Kay Prüfer
Group leader
Department of Archaeogenetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig
phone: +49 (0) 341 3550 506
e-mail:
pruefer@[>>> Please remove the text! <<<]eva.mpg.de
Publications
2024
Michel, M., Skourtanioti, E., Pierini, F., Guevara, E. K., Mötsch, A., Kocher, A., Barquera, R., Bianco, R. A., Carlhoff, S., Coppola Bove, L., Freilich, S., Giffin, K., Hermes, T., Hiß, A. N., Knolle, F., Nelson, E. A., Neumann, G., Papac, L., Penske, S., Rohrlach, A. B., Salem, N., Semerau, L., Villalba-Mouco, V., Abadie, I., Aldenderfer, M., Beckett, J. F., Brown, M., Campus, F. G. R., Chenghwa, T., Cruz Berrocal, M., Damašek, L., Duffett Carlson, K. S., Durand, R., Ernée, M., Fântăneanu, C., Frenzel, H., García Atiénzar, G., Guillén, S., Hsieh, E., Karwowski, M., Kelvin, D., Kelvin, N., Khokhlov, A., Kinaston, R. L., Korolev, A., Krettek, K.-L., Küßner, M., Lai, L., Look, C., Majander, K., Mandl, K., Mazzarello, V., McCormick, M., de Miguel Ibáñez, P., Murphy, R., Németh, R. E., Nordqvist, K., Novotny, F., Obenaus, M., Olmo-Enciso, L., Onkamo, P., Orschiedt, J., Patrushev, V., Peltola, S., Romero, A., Rubino, S., Sajantila, A., Salazar-García, D. C., Serrano, E., Shaydullaev, S., Sias, E., Šlaus, M., Stančo, L., Swanston, T., Teschler-Nicola, M., Valentin, F., Van de Vijver, K., Varney, T. L., Vigil-Escalera Guirado, A., Waters, C. K., Weiss-Krejci, E., Winter, E., Lamnidis, T. C., Prüfer, K., Nägele, K., Spyrou, M., Schiffels, S., Stockhammer, P. W., Haak, W., Posth, C., Warinner, C., Bos, K. I., Herbig, A., & Krause, J. (2024). Ancient Plasmodium genomes shed light on the history of human malaria. Nature, 631(8019), 125-133. |
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Mylopotamitaki, D., Weiss, M., Fewlass, H., Zavala, E. I., Rougier, H., Sümer, A., Hajdinjak, M., Smith, G. M., Ruebens, K., Sinet-Mathiot, V., Pederzani, S., Essel, E., Harking, F. S., Xia, H., Hansen, J., Kirchner, A., Lauer, T., Stahlschmidt, M., Hein, M., Talamo, S., Wacker, L., Meller, H., Dietl, H., Orschiedt, J., Olsen, J. V., Zeberg, H., Prüfer, K., Krause, J., Meyer, M., Welker, F., McPherron, S. P., Schüler, T., & Hublin, J.-J. (2024). Homo sapiens reached the higher latitudes of Europe by 45,000 years ago. Nature, 626, 341-346. |
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Rohrlach, A. B., Rivollat, M., de-Miguel-Ibáñez, P., Moilanen, U., Liira, A.-M., Teixeira, J. C., Roca-Rada, X., Armendáriz-Martija, J., Boyadzhiev, K., Boyadzhiev, Y., Llamas, B., Tiliakou, A., Mötsch, A., Tuke, J., Prevedorou, E.-A., Polychronakou-Sgouritsa, N., Buikstra, J., Onkamo, P., Stockhammer, P. W., Heyne, H. O., Lemke, J. R., Risch, R., Schiffels, S., Krause, J., Haak, W., & Prüfer, K. (2024). Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA. Nature Communications, 15: 1294. |
Open Access2023
Begg, T. J. A., Schmidt, A., Kocher, A., Larmuseau, M. H., Runfeldt, G., Maier, P. A., Wilson, J. D., Barquera, R., Maj, C., Szolek, A., Sager, M., Clayton, S., Peltzer, A., Hui, R., Ronge, J., Reiter, E., Freund, C., Burri, M., Aron, F., Tiliakou, A., Osborn, J., Behar, D. M., Boecker, M., Brandt, G., Cleynen, I., Strassburg, C., Prüfer, K., Kühnert, D., Meredith, W. R., Nöthen, M. M., Attenborough, R. D., Kivisild, T., & Krause, J. (2023). Genomic analyses of hair from Ludwig van Beethoven. Current Biology, 33(8), 1431-1447.e22. |
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Wang, K., Prüfer, K., Krause-Kyora, B., Childebayeva, A., Schuenemann, V. J., Coia, V., Maixner, F., Zink, A., Schiffels, S., & Krause, J. (2023). High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry. Cell Genomics, 3(9): 100377. |
2022
Childebayeva, A., Rohrlach, A. B., Barquera Lozano, R. J., Rivollat, M., Aron, F., Szolek, A., Kohlbacher, O., Nicklisch, N., Alt, K., Gronenborn, D., Meller, H., Friederich, S., Prüfer, K., Deguilloux, M.-F., Krause, J., & Haak, W. (2022). Population genetics and signatures of selection in early Neolithic European farmers. Molecular Biology and Evolution, 39(6): msac108. |
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Yu, H., Loosdrecht, M. S. v. d., Mannino, M. A., Talamo, S., Rohrlach, A. B., Childebayeva, A., Villalba-Mouco, V., Aron, F., Brandt, G., Burri, M., Freund, C., Radzeviciute, R., Stahl, R., Wissgott, A., Fewlass, H., Tagliacozzo, A., Piperno, M., Tusa, S., Collina, C., Schimmenti, V., Di Salvo, R., Prüfer, K., Posth, C., Hublin, J.-J., Gronenborn, D., Binder, D., Jeong, C., Haak, W., & Krause, J. (2022). Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily. iScience, 5(25): 104244. |
2021
Carlhoff, S., Duli, A., Nägele, K., Nur, M., Skov, L., Sumantri, I., Oktaviana, A. A., Hakim, B., Burhan, B., Syahdar, F. A., McGahan, D. P., Bulbeck, D., Perston, Y. L., Newman, K., Saiful, A. M., Ririmasse, M., Chia, S., Hasanuddin, Pulubuhu, D. A. T., Suryatman, Supriadi, Jeong, C., Peter, B. M., Prüfer, K., Powell, A., Krause, J., Posth, C., & Brumm, A. (2021). Genome of a middle Holocene hunter-gatherer from Wallacea. Nature, 596, 543-547. |
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Kocher, A., Papac, L., Barquera, R., Key, F. M., Spyrou, M. A., Hübler, R., Rohrlach, A. B., Aron, F., Stahl, R., Wissgott, A., van Bömmel, F., Pfefferkorn, M., Mittnik, A., Villalba-Mouco, V., Neumann, G. U., Rivollat, M., Loosdrecht, M. S. v. d., Majander, K., Tukhbatova, R. I., Musralina, L., Ghalichi, A., Penske, S., Sabin, S., Michel, M., Gretzinger, J., Nelson, E. A., Ferraz, T., Nägele, K., Parker, C. E., Keller, M., Guevara, E., Feldman, M., Eisenmann, S., Skourtanioti, E., Giffin, K., Gnecchi-Ruscone, G. A., Friederich, S., Schimmenti, V., Khartanovich, V., Karapetian, M. K., Chaplygin, M. S., Kufterin, V. V., Khokhlov, A. A., Chizhevsky, A. A., Stashenkov, D. A., Kochkina, A. F., Tejedor-Rodríguez, C., de Lagrán, Í.-G.-M., Arcusa-Magallón, H., Garrido-Pena, R., Royo-Guillén, J. I., Novácek, J., Rottier, S., Kacki, S., Saintot, S., Kaverzneva, E., Belinskiy, A. B., Velemínský, P., Limburský, P., Kostka, M., Loe, L., Popescu, E., Clarke, R., Lyons, A., Mortimer, R., Sajantila, A., de Armas, Y. C., Godoy, S. T. H., Hernández-Zaragoza, D. I., Pearson, J., Binder, D., Lefranc, P., Kantorovich, A. R., Maslov, V. E., Lai, L., Zoledziewska, M., Beckett, J. F., Langová, M., Danielisová, A., Ingman, T., Atiénzar, G. G., de Ibáñez, M. P. M., Romero, A., Sperduti, A., Beckett, S., Salter, S. J., Zilivinskaya, E. D., Vasilev, D. V., von Heyking, K., Burger, R. L., Salazar, L. C., Amkreutz, L., Navruzbekov, M., Rosenstock, E., Alonso-Fernández, C., Slavchev, V., Kalmykov, A. A., Atabiev, B. C., Batieva, E., Calmet, M. A., Llamas, B., Schultz, M., Krauß, R., Jiménez-Echevarría, J., Francken, M., Shnaider, S., de Knijff, P., Altena, E., de Vijver, K. V., Fehren-Schmitz, L., Tung, T. A., Lösch, S., Dobrovolskaya, M., Makarov, N., Read, C., Twest, M. V., Sagona, C., Ramsl, P. C., Akar, M., Yener, K. A., Ballestero, E. C., Cucca, F., Mazzarello, V., Utrilla, P., Rademaker, K., Fernández-Domínguez, E., Baird, D., Semal, P., Márquez-Morfín, L., Roksandic, M., Steiner, H., Salazar-García, D. C., Shishlina, N., Erdal, Y. S., Hallgren, F., Boyadzhiev, Y., Boyadzhiev, K., Küßner, M., Sayer, D., Onkamo, P., Skeates, R., Rojo-Guerra, M., Buzhilova, A., Khussainova, E., Djansugurova, L. B., Beisenov, A. Z., Samashev, Z., Massy, K., Mannino, M., Moiseyev, V., Mannermaa, K., Balanovsky, O., Deguilloux, M.-F., Reinhold, S., Hansen, S., Kitov, E. P., Dobeš, M., Ernée, M., Meller, H., Alt, K. W., Prüfer, K., Warinner, C., Schiffels, S., Stockhammer, P. W., Bos, K., Posth, C., Herbig, A., Haak, W., Krause, J., & Kühnert, D. (2021). Ten millennia of hepatitis B virus evolution. Science, 374(6564), 182-188. |
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Prüfer, K., Posth, C., Yu, H., Stoessel, A., Spyrou, M. A., Deviese, T., Mattonai, M., Ribechini, E., Higham, T., Velemínský, P., Brůžek, J., & Krause, J. (2021). A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia. Nature Ecology & Evolution, 5, 820-825. |
2020
Cole, C. B., Zhu, S. J., Mathieson, I., Prüfer, K., & Lunter, G. (2020). Ancient Admixture into Africa from the ancestors of non-Africans. bioRxiv. |
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Khan, N., de Manuel, M., Peyrégne, S., Do, R., Prüfer, K., Marques-Bonet, T., Varki, N., Gagneux, P., & Varki, A. (2020). Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins. Genome Biology and Evolution, 12(7), 1040-1050. |
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Loosdrecht, M. S. v. d., Mannino, M. A., Talamo, S., Villalba-Mouco, V., Posth, C., Aron, F., Brandt, G., Burri, M., Freund, C., Radzeviciute, R., Stahl, R., Wissgott, A., Klausnitzer, L., Nagel, S., Meyer, M., Tagliacozzo, A., Piperno, M., Tusa, S., Collina, C., Schimmenti, V., Salvo, R. D., Prüfer, K., Hublin, J.-J., Schiffels, S., Jeong, C., Haak, W., & Krause, J. (2020). Genomic and dietary transitions during the Mesolithic and Early Neolithic in Sicily. bioRxiv, 986158. |
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Mafessoni, F., Grote, S., de Filippo, C., Slon, V., Kolobova, K. A., Viola, B., Markin, S. V., Chintalapati, M., Peyrégne, S., Skov, L., Skoglund, P., Krivoshapkin, A. I., Derevianko, A. P., Meyer, M., Kelso, J., Peter, B., Prüfer, K., & Pääbo, S. (2020). A high-coverage Neandertal genome from Chagyrskaya Cave. Proceedings of the National Academy of Sciences, 117(26), 15132-15136. |
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Peyrégne, S., & Prüfer, K. (2020). Present-Day DNA contamination in ancient DNA datasets. BioEssays, 42: 2000081. |
2019
Bokelmann, L., Hajdinjak, M., Peyrégne, S., Brace, S., Essel, E., de Filippo, C., Glocke, I., Grote, S., Mafessoni, F., Nagel, S., Kelso, J., Prüfer, K., Vernot, B., Barnes, I., Pääbo, S., Meyer, M., & Stringer, C. (2019). A genetic analysis of the Gibraltar Neanderthals. Proceedings of the National Academy of Sciences, 116(31), 15610-15615. |
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Peyrégne, S., Slon, V., Mafessoni, F., de Filippo, C., Hajdinjak, M., Nagel, S., Nickel, B., Essel, E., Le Cabec, A., Wehrberger, K., Conard, N. J., Kind, C. J., Posth, C., Krause, J., Abrams, G., Bonjean, D., Di Modica, K., Toussaint, M., Kelso, J., Meyer, M., Pääbo, S., & Prüfer, K. (2019). Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe. Science Advances, 5(6): eaaw5873. |
2018
de Filippo, C., Meyer, M., & Prüfer, K. (2018). Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences. BMC Biology, 16: 121. |
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Hajdinjak, M., Fu, Q., Hübner, A., Petr, M., Mafessoni, F., Grote, S., Skoglund, P., Narasimham, V., Rougier, H., Crevecoeur, I., Semal, P., Soressi, M., Talamo, S., Hublin, J.-J., Gušic, I., Kucan, Ž., Rudan, P., Golovanova, L. V., Doronichev, V. B., Posth, C., Krause, J., Korlevic, P., Nagel, S., Nickel, B., Slatkin, M., Patterson, N., Reich, D., Prüfer, K., Meyer, M., Pääbo, S., & Kelso, J. (2018). Reconstructing the genetic history of late Neanderthals. Nature, 555(7698), 652-656. |
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Mafessoni, F., de Filippo, C., Slon, V., Grote, S., Chintalapati, M., Peter, B., Viola, B., Markin, S. V., Vasilyev, S. K., Rudaya, N. A., Kolobova, K. A., Shunkov, M. V., Derevianko, A. P., Kelso, J., Meyer, M., Prüfer, K., & Pääbo, S. (2018). A high-coverage Neandertal genome from Chagyrskaya Cave. In T. A. Klimenkova ( |
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Mafessoni, F., Prasad, R. B., Groop, L., Hansson, O., & Prüfer, K. (2018). Turning Vice into Virtue: Using Batch-Effects to Detect Errors in Large Genomic Data Sets. Genome Biology and Evolution, 10(10), 2697-2708. |
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Prüfer, K. (2018). snpAD: An ancient DNA genotype caller. Bioinformatics, 34(24), 4165-4171. |
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Slon, V., Mafessoni, F., Vernot, B., de Filippo, C., Grote, S., Viola, B., Hajdinjak, M., Peyrégne, S., Nagel, S., Brown, S., Douka, K., Higham, T., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Kelso, J., Meyer, M., Prüfer, K., & Pääbo, S. (2018). Denisova 11: The daughter of a Neandertal and a Denisovan. In T. A. Klimenkova ( |
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Slon, V., Mafessoni, F., Vernot, B., de Filippo, C., Grote, S., Viola, T. B., Hajdinjak, M., Peyrégne, S., Nagel, S., Brown, S., Douka, K., Higham, T., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Kelso, J., Meyer, M., Prüfer, K., & Pääbo, S. (2018). The genome of the offspring of a Neanderthal mother and a Denisovan father. Nature, 561(7721), 113-116. |
2017
Chintalapati, M., Dannemann, M., & Prüfer, K. (2017). Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans. BMC Evolutionary Biology, 17: 179. |
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Dannemann, M., Prüfer, K., & Kelso, J. (2017). Functional implications of Neandertal introgression in modern humans. Genome Biology, 18: 61. |
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Hajdinjak, M., Fu, Q., Stenzel, U., Hübner, A., Petr, M., Mafessoni, F., Grote, S., Rougier, H., Crevecoeur, I., Semal, P., Soressi, M., Talamo, S., Hublin, J.-J., Gušić, I., Kućan, Ž., Rudan, P., Golovanova, L. V., Doronichev, V. B., Posth, C., Krause, J., Korlević, P., Nagel, S., Nickel, B., Prüfer, K., Kelso, J., Meyer, M., & Pääbo, S. (2017). Population history of late Neandertals. In Proceedings of the European Society for the study of Human Evolution (PESHE) (6, pp. 83). |
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Mafessoni, F., & Prüfer, K. (2017). Better support for a small effective population size of Neandertals and a long shared history of Neandertals and Denisovans. Proceedings of the National Academy of Sciences, 114(48), E10256-E10257. |
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Peyrégne, S., Dannemann, M., & Prüfer, K. (2017). Detecting ancient positive selection in humans using extended lineage sorting. Genome Research, 27(9), 1563-1572. |
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Prüfer, K., Filippo, C. d., Grote, S., Mafessoni, F., Korlevic, P., Hajdinjak, M., Vernot, B., Skov, L., Hsieh, P., Peyrégne, S., Reher, D., Hopfe, C., Nagel, S., Maricic, T., Fu, Q., Theunert, C., Rogers, R., Skoglund, P., Chintalapati, M., Dannemann, M., Nelson, B. J., Key, F. M., Rudan, P., Kucan, Ž., Gušic, I., Golovanova, L. V., Doronichev, V. B., Patterson, N., Reich, D., Eichler, E. E., Slatkin, M., Schierup, M. H., Andrés, A. M., Kelso, J., Meyer, M., & Pääbo, S. (2017). A high-coverage Neandertal genome from Vindija Cave in Croatia. Science, 358(6363), 655-658. |
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Slon, V., Hopfe, C., Weiß, C. L., Mafessoni, F., de la Rasilla, M., Lalueza-Fox, C., Rosas, A., Soressi, M., Knul, M. V., Miller, R., Stewart, J. R., Derevianko, A. P., Jacobs, Z., Li, B., Roberts, R. G., Shunkov, M. V., de Lumley, H., Perrenoud, C., Gušic, I., Kucan, Ž., Rudan, P., Ayinuer-Petri, A., Essel, E., Nagel, S., Nickel, B., Schmidt, A., Prüfer, K., Kelso, J., Burbano, H. A., Pääbo, S., & Meyer, M. (2017). Neandertal and Denisovan DNA from Pleistocene sediments. Science, 356(6338), 605-608. |
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Slon, V., Viola, B., Renaud, G., Gansauge, M.-T., Benazzi, S., Sawyer, S., Hublin, J.-J., Shunkov, M. V., Derevianko, A. P., Kelso, J., Prüfer, K., Meyer, M., & Pääbo, S. (2017). A fourth Denisovan individual. Science Advances, 3(7): e1700186. |
2016
Cagan, A., Theunert, C., Laayouni, H., Santpere, G., Pybus, M., Casals, F., Prüfer, K., Navarro, A., Marques-Bonet, T., Bertranpetit, J., & Andrés, A. M. (2016). Natural selection in the great apes. Molecular Biology and Evolution, 33(12), 3268-3283. |
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Grote, S., Prüfer, K., Kelso, J., & Dannemann, M. (2016). ABAEnrichment: An R package to test for gene set expression enrichment in the adult and developing human brain. Bioinformatics, 32(20), 3201-3203. |
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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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Prüfer, K. (2016). The high-quality genomes of a Neandertal and a Denisovan. American Journal of Physical Anthropology, 159(S62), 257-258. |
2015
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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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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Le Duc, D., Renaud, G., Krishnan, A., Almén, M. S., Huynen, L., Prohaska, S. J., Ongyerth, M., Bitarello, B. D., Schiöth, H. B., Hofreiter, M., Stadler, P. F., Prüfer, K., Lambert, D., Kelso, J., & Schöneberg, T. (2015). Kiwi genome provides insights into evolution of a nocturnal lifestyle. Genome Biology, 16: 147. |
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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), 835-835. |
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Ronke, C., Dannemann, M., Halbwax, M., Fischer, A., Helmschrodt, C., Brügel, M., André, C., Atencia, R., Mugisha, L., Scholz, M., Ceglarek, U., Thiery, J., Pääbo, S., Prüfer, K., & Kelso, J. (2015). Lineage-specific changes in biomarkers in great apes and humans. PLoS One, 10(8): e0134548. |
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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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Weiß, C. L., Dannemann, M., Prüfer, K., & Burbano, H. A. (2015). Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data. eLife, 4: e10005. |
2014
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., 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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Gokhman, D., Lavi, E., Prüfer, K., Fraga, M. F., Riancho, J. A., Kelso, J., 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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Hajdinjak, M., Korlević, P., Gansauge, M.-T., Dabney, J., Slon, V., Glocke, I., Sawyer, S., Nickel, B., Nagel, S., Gerber, T., Hopfe, C., Stenzel, U., Renaud, G., Andrés, A. M., Castellano, S., Kelso, J., Prüfer, K., Meyer, M., & Pääbo, S. (2014). Neandertal genetic diversity. Poster presented at XVII World UISPP Congress, Burgos, Spain. |
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Kelso, J., & Prüfer, K. (2014). Ancient humans and the origin of modern humans. Current Opinion in Genetics & Development, 29, 133-138. |
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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., 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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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., Kucinskas, 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., 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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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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Sankararaman, S., Mallick, S., Dannemann, M., Prüfer, K., Kelso, J., Pääbo, S., Patterson, N., & Reich, D. (2014). The genomic landscape of Neanderthal ancestry in present-day humans. Nature, 507(7492), 354-357. |
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The SIGMA Type 2 Diabetes Consortium, including authors, Prüfer, K., Sawyer, S., Stenzel, U., Kelso, J., Pääbo, S., & and others (2014). Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature, 506, 97-101. |
2013
Gokhman, D., Prüfer, K., Lavi, E., Kelso, J., Pääbo, S., Meshorer, E., & Carmel, L. (2013). Paleoepigenetics: Reconstructing the DNA methylation maps of archaic hominins. In European Society for the study of Human Evolution ( |
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Prado-Martinez, J., Sudmant, P. H., Kidd, J. M., Li, H., Kelley, J. L., Lorente-Galdos, B., Veeramah, K. R., Woerner, A. E., O’Connor, T. D., Santpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H., Munch, K., Hobolth, A., Halager, A. E., Malig, M., Hernandez-Rodriguez, J., Hernando-Herraez, I., Prüfer, K., Pybus, M., Johnstone, L., Lachmann, M., Alkan, C., Twigg, D., Petit, N., Baker, C., Hormozdiari, F., Fernandez-Callejo, M., Dabad, M., Wilson, M. L., Stevison, L., Camprubí, C., Carvalho, T., Ruiz-Herrera, A., Vives, L., Mele, M., Abello, T., Kondova, I., Bontrop, R. E., Pusey, A., Lankester, F., Kiyang, J. A., Bergl, R. A., Lonsdorf, E., Myers, S., Ventura, M., Gagneux, P., Comas, D., Siegismund, H., Blanc, J., Agueda-Calpena, L., Gut, M., Fulton, L., Tishkoff, S. A., Mullikin, J. C., Wilson, R. K., Gut, I. G., Gonder, M. K., Ryder, O. A., Hahn, B. H., Navarro, A., Akey, J. M., Bertranpetit, J., Reich, D., Mailund, T., Schierup, M. H., Hvilsom, C., Andrés, A. M., Wall, J. D., Bustamante, C. D., Hammer, M. F., Eichler, E. E., & Marques-Bonet, T. (2013). Great ape genetic diversity and population history. Nature, 499, 471-475. |
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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. |
2012
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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Groß, A., Hartung, M., Prüfer, K., Kelso, J., & Rahm, E. (2012). Impact of ontology evolution on functional analyses. Bioinformatics, 28(20), 2671-2677. |
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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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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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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. |
2011
Fischer, A., Prüfer, K., Good, J. M., Halbwax, M., Wiebe, V., André, C., Atencia, R., Mugisha, L., Ptak, S. E., & Pääbo, S. (2011). Bonobos fall within the genomic variation of chimpanzees. PLoS One, 6(6): e21605. |
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Prüfer, K. (2011). Computational approaches to ancient genome analysis. PhD Thesis, Universität, Leipzig. |
2010
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.-H.-Y., Hansen, N. F., Durand, E. Y., Malaspinas, A.-S., Jensen, J. D., Marques-Bonet, T., Alkan, C., Prüfer, K., Meyer, M., Burbano, H. A., Good, J. M., Schultz, R., Aximu-Petri, A., Butthoff, A., Höber, B., Höffner, B., Siegemund, M., Weihmann, A., Nusbaum, C., Lander, E. S., Russ, C., Novod, N., Affourtit, J., Egholm, M., Verna, C., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Doronichev, V. B., Golovanova, L. V., Lalueza-Fox, C., Rasilla, M. d. l., Fortea, J., Rosas, A., Schmitz, R. W., Johnson, P. L. F., Eichler, E. E., Falush, D., Birney, E., Mullikin, J. C., Slatkin, M., Nielsen, R., Kelso, J., Lachmann, M., Reich, D., & Pääbo, S. (2010). A draft sequence of the Neandertal genome. Science, 328(5979), 710-722. |
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Kelso, J., Hoehndorf, R., & Prüfer, K. (2010). Ontologies in biology. In R. Poli, M. Healy, & A. Kameas ( |
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Prüfer, K., Stenzel, U., Hofreiter, M., Pääbo, S., Kelso, J., & Green, R. E. (2010). Computational challenges in the analysis of ancient DNA. Genome Biology, 11(5): R47. |
2009
Green, R. E., Briggs, A. W., Krause, J., Prüfer, K., Burbano, H. A., Siebauer, M., Lachmann, M., & Pääbo, S. (2009). The Neandertal genome and ancient DNA authenticity. EMBO Journal, 28(17), 2494-2502. |
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Hoehndorf, R., Bacher, J., Backhaus, M., Gregorio, S. E. J., Loebe, F., Pruefer, K., Uciteli, A., Visagie, J., Herre, H., & Kelso, J. (2009). BOWiki: An ontology-based wiki for annotation of data and integration of knowledge in biology. BMC Bioinformatics, 10: S5. |
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Krause, J., Green, R. E., Briggs, A. W., Stenzel, U., Prüfer, K., Maricic, T., Kichner, M., Kelso, J. F., Reich, D., Mullikin, J. C., Egholm, M., & Pääbo, S. (2009). Insights from sequencing the Neanderthal genome. American Journal of Physical Anthropology, 138(S48), 170-170. |
2008
Green, R. E., Malaspinas, A.-S., Krause, J., Briggs, A. W., Johnson, P. L. F., Uhler, C., Meyer, M., Good, J. M., Maricic, T., Stenzel, U., Prüfer, K., Siebauer, M., Burbano, H. A., Ronan, M. T., Rothberg, J. M., Egholm, M., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Wikström, M., Laakkonen, L., Kelso, J., Slatkin, M., & Pääbo, S. (2008). A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell, 134(3), 416-426. |
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Prüfer, K., Stenzel, U., Dannemann, M., Green, R. E., Lachmann, M., & Kelso, J. (2008). PatMaN: Rapid alignment of short sequences to large databases. Bioinformatics, 24(13), 1530-1533. |
2007
Briggs, A. W., Stenzel, U., Johnson, P. L. F., Green, R. E., Kelso, J., Prüfer, K., Meyer, M., Krause, J., Ronan, M. T., Lachmann, M., & Pääbo, S. (2007). Patterns of damage in genomic DNA sequences from a Neandertal. Proceedings of the National Academy of Sciences of the United States of America, 104(37), 14616-14621. |
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Krause, J., Orlando, L., Serre, D., Viola, B., Prüfer, K., Richards, M. P., Hublin, J.-J., Hänni, C., Derevianko, A. P., & Pääbo, S. (2007). Neanderthals in central Asia and Siberia. Nature, 449(7164), 902-904. |
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Meyer, M., Stenzel, U., Myles, S., Prüfer, K., & Hofreiter, M. (2007). Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Research, 35(15): e97. |
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Prüfer, K., Muetzel, B., Do, H.-H., Weiss, G., Khaitovich, P., Rahm, E., Pääbo, S., Lachmann, M., & Enard, W. (2007). FUNC: A package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics, 8: 41. |
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Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., Batzer, M. A., Bustamante, C. D., Eichler, E. E., Hahn, M. W., Hardison, R. C., Makova, K. D., Miller, W., Milosavljevic, A., Palermo, R. E., Siepel, A., Sikela, J. M., Attaway, T., Bell, S., Bernard, K. E., Buhay, C. J., Chandrabose, M. N., Dao, M., Davis, C., Delehaunty, K. D., Ding, Y., Dinh, H. H., Dugan-Rocha, S., Fulton, L. A., Gabisi, R. A., Garner, T. T., Godfrey, J., Hawes, A. C., Hernandez, J., Hines, S., Holder, M., Hume, J., Jhangiani, S. N., Joshi, V., Khan, Z. M., Kirkness, E. F., Cree, A., Fowler, R. G., Lee, S., Lewis, L. R., Li, Z., Liu, Y.-s., Moore, S. M., Muzny, D., Nazareth, L. V., Ngo, D. N., Okwuonu, G. O., Pai, G., Parker, D., Paul, H. A., Pfannkoch, C., Pohl, C. S., Rogers, Y.-H., Ruiz, S. J., Sabo, A., Santibanez, J., Schneider, B. W., Smith, S. M., Sodergren, E., Svatek, A. F., Utterback, T. R., Vattathil, S., Warren, W., White, C. S., Chinwalla, A. T., Feng, Y., Halpern, A. L., Hillier, L. W., Huang, X., Minx, P., Nelson, J. O., Pepin, K. H., Qin, X., Sutton, G. G., Venter, E., Walenz, B. P., Wallis, J. W., Worley, K. C., Yang, S.-P., Jones, S. M., Marra, M. A., Rocchi, M., Schein, J. E., Baertsch, R., Clarke, L., Csürös, M., Glasscock, J., Harris, R. A., Havlak, P., Jackson, A. R., Jiang, H., Liu, Y., Messina, D. N., Shen, Y., Song, H.-X.-Z., Wylie, T., Zhang, L., Birney, E., Han, K., Konkel, M. K., Lee, J., Smit, A. F. A., Ullmer, B., Wang, H., Xing, J., Burhans, R., Cheng, Z., Karro, J. E., Ma, J., Raney, B., She, X., Cox, M. J., Demuth, J. P., Dumas, L. J., Han, S.-G., Hopkins, J., Karimpour-Fard, A., Kim, Y. H., Pollack, J. R., Vinar, T., Addo-Quaye, C., Degenhardt, J., Denby, A., Hubisz, M. J., Indap, A., Kosiol, C., Lahn, B. T., Lawson, H. A., Marklein, A., Nielsen, R., Vallender, E. J., Clark, A. G., Ferguson, B., Hernandez, R. D., Hirani, K., Kehrer-Sawatzki, H., Kolb, J., Patil, S., Pu, L.-L., Ren, Y., Smith, D. G., Wheeler, D. A., Schenck, I., Ball, E. V., Chen, R., Cooper, D. N., Giardine, B., Hsu, F., Kent, W. J., Lesk, A., Nelson, D. L., O'Brien, W. E., Prüfer, K., Stenson, P. D., Wallace, J. C., Ke, H., Liu, X.-M., Wang, P., Xiang, A. P., Yang, F., Barber, G. P., Haussler, D., Karolchik, D., Kern, A. D., Kuhn, R. M., Smith, K. E., & Zwieg, A. S. (2007). Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316(5822), 222-234. |
2006
Hoehndorf, R., Prüfer, K., Backhaus, M., Herre, H., Kelso, J., Loebe, F., & Visagie, J. (2006). A proposal for a gene functions wiki. In R. Meersman, Z. Tari, & P. Herrero ( |
2005
Hellmann, I., Prüfer, K., Ji, H. K., Zody, M. C., Pääbo, S., & Ptak, S. E. (2005). Why do human diversity levels vary at a megabase scale? Genome Research, 15(9), 1222-1231. |
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Prüfer, K. (2005). Bioinformatische Werkzeuge für den Genom-Vergleich zwischen Mensch und Schimpanse. Diploma Thesis, Universität Leipzig, 2015. |
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The Chimpanzee Sequencing and Analysis Consortium, Mikkelsen, T. S., Hillier, L. W., Eichler, E. E., Zody, M. C., Jaffe, D. B., Yang, S.-P., Enard, W., Hellmann, I., Lindblad-Toh, K., Altheide, T. K., Archidiacono, N., Bork, P., Butler, J., Chang, J. L., Cheng, Z., Chinwalla, A. T., de Jong, P., Delehaunty, K. D., Fronick, C. C., Fulton, L. L., Gilad, Y., Glusman, G., Gnerre, S., Graves, T. A., Hayakawa, T., Hayden, K. E., Huang, X., Ji, H., Kent, W. J., King, M.-C., Kulbokasl, E. J., Lee, M. K., Liu, G., Lopez-Otin, C., Makova, K. D., Man, O., Mardis, E. R., Mauceli, E., Miner, T. L., Nash, W. E., Nelson, J. O., Pääbo, S., Patterson, N. J., Pohl, C. S., Pollard, K. S., Prüfer, K., Puente, X. S., Reich, D., Rocchi, M., Rosenbloom, K., Ruvolo, M., Richter, D. J., Schaffner, S. F., Smit, A. F. A., Smith, S. M., Suyama, M., Taylor, J., Torrents, D., Tuzun, E., Varki, A., Velasco, G., Ventura, M., Wallis, J. W., Wendl, M. C., Wilson, R. K., Lander, E. S., & Waterston, R. H. (2005). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437(7055), 69-87. |