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Recent Department Publications

Last update: June 29th, 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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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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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.
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Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., Berger, B., Economou, C., Bollongino, R., Fu, Q., Bos, K. I., Nordenfelt, S., Li, H., de Filippo, C., Prüfer, K., Sawyer, S., Posth, C., Haak, W., Hallgren, F., Fornander, E., Rohland, N., Delsate, D., Francken, M., Guinet, J.-M., Wahl, J., Ayodo, G., Babiker, H. A., Bailliet, G., Balanovska, E., Balanovsky, O., Barrantes, R., Bedoya, G., Ben-Ami, H., Bene, J., Berrada, F., Bravi, C. M., Brisighelli, F., Busby, G. B. J., Cali, F., Churnosov, M., Cole, D. E. C., Corach, D., Damba, L., van Driem, G., Dryomov, S., Dugoujon, J.-M., Fedorova, S. A., Romero, I. G., Gubina, M., Hammer, M., Henn, B. M., Hervig, T., Hodoglugil, U., Jha, A. R., Karachanak-Yankova, S., Khusainova, R., Khusnutdinova, E., Kittles, R., Kivisild, T., Klitz, W., Kučinskas, V., Kushniarevich, A., Laredj, L., Litvinov, S., Loukidis, T., Mahley, R. W., Melegh, B., Metspalu, E., Molina, J., Mountain, J., Näkkäläjärvi, K., Nesheva, D., Nyambo, T., Osipova, L., Parik, J., Platonov, F., Posukh, O., Romano, V., Rothhammer, F., Rudan, I., Ruizbakiev, R., Sahakyan, H., Sajantila, A., Salas, A., Starikovskaya, E. B., Tarekegn, A., Toncheva, D., Turdikulova, S., Uktveryte, I., Utevska, O., Vasquez, R., Villena, M., Voevoda, M., Winkler, C. A., Yepiskoposyan, L., Zalloua, P., Zemunik, T., Cooper, A., Capelli, C., Thomas, M. G., Ruiz-Linares, A., Tishkoff, S. A., Singh, L., Thangaraj, K., Villems, R., Comas, D., Sukernik, R., Metspalu, M., Meyer, M., Eichler, E. E., Burger, J., Slatkin, M., Pääbo, S., Kelso, J. F., Reich, D., & Krause, J. (2014). Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature, 513(7518), 409-413.
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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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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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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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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, 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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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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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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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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2011

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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Albert, F. W., Hodges, E., Jensen, J. D., Besnier, F., Xuan, Z., Rooks, M., Bhattacharjee, A., Brizuela, L., Good, J. M., Green, R. E., Burbano, H. A., Plyusnina, I. Z., Trut, L., Andersson, L., Schöneberg, T., Carlborg, Ö., Hannon, G. J., & Pääbo, S. (2011). Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity, 107(3), 205-214.
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Döppes, D., Rabeder, G., & Stiller, M. (2011). Was the Middle Würmian in the High Alps warmer than today? Quaternary International, 245(2), 193-200.
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Fu, X., Giavalisco, P., Liu, X., Catchpole, G., Fu, N., Ning, Z.-B., Guo, S., Yan, Z., Somel, M., Pääbo, S., Zeng, R., Willmitzer, L., & Khaitovich, P. (2011). Rapid metabolic evolution in human prefrontal cortex. Proceedings of the National Academy of Sciences of the United States of America, 108(15), 6181-6186.
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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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Horn, S., Durka, W., Wolf, R., Ermala, A., Stubbe, A., Stubbe, M., & Hofreiter, M. (2011). Mitochondrial Genomes Reveal Slow Rates of Molecular Evolution and the Timing of Speciation in Beavers (Castor), One of the Largest Rodent Species. PLoS ONE, 6(1): e14622.
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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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Jin, C., Li, J., Green, C. D., Yu, X., Tang, X., Han, D., Xian, B., Wang, D., Huang, X., Cao, X., Yan, Z., Hou, L., Liu, J., Shukeir, N., Khaitovich, P., Chen, C. D., Zhang, H., Jenuwein, T., & Han, J.-D.-J. (2011). Histone Demethylase UTX-1 Regulates C. elegans Life Span by Targeting the Insulin/IGF-1 Signaling Pathway. Cell Metabolism, 14(2), 161-172.
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Jordan, S., Krause, J., Prager, A., Mitrovic, M., Jonjic, S., Koszinowski, U. H., & Adler, B. (2011). Virus Progeny of Murine Cytomegalovirus Bacterial Artificial Chromosome pSM3fr Show Reduced Growth in Salivary Glands due to a Fixed Mutation of MCK-2. Journal of Virology, 85(19), 10346-10353.
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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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Lehnertz, B., Rogalski, J. C., Schulze, F. M., Yi, L., Lin, S., Kast, J., & Rossi, F. M. (2011). p53-dependent transcription and tumor suppression are not affected in set7/9-deficient mice. Molecular Cell, 43(4), 673-680.
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Lerner, H. R. L., Meyer, M., James, H. F., Hofreiter, M., & Fleischer, R. C. (2011). Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers. Current Biology, 21(21), 1838-1844.
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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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Li, M., & Chen, S.-S. (2011). The tendency to recreate ancestral CG dinucleotides in the human genome. BMC Evolutionary Biology, 11: 3.
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Liebscher, I., Müller, U., Teupser, D., Engemaier, E., Engel, K. M. Y., Ritscher, L., Thor, D., Sangkuhl, K., Ricken, A., Wurm, A., Piehler, D., Schmutzler, S., Fuhrmann, H., Albert, F. W., Reichenbach, A., Thiery, J., Schöneberg, T., & Schulz, A. (2011). Altered Immune Response in Mice Deficient for the G Protein-coupled Receptor GPR34. The Journal of Biological Chemistry, 286(3), 2101-2110.
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Lippold, S., Knapp, M., Kuznetsova, T., Leonard, J. A., Benecke, N., Ludwig, A., Rasmussen, M., Cooper, A., Weinstock, J., Willerslev, E., Shapiro, B., & Hofreiter, M. (2011). Discovery of lost diversity of paternal horse lineages using ancient DNA. Nature Communications, 2: 450, pp. 1-6.
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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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Myles, S., Lea, R. A., Ohashi, J., Chambers, G. K., Weiss, J. G., Hardouin, E., Engelken, J., Macartney-Coxson, D. P., Eccles, D. A., Naka, I., Kimura, R., Inaoka, T., Matsumura, Y., & Stoneking, M. (2011). Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans. BMC Medical Genetics, 12(1): 10, pp. 1-7.
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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.
Nasidze, I., Li, J., Schroeder, R., Creasey, J. L., Li, M., & Stoneking, M. (2011). High diversity of the saliva microbiome in Batwa pygmies. PLoS ONE, 6(8): e23352.
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Oña, L., & Lachmann, M. (2011). Ant aggression and evolutionary stability in plant–ant and plant–pollinator mutualistic interactions. Journal of Evolutionary Biology, 24(3), 617-629.
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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., Saitou, N., Wollstein, A., Kayser, M., Pääbo, S., & Stoneking, M. (2011). Denisova admixture and the first modern human dispersals into southeast Asia and Oceania. The American Journal of Human Genetics, 89(4), 516-528.
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Reimers-Kipping, S., Hevers, W., Pääbo, S., & Enard, W. (2011). Humanized Foxp2 specifically affects cortico-basal ganglia circuits. Neuroscience, 175, 75-84.
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Reinartz, R., Lippold, S., Lieckfeldt, D., & Ludwig, A. (2011). Population genetic analyses of Acipenser ruthenus as a prerequisite for the conservation of the uppermost Danube population. Journal of Applied Ichthyology, 27(2), 477-483.
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Schönberg, A., Theunert, C., Li, M., Stoneking, M., & Nasidze, I. (2011). High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: High diversity and demographic inferences. European Journal of Human Genetics, 19(9), 988-994.
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Stewart, J. R., Aspinall, S., Beech, M., Fenberg, P., Hellyer, P., Larkin, N., Lokier, S. W., Marx, F. G., Meyer, M., Miller, R., Rainbow, P. S., Taylor, J. D., Whittaker, J. E., Al-Mehsin, K., & Strohmenger, C. J. (2011). Biotically constrained palaeoenvironmental conditions of a mid-Holocene intertidal lagoon on the southern shore of the Arabian Gulf: Evidence associated with a whale skeleton at Musaffah, Abu Dhabi, UAE. Quaternary Science Reviews, 30(25-26), 3675-3690.
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Stoneking, M., & Krause, J. (2011). Learning about human population history from ancient and modern genomes. Nature Reviews Genetics, 12(9), 603-614.
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Thalmann, O., Wegmann, D., Spitzner, M., Arandjelovic, M., Guschanski, K., Leuenberger, C., Bergl, R. A., & Vigilant, L. (2011). Historical sampling reveals dramatic demographic changes in western gorilla populations. BMC Evolutionary Biology, 11: 85, pp. 1-10.
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Viola, B., Markin, S. V., Zenin, A., Shunkov, V., & Derevianko, A. V. (2011). Late Pleistocene hominins from the Altai Mountains, Russia. In Verchnij paleolit v Afrike i Evrazii i formirovanie čeloveka sovremennogo anatomičeskogo tipa: meždunarodnyj simpozium "Osobennosti perechoda k verchnemu paleolitu v Evrazii: kulʹturnaja dinamika i razvitie roda Nomo" (Denisova peščera, Altaj, 4-10 ijulja 2011 g.) = The Upper paleolithic in Africa and Eurasia and the origin of anatomically modern Humans: International Symposium "Features of the Upper Paleolithic Transition in Eurasia: Cultural dynamics and the Evolution of the Genus Homo" (Denisova Cave, the Altai, 4-10 July, 2011) (pp. 207-213). Novosibirsk: Izdatelʹstvo Instituta archeologii i ėtnografii SO RAN.
Yan, Z., Hu, H. Y., Jiang, X., Maierhofer, V., Neb, E., He, L., Hu, Y., Hu, H., Li, N., Chen, W., & Khaitovich, P. (2011). Widespread expression of piRNA-like molecules in somatic tissues. Nucleic Acids Research, 39(15), 6596-6607.
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Yuan, Y., Chen, Y.-P.-P., Ni, S., Xu, G. A., Tang, L., Vingron, M., Somel, M., & Khaitovich, P. (2011). Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series. BMC Bioinformatics, 12: 347.
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