24.07.2014 - 06:22
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Publications

2014

Gokhman, D., E. Lavi, K. Prüfer, M.F. Fraga, J.A. Riancho, J. Kelso, S. Pääbo, E. Meshorer and L. Carmel: Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science 344, 523-527 (2014).

Khrameeva, E.E., K.Bozek, L. He, Z. Yan, X. Jiang, Y. Wei, K. Tang, M.S. Gelfand, K. Prüfer, J. Kelso, S. Pääbo, P. Giavalisco, M. Lachmann and P. Khaitovich: Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. Nature Communications 5:3584, doi:10.1038/ncomms4584 (2014).

Prüfer, K., F. Racimo, N. Patterson, F. Jay, S. Sankararaman, S. Sawyer, A. Heinze, G. Renaud, P.H. Sudmant, C. de Filippo, H. Li, S. Mallick, M. Dannemann, Q. Fu, M. Kircher, M. Kuhlwilm, M. Lachmann, M. Meyer, M. Ongyerth, M. Siebauer, C. Theunert, A. Tandon, P. Moorjani, J. Pickrell, J.C. Mullikin, S.H. Vohr, R.E. Green, I. Hellmann, P.L.F. Johnson, H. Blanche, H. Cann, J.O. Kitzman, J. Shendure, E.E. Eichler, E.S. Lein, T.E. Bakken, L.V. Golovanova, V.B. Doronichev, M.V. Shunkov, A.P. Derevianko, B. Viola, M. Slatkin, D. Reich, J. Kelso and S. Pääbo: The complete genome sequence of a Neandertal from the Altai Mountains. Nature 505, 43-49 (2014). 

Sankararaman, S., S. Mallick, M. Dannemann, K. Prüfer, J. Kelso, S. Pääbo, N. Patterson and D. Reich: The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507, 354-357 (2014).

2013

Prado-Martinez, J., P.H. Sudmant, J.M. Kidd, H. Li, J.L. Kelley, B. Lorente-Galdos, K.R. Veeramah, A.E. Woerner, T.D. O'Connor, G. Santpere, A. Cagan, C. Theunert, F. Casals, H. Laayouni, K. Munch, A. Hobolth, A.E. Halager, M. Malig, J. Hernandez-Rodriguez, I. Hernando-Herraez, K. Prüfer, M. Pybus, L. Johnstone, M. Lachmann, C. Alkan, D. Twigg, N. Petit, C. Baker, F. Hormozdiari, M. Fernandez-Callejo, M. Dabad, M.L. Wilson, L. Stevison, C. Camprubi, T. Carvalho, A. Ruiz-Herrera, L. Vives, M. Mele, T. Abello, I. Kondova, R.E. Bontrop, A. Pusey, F. Lankester, J.A. Kiyang, R.A. Bergl, E. Lonsdorf, S. Myers, M. Ventura, P. Gagneux, D. Comas, H. Siegismund, J. Blanc, L. Agueda-Calpena, M. Gut, L. Fulton, S.A. Tishkoff, J.C. Mullikin, R.K. Wilson, I.G. Gut, M.K. Gonder, O.A. Ryder, B.H. Hahn, A. Navarro, J.M. Akey, J. Bertranpetit, D. Reich, T. Mailund, M.H. Schierup, C. Hvilsom, A.M. Andrés, J.D. Wall, C.D. Bustamante, M.F. Hammer, E.E. Eichler and T. Marques-Bonet: Great ape genetic diversity and population history. Nature 499, 471-75 (2013).

Prüfer K, Langergraber KE, Pääbo S, Vigilant L. Reply to Gibb and Hills: Divergence times, generation lengths and mutation rates in great apes and humans.  Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):E612.

2012

Groß A, Hartung M, Prüfer K, Kelso J, Rahm E. Impact of ontology evolution on functional analyses. Bioinformatics. 2012 Oct 15;28(20):2671-7.

Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012 Oct 12;338(6104):222-6.

Langergraber KE, Prüfer K, Rowney C, Boesch C, Crockford C, Fawcett K, Inoue E, Inoue-Muruyama M, Mitani JC, Muller MN, Robbins MM, Schubert G, Stoinski TS, Viola B, Watts D, Wittig RM, Wrangham RW, Zuberbühler K, Pääbo S, Vigilant L.  Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):15716-21.

Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S. The bonobo genome compared with the chimpanzee and human genomes. Nature. 2012 Jun 28;486(7404):527-31.

Dannemann M, Prüfer K, Lizano E, Nickel B, Burbano HA, Kelso J. Transcription factors are targeted by differentially expressed miRNAs in primates. Genome Biol Evol. 2012;4(4):552-64.

Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A, Schierup MH. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet. 2012;8(12):e1003125.

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2011

Fischer A, Prüfer K, Good JM, Halbwax M, Wiebe V, André C, Atencia R, Mugisha L, Ptak SE, Pääbo S. Bonobos fall within the genomic variation of chimpanzees.  PLoS One. 2011;6(6):e21605.

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2010

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome. Science. 2010 May 7;328(5979):710-22.

Prüfer K, Stenzel U, Hofreiter M, Pääbo S, Kelso J, Green RE. Computational challenges in the analysis of ancient DNA. Genome Biol. 2010;11(5):R47.

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2009

Green RE, Briggs AW, Krause J, Prüfer K, Burbano HA, Siebauer M, Lachmann M, Pääbo S. The Neandertal genome and ancient DNA authenticity. EMBO J. 2009 Sep 2;28(17):2494-502.

Kelso, J, Hoehndorf R and Prüfer K: Ontologies in biology. In: Theory and Applications of Ontologies. Second Volume. Ontology: The Information-science Stance. (Eds) M. Healey, A. Kameas and R. Poli, Springer-Verlag 2010, 347-371.

Hoehndorf R, Bacher J, Backhaus M, Gregorio SE Jr, Loebe F, Prüfer K, Uciteli A, Visagie J, Herre H, Kelso J. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology. BMC Bioinformatics. 2009 May 6;10 Suppl 5:S5.

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2008

Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković D, Kućan Z, Gusić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell. 2008 Aug 8;134(3):416-26.

Prüfer K, Stenzel U, Dannemann M, Green RE, Lachmann M, Kelso J. PatMaN: rapid alignment of short sequences to large databases. Bioinformatics. 2008 Jul 1;24(13):1530-1.

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2007

Krause J, Orlando L, Serre D, Viola B, Prüfer K, Richards MP, Hublin JJ, Hänni C, Derevianko AP, Pääbo S. Neanderthals in central Asia and Siberia. Nature. 2007 Oct 18;449(7164):902-4.

Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14616-21.

Rhesus Macaque Genome Sequencing and Analysis Consortium, Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csürös M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'brien WE, Prüfer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007 Apr 13;316(5822):222-34.

Prüfer K, Muetzel B, Do HH, Weiss G, Khaitovich P, Rahm E, Pääbo S, Lachmann M, Enard W. FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics. 2007 Feb 6;8:41.

Meyer M, Stenzel U, Myles S, Prüfer K, Hofreiter M. Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res. 2007;35(15):e97.

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2005

Hellmann I, Prüfer K, Ji H, Zody MC, Pääbo S, Ptak SE. Why do human diversity levels vary at a megabase scale? Genome Res. 2005 Sep;15(9):1222-31.

Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005 Sep 1;437(7055):69-87.