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Items: 1 to 50 of 72

1.

snpAD: An ancient DNA genotype caller.

Prüfer K.

Bioinformatics. 2018 Jun 21. doi: 10.1093/bioinformatics/bty507. [Epub ahead of print]

PMID:
29931305
2.

Uncoupling human and climate drivers of late Holocene vegetation change in southern Brazil.

Robinson M, De Souza JG, Maezumi SY, Cárdenas M, Pessenda L, Prufer K, Corteletti R, Scunderlick D, Mayle FE, De Blasis P, Iriarte J.

Sci Rep. 2018 May 17;8(1):7800. doi: 10.1038/s41598-018-24429-5.

3.

Reconstructing the genetic history of late Neanderthals.

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 JJ, Gušić I, Kućan Ž, Rudan P, Golovanova LV, Doronichev VB, Posth C, Krause J, Korlević P, Nagel S, Nickel B, Slatkin M, Patterson N, Reich D, Prüfer K, Meyer M, Pääbo S, Kelso J.

Nature. 2018 Mar 29;555(7698):652-656. doi: 10.1038/nature26151. Epub 2018 Mar 21.

PMID:
29562232
4.

Better support for a small effective population size of Neandertals and a long shared history of Neandertals and Denisovans.

Mafessoni F, Prüfer K.

Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):E10256-E10257. doi: 10.1073/pnas.1716918114. Epub 2017 Nov 14. No abstract available.

5.

A high-coverage Neandertal genome from Vindija Cave in Croatia.

Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević 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 BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S.

Science. 2017 Nov 3;358(6363):655-658. doi: 10.1126/science.aao1887. Epub 2017 Oct 5.

PMID:
28982794
6.

A regime shift in the Sun-Climate connection with the end of the Medieval Climate Anomaly.

Smirnov DA, Breitenbach SFM, Feulner G, Lechleitner FA, Prufer KM, Baldini JUL, Marwan N, Kurths J.

Sci Rep. 2017 Sep 11;7(1):11131. doi: 10.1038/s41598-017-11340-8.

7.

Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans.

Chintalapati M, Dannemann M, Prüfer K.

BMC Evol Biol. 2017 Aug 4;17(1):179. doi: 10.1186/s12862-017-1018-8.

8.

Detecting ancient positive selection in humans using extended lineage sorting.

Peyrégne S, Boyle MJ, Dannemann M, Prüfer K.

Genome Res. 2017 Sep;27(9):1563-1572. doi: 10.1101/gr.219493.116. Epub 2017 Jul 18.

9.

A fourth Denisovan individual.

Slon V, Viola B, Renaud G, Gansauge MT, Benazzi S, Sawyer S, Hublin JJ, Shunkov MV, Derevianko AP, Kelso J, Prüfer K, Meyer M, Pääbo S.

Sci Adv. 2017 Jul 7;3(7):e1700186. doi: 10.1126/sciadv.1700186. eCollection 2017 Jul.

10.

Neandertal and Denisovan DNA from Pleistocene sediments.

Slon V, Hopfe C, Weiß CL, Mafessoni F, de la Rasilla M, Lalueza-Fox C, Rosas A, Soressi M, Knul MV, Miller R, Stewart JR, Derevianko AP, Jacobs Z, Li B, Roberts RG, Shunkov MV, de Lumley H, Perrenoud C, Gušić I, Kućan Ž, Rudan P, Aximu-Petri A, Essel E, Nagel S, Nickel B, Schmidt A, Prüfer K, Kelso J, Burbano HA, Pääbo S, Meyer M.

Science. 2017 May 12;356(6338):605-608. doi: 10.1126/science.aam9695. Epub 2017 Apr 27.

PMID:
28450384
11.

Tropical rainfall over the last two millennia: evidence for a low-latitude hydrologic seesaw.

Lechleitner FA, Breitenbach SF, Rehfeld K, Ridley HE, Asmerom Y, Prufer KM, Marwan N, Goswami B, Kennett DJ, Aquino VV, Polyak V, Haug GH, Eglinton TI, Baldini JU.

Sci Rep. 2017 Apr 5;7:45809. doi: 10.1038/srep45809.

12.

Functional implications of Neandertal introgression in modern humans.

Dannemann M, Prüfer K, Kelso J.

Genome Biol. 2017 Apr 3;18(1):61. doi: 10.1186/s13059-017-1181-7.

13.

Persistent northward North Atlantic tropical cyclone track migration over the past five centuries.

Baldini LM, Baldini JU, McElwaine JN, Frappier AB, Asmerom Y, Liu KB, Prufer KM, Ridley HE, Polyak V, Kennett DJ, Macpherson CG, Aquino VV, Awe J, Breitenbach SF.

Sci Rep. 2016 Nov 23;6:37522. doi: 10.1038/srep37522.

14.

Natural Selection in the Great Apes.

Cagan A, Theunert C, Laayouni H, Santpere G, Pybus M, Casals F, Prüfer K, Navarro A, Marques-Bonet T, Bertranpetit J, Andrés AM.

Mol Biol Evol. 2016 Dec;33(12):3268-3283. Epub 2016 Oct 30.

15.

ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain.

Grote S, Prüfer K, Kelso J, Dannemann M.

Bioinformatics. 2016 Oct 15;32(20):3201-3203. Epub 2016 Jun 26.

16.

Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins.

Meyer M, Arsuaga JL, de Filippo C, Nagel S, Aximu-Petri A, Nickel B, Martínez I, Gracia A, Bermúdez de Castro JM, Carbonell E, Viola B, Kelso J, Prüfer K, Pääbo S.

Nature. 2016 Mar 24;531(7595):504-7. doi: 10.1038/nature17405. Epub 2016 Mar 14.

PMID:
26976447
17.

Nuclear and mitochondrial DNA sequences from two Denisovan individuals.

Sawyer S, Renaud G, Viola B, Hublin JJ, Gansauge MT, Shunkov MV, Derevianko AP, Prüfer K, Kelso J, Pääbo S.

Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):15696-700. doi: 10.1073/pnas.1519905112. Epub 2015 Nov 16.

18.

Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data.

Weiß CL, Dannemann M, Prüfer K, Burbano HA.

Elife. 2015 Nov 3;4. pii: e10005. doi: 10.7554/eLife.10005.

19.

Lineage-Specific Changes in Biomarkers in Great Apes and Humans.

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.

PLoS One. 2015 Aug 6;10(8):e0134548. doi: 10.1371/journal.pone.0134548. eCollection 2015.

20.

Kiwi genome provides insights into evolution of a nocturnal lifestyle.

Le Duc D, Renaud G, Krishnan A, Almén MS, Huynen L, Prohaska SJ, Ongyerth M, Bitarello BD, Schiöth HB, Hofreiter M, Stadler PF, Prüfer K, Lambert D, Kelso J, Schöneberg T.

Genome Biol. 2015 Jul 23;16:147. doi: 10.1186/s13059-015-0711-4.

21.

An early modern human from Romania with a recent Neanderthal ancestor.

Fu Q, Hajdinjak M, Moldovan OT, 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.

Nature. 2015 Aug 13;524(7564):216-9. doi: 10.1038/nature14558. Epub 2015 Jun 22.

22.

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion.

Florio M, Albert M, Taverna E, Namba T, Brandl H, Lewitus E, Haffner C, Sykes A, Wong FK, Peters J, Guhr E, Klemroth S, Prüfer K, Kelso J, Naumann R, Nüsslein I, Dahl A, Lachmann R, Pääbo S, Huttner WB.

Science. 2015 Mar 27;347(6229):1465-70. doi: 10.1126/science.aaa1975. Epub 2015 Feb 26.

23.

Anthropology. Comment on "Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans".

Prüfer K, Meyer M.

Science. 2015 Feb 20;347(6224):835. doi: 10.1126/science.1260617.

24.

Genome sequence of a 45,000-year-old modern human from western Siberia.

Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM, Bondarev AA, Johnson PL, Aximu-Petri A, Prüfer K, de Filippo C, Meyer M, Zwyns N, Salazar-García DC, Kuzmin YV, Keates SG, Kosintsev PA, Razhev DI, Richards MP, Peristov NV, Lachmann M, Douka K, Higham TF, Slatkin M, Hublin JJ, Reich D, Kelso J, Viola TB, Pääbo S.

Nature. 2014 Oct 23;514(7523):445-9. doi: 10.1038/nature13810.

25.

Ancient humans and the origin of modern humans.

Kelso J, Prüfer K.

Curr Opin Genet Dev. 2014 Dec;29:133-8. doi: 10.1016/j.gde.2014.09.004. Epub 2014 Oct 3. Review.

PMID:
25286439
26.

Ancient human genomes suggest three ancestral populations for present-day Europeans.

Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, Berger B, Economou C, Bollongino R, Fu Q, Bos KI, 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 JM, Wahl J, Ayodo G, Babiker HA, Bailliet G, Balanovska E, Balanovsky O, Barrantes R, Bedoya G, Ben-Ami H, Bene J, Berrada F, Bravi CM, Brisighelli F, Busby GB, Cali F, Churnosov M, Cole DE, Corach D, Damba L, van Driem G, Dryomov S, Dugoujon JM, Fedorova SA, Gallego Romero I, Gubina M, Hammer M, Henn BM, Hervig T, Hodoglugil U, Jha AR, Karachanak-Yankova S, Khusainova R, Khusnutdinova E, Kittles R, Kivisild T, Klitz W, Kučinskas V, Kushniarevich A, Laredj L, Litvinov S, Loukidis T, Mahley RW, 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 EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Vasquez R, Villena M, Voevoda M, Winkler CA, Yepiskoposyan L, Zalloua P, Zemunik T, Cooper A, Capelli C, Thomas MG, Ruiz-Linares A, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, Krause J.

Nature. 2014 Sep 18;513(7518):409-13. doi: 10.1038/nature13673.

27.

Reconstructing the DNA methylation maps of the Neandertal and the Denisovan.

Gokhman D, Lavi E, Prüfer K, Fraga MF, Riancho JA, Kelso J, Pääbo S, Meshorer E, Carmel L.

Science. 2014 May 2;344(6183):523-7. doi: 10.1126/science.1250368. Epub 2014 Apr 17.

28.

Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans.

Khrameeva EE, Bozek K, He L, Yan Z, Jiang X, Wei Y, Tang K, Gelfand MS, Prufer K, Kelso J, Paabo S, Giavalisco P, Lachmann M, Khaitovich P.

Nat Commun. 2014 Apr 1;5:3584. doi: 10.1038/ncomms4584.

29.

The genomic landscape of Neanderthal ancestry in present-day humans.

Sankararaman S, Mallick S, Dannemann M, Prüfer K, Kelso J, Pääbo S, Patterson N, Reich D.

Nature. 2014 Mar 20;507(7492):354-7. doi: 10.1038/nature12961. Epub 2014 Jan 29.

30.

The complete genome sequence of a Neanderthal from the Altai Mountains.

Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PL, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S.

Nature. 2014 Jan 2;505(7481):43-9. doi: 10.1038/nature12886. Epub 2013 Dec 18.

31.

Great ape genetic diversity and population history.

Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, 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 ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T.

Nature. 2013 Jul 25;499(7459):471-5. doi: 10.1038/nature12228. Epub 2013 Jul 3.

32.

Reply to Gibb and Hills: Divergence times, generation lengths and mutation rates in great apes and humans.

Prüfer K, Langergraber KE, Pääbo S, Vigilant L.

Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):E612. No abstract available.

33.

A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.

Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, Lunter G, Prüfer K, Scally A, Hobolth A, Schierup MH.

PLoS Genet. 2012;8(12):e1003125. doi: 10.1371/journal.pgen.1003125. Epub 2012 Dec 20.

34.

Development and disintegration of Maya political systems in response to climate change.

Kennett DJ, Breitenbach SF, Aquino VV, Asmerom Y, Awe J, Baldini JU, Bartlein P, Culleton BJ, Ebert C, Jazwa C, Macri MJ, Marwan N, Polyak V, Prufer KM, Ridley HE, Sodemann H, Winterhalder B, Haug GH.

Science. 2012 Nov 9;338(6108):788-91. doi: 10.1126/science.1226299.

35.

Impact of ontology evolution on functional analyses.

Groß A, Hartung M, Prüfer K, Kelso J, Rahm E.

Bioinformatics. 2012 Oct 15;28(20):2671-7. doi: 10.1093/bioinformatics/bts498. Epub 2012 Sep 6.

PMID:
22954631
36.

A high-coverage genome sequence from an archaic Denisovan individual.

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.

Science. 2012 Oct 12;338(6104):222-6. doi: 10.1126/science.1224344. Epub 2012 Aug 30.

37.

Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution.

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.

Proc Natl Acad Sci U S A. 2012 Sep 25;109(39):15716-21. Epub 2012 Aug 13. Review.

38.

The bonobo genome compared with the chimpanzee and human genomes.

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.

Nature. 2012 Jun 28;486(7404):527-31. doi: 10.1038/nature11128.

39.

Transcription factors are targeted by differentially expressed miRNAs in primates.

Dannemann M, Prüfer K, Lizano E, Nickel B, Burbano HA, Kelso J.

Genome Biol Evol. 2012;4(4):552-64. doi: 10.1093/gbe/evs033. Epub 2012 Mar 27.

40.

Bonobos fall within the genomic variation of chimpanzees.

Fischer A, Prüfer K, Good JM, Halbwax M, Wiebe V, André C, Atencia R, Mugisha L, Ptak SE, Pääbo S.

PLoS One. 2011;6(6):e21605. doi: 10.1371/journal.pone.0021605. Epub 2011 Jun 29.

41.

A draft sequence of the Neandertal genome.

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 Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S.

Science. 2010 May 7;328(5979):710-722. doi: 10.1126/science.1188021.

42.

Computational challenges in the analysis of ancient DNA.

Prüfer K, Stenzel U, Hofreiter M, Pääbo S, Kelso J, Green RE.

Genome Biol. 2010;11(5):R47. doi: 10.1186/gb-2010-11-5-r47. Epub 2010 May 6.

43.

The Neandertal genome and ancient DNA authenticity.

Green RE, Briggs AW, Krause J, Prüfer K, Burbano HA, Siebauer M, Lachmann M, Pääbo S.

EMBO J. 2009 Sep 2;28(17):2494-502. doi: 10.1038/emboj.2009.222. Epub 2009 Aug 6. Review.

44.

BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.

Hoehndorf R, Bacher J, Backhaus M, Gregorio SE Jr, Loebe F, Prüfer K, Uciteli A, Visagie J, Herre H, Kelso J.

BMC Bioinformatics. 2009 May 6;10 Suppl 5:S5. doi: 10.1186/1471-2105-10-S5-S5.

45.

Liver X receptor beta with mutations in the activation function-2 region is excluded from the nucleolus.

Lall R, Kuruvilla S, Prüfer K.

Cell Biol Int. 2009 Mar;33(3):447-52. doi: 10.1016/j.cellbi.2009.01.015. Epub 2009 Jan 31.

PMID:
19356704
46.

The N-terminal nuclear localization sequences of liver X receptors alpha and beta bind to importin alpha and are essential for both nuclear import and transactivating functions.

Miller A, Crumbley C, Prüfer K.

Int J Biochem Cell Biol. 2009 Apr;41(4):834-43. doi: 10.1016/j.biocel.2008.08.016. Epub 2008 Aug 19.

PMID:
18773967
47.

A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing.

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.

Cell. 2008 Aug 8;134(3):416-26. doi: 10.1016/j.cell.2008.06.021.

48.

Mutations in the AF-2 region abolish ligand-induced intranuclear immobilization of the liver X receptor alpha.

Prüfer K, Hernandez C, Gilbreath M.

Exp Cell Res. 2008 Aug 15;314(14):2652-60. doi: 10.1016/j.yexcr.2008.05.005. Epub 2008 May 27.

PMID:
18599038
49.

PatMaN: rapid alignment of short sequences to large databases.

Prüfer K, Stenzel U, Dannemann M, Green RE, Lachmann M, Kelso J.

Bioinformatics. 2008 Jul 1;24(13):1530-1. doi: 10.1093/bioinformatics/btn223. Epub 2008 May 8.

50.

Neanderthals in central Asia and Siberia.

Krause J, Orlando L, Serre D, Viola B, Prüfer K, Richards MP, Hublin JJ, Hänni C, Derevianko AP, Pääbo S.

Nature. 2007 Oct 18;449(7164):902-4. Epub 2007 Sep 30.

PMID:
17914357

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