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Items: 1 to 20 of 21

1.

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach.

Renaud G, Stenzel U, Maricic T, Wiebe V, Kelso J.

Bioinformatics. 2015 Mar 1;31(5):770-2. doi: 10.1093/bioinformatics/btu719. Epub 2014 Oct 30.

2.

leeHom: adaptor trimming and merging for Illumina sequencing reads.

Renaud G, Stenzel U, Kelso J.

Nucleic Acids Res. 2014 Oct;42(18):e141. doi: 10.1093/nar/gku699. Epub 2014 Aug 6.

3.

Patterns of coding variation in the complete exomes of three Neandertals.

Castellano S, Parra G, Sánchez-Quinto FA, Racimo F, Kuhlwilm M, Kircher M, Sawyer S, Fu Q, Heinze A, Nickel B, Dabney J, Siebauer M, White L, Burbano HA, Renaud G, Stenzel U, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajković D, Kucan Ž, Gušic I, Shunkov MV, Derevianko AP, Viola B, Meyer M, Kelso J, Andrés AM, Pääbo S.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6666-71. doi: 10.1073/pnas.1405138111. Epub 2014 Apr 21.

4.

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers.

Renaud G, Kircher M, Stenzel U, Kelso J.

Bioinformatics. 2013 May 1;29(9):1208-9. doi: 10.1093/bioinformatics/btt117. Epub 2013 Mar 6.

5.

DNA analysis of an early modern human from Tianyuan Cave, China.

Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Pääbo S.

Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2223-7. doi: 10.1073/pnas.1221359110. Epub 2013 Jan 22.

6.

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.

7.

Genetic history of an archaic hominin group from Denisova Cave in Siberia.

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, Pääbo S.

Nature. 2010 Dec 23;468(7327):1053-60. doi: 10.1038/nature09710.

8.

Road blocks on paleogenomes--polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA.

Heyn P, Stenzel U, Briggs AW, Kircher M, Hofreiter M, Meyer M.

Nucleic Acids Res. 2010 Sep;38(16):e161. doi: 10.1093/nar/gkq572. Epub 2010 Jun 28.

9.

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 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.

Science. 2010 May 7;328(5979):710-22. doi: 10.1126/science.1188021.

10.

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.

11.

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA.

Briggs AW, Stenzel U, Meyer M, Krause J, Kircher M, Pääbo S.

Nucleic Acids Res. 2010 Apr;38(6):e87. doi: 10.1093/nar/gkp1163. Epub 2009 Dec 22.

12.

Primer extension capture: targeted sequence retrieval from heavily degraded DNA sources.

Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Pääbo S.

J Vis Exp. 2009 Sep 3;(31):1573. doi: 10.3791/1573.

13.

Improved base calling for the Illumina Genome Analyzer using machine learning strategies.

Kircher M, Stenzel U, Kelso J.

Genome Biol. 2009;10(8):R83. doi: 10.1186/gb-2009-10-8-r83. Epub 2009 Aug 14.

14.

Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA.

Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M.

Genome Res. 2009 Oct;19(10):1843-8. doi: 10.1101/gr.095760.109. Epub 2009 Jul 27.

15.

Targeted retrieval and analysis of five Neandertal mtDNA genomes.

Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S.

Science. 2009 Jul 17;325(5938):318-21. doi: 10.1126/science.1174462.

16.

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.

17.

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.

18.

Parallel tagged sequencing on the 454 platform.

Meyer M, Stenzel U, Hofreiter M.

Nat Protoc. 2008;3(2):267-78. doi: 10.1038/nprot.2007.520.

PMID:
18274529
19.

Patterns of damage in genomic DNA sequences from a Neandertal.

Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S.

Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14616-21. Epub 2007 Aug 21.

20.

Targeted high-throughput sequencing of tagged nucleic acid samples.

Meyer M, Stenzel U, Myles S, Prüfer K, Hofreiter M.

Nucleic Acids Res. 2007;35(15):e97. Epub 2007 Aug 1.

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