M. (2011). Population-genetic comparison of the Sorbian isolate population in Germany with the German KORA population using genome-wide SNP arrays. BMC Genetics, 12: 67.
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Grossmann, T., Johnson, M. H., Vaish, A., Hughes, D. A., Quinque, D., Stoneking, M., & Friederici, A. D. (2011). Genetic and neural dissociation of individual responses to emotional expressions in human infants. Developmental Cognitive Neuroscience, 1(1), 57-66.
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Gunnarsdóttir, E. D., Li, M., Bauchet, M., Finstermeier, K., & Stoneking, M. (2011). High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Research, 21(1), 1-11.
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Gunnarsdóttir, E. D., Nandineni, M. R., Li, M., Myles, S., Gil, D., Pakendorf, B., & Stoneking, M. (2011). Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra. Nature Communications, 2: 228.
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Harrison, A., Lemey, P., Hurles, M., Moyes, C., Horn, S., Pryor, J., Malani, J., Supuri, M., Masta, A., Teriboriki, B., Toatu, T., Penny, D., Rambaut, A., & Shapiro, B. (2011). Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation. Viruses, 3(2), 83-101.
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Haun, D. B. M., & Tomasello, M. (2011). Conformity to Peer Pressure in Preschool Children. Child Development, 82(6), 1759-1767.
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Hu, H. Y., Guo, S., Xi, J., Yan, Z., Fu, N., Zhang, X., Menzel, C., Liang, H., Yang, H., Zhao, M., Zeng, R., Chen, W., Pääbo, S., & Khaitovich, P. (2011). MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PLoS Genetics, 7(10): e1002327, pp. 1-14.
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Ka, S., Albert, F. W., Denbow, D. M., Pääbo, S., Siegel, P. B., Andersson, L., & Hallböök, F. (2011). Differentially expressed genes in hypothalamus in relation to genomic regions under selection in two chicken lines resulting from divergent selection for high or low body weight. Neurogenetics, 12(3), 211-221.
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Kircher, M. (2011). Understanding and improving high-throughput sequencing data production and analysis. PhD Thesis, Univ., Leipzig.
      
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Li, J., Zhang, L., Zhou, H., Stoneking, M., & Tang, K. (2011). Global patterns of genetic diversity and signals of natural selection for human ADME genes. Human Molecular Genetics, 20(3), 528-540.
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Lippold, S., Matzke, N. J., Reissmann, M., & Hofreiter, M. (2011). Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evolutionary Biology, 11: 328.
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Liu, Y., Han, D., Han, Y., Yan, Z., Xie, B., Li, J., Qiao, N., Hu, H., Khaitovich, P., Gao, Y., & Han, J.-D.-J. (2011). Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Research, 39(4), 1408-1418.
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Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011). Deep proteome and transcriptome mapping of a human cancer cell line. Molecular Systems Biology, 7: 548.
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Nasidze, I., & Stoneking, M. (2011). Microbiome diversity in human saliva. In F. J. d. Bruijn (Ed.), Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats (pp. 335-339). New York: Wiley.
      
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