25.08.2016 - 20:26
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Some recent papers from the Pääbo laboratory

Gokce, O., Stanley, G. M., Treutlein, B., Neff, N. F., Camp, J. G., Malenka, R. C., Rothwell, P. E., Fuccillo, M. V., Südhof, T. C., & Quake, S. R. (2016). Cellular taxonomy of the mouse striatum as revealed by single-cell RNA-seq. Cell Reports, 16(4), 1126-1137.
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Treutlein, B., Lee, Q. Y., Camp, J. G., Mall, M., Koh, W., Shariati, S. A. M., Sim, S., Neff, N. F., Skotheim, J. M., Wernig, M., & Quake, S. R. (2016). Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq. Nature, 534(7607), 391-395.
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Fu, Q., Posth, C., Hajdinjak, M., Petr, M., Mallick, S., Fernandes, D., Furtwängler, A., Haak, W., Meyer, M., Mittnik, A., Nickel, B., Peltzer, A., Rohland, N., Slon, V., Talamo, S., Lazaridis, I., Lipson, M., Mathieson, I., Schiffels, S., Skoglund, P., Derevianko, A. P., Drozdov, N., Slavinsky, V., Tsybankov, A., Cremonesi, R. G., Mallegni, F., Gély, B., Vacca, E., Morales, M. R. G., Straus, L. G., Neugebauer-Maresch, C., Teschler-Nicola, M., Constantin, S., Moldovan, O. T., Benazzi, S., Peresani, M., Coppola, D., Lari, M., Ricci, S., Ronchitelli, A., Valentin, F., Thevenet, C., Wehrberger, K., Grigorescu, D., Rougier, H., Crevecoeur, I., Flas, D., Semal, P., Mannino, M. A., Cupillard, C., Bocherens, H., Conard, N. J., Harvati, K., Moiseyev, V., Drucker, D. G., Svoboda, J., Richards, M. P., Caramelli, D., Pinhasi, R., Kelso, J., Patterson, N., Krause, J., Pääbo, S., & Reich, D. (2016). The genetic history of Ice Age Europe. Nature, 534(7606), 200-205.
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de Filippo, C., Key, F. M., Ghirotto, S., Benazzo, A., Meneu, J. R., Weihmann, A., NISC Comparative Sequence Program, Parra, G., Green, E. D., & Andrés, A. M. (2016). Recent selection changes in human genes under long-term balancing selection. Molecular Biology and Evolution, 33(6), 1435-1447.
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Suh, A., Witt, C. C., Menger, J., Sadanandan, K. R., Podsiadlowski, L., Gerth, M., Weigert, A., McGuire, J. A., Mudge, J., Edwards, S. V., & Rheindt, F. E. (2016). Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes. Nature Communications, 7: 11396.
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Vernot, B., Tucci, S., Kelso, J., Schraiber, J., Wolf, A., Gittelman, R., Dannemann, M., Grote, S., McCoy, R., Norton, H., Scheinfeldt, L., Merriwether, D., Koki, G., Friedlaender, J., Wakefield, J., Pääbo, S., & Akey, J. (2016). Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science, 352(6282), 235-239.
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Brown, S., Higham, T., Slon, V., Pääbo, S., Meyer, M., Douka, K., Brock, F., Comeskey, D., Procopio, N., Shunkov, M., Derevianko, A., & Buckley, M. (2016). Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis. Scientific Reports, 6: 23559.
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Meyer, M., Arsuaga, J.-L., de Filippo, C., Nagel, S., Aximu-Petri, A., Nickel, B., Martínez, I., Gracia, A., Bermúdez de Castro, J. M., Carbonell, E., Viola, B., Kelso, J., Prüfer, K., & Pääbo, S. (2016). Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature, 531(7595), 504-507.
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Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Rudan, P., Brajkovic, D., Kucan, Ž., Gušic, I., Marques-Bonet, T., Andrés, A. M., Viola, B., Pääbo, S., Meyer, M., Siepel, A., & Castellano, S. (2016). Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, 530(7591), 429-433.
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Sawyer, S., Renaud, G., Viola, B., Hublin, J.-J., Gansauge, M.-T., Shunkov, M. V., Derevianko, A. P., Prüfer, K., Kelso, J., & Pääbo, S. (2015). Nuclear and mitochondrial DNA sequences from two Denisovan individuals. Proceedings of the National Academy of Sciences of the United States of America, 112(51), 15696-15700.
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Renaud, G., Slon, V., Duggan, A. T., & Kelso, J. (2015). Schmutzi: Estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biology, 16: 224.
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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., Reich, D., & Pääbo, S. (2015). An early modern human from Romania with a recent Neanderthal ancestor. Nature, 524(7564), 216-219.
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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., 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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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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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., & Pääbo, S. (2014). The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505(7481), 43-49.
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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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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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