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Items: 1 to 20 of 99

1.

Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis.

Gilbert MT, Binladen J, Miller W, Wiuf C, Willerslev E, Poinar H, Carlson JE, Leebens-Mack JH, Schuster SC.

Nucleic Acids Res. 2007;35(1):1-10. Epub 2006 Aug 18.

2.

Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions.

Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, Cooper A.

Nucleic Acids Res. 2007;35(17):5717-28. Epub 2007 Aug 22.

3.

Postmortem miscoding lesions in sequence analysis of human ancient mitochondrial DNA.

Lamers R, Hayter S, Matheson CD.

J Mol Evol. 2009 Jan;68(1):40-55. doi: 10.1007/s00239-008-9184-3. Epub 2008 Dec 6.

PMID:
19067027
4.

Assessing the fidelity of ancient DNA sequences amplified from nuclear genes.

Binladen J, Wiuf C, Gilbert MT, Bunce M, Barnett R, Larson G, Greenwood AD, Haile J, Ho SY, Hansen AJ, Willerslev E.

Genetics. 2006 Feb;172(2):733-41. Epub 2005 Nov 19.

5.

Characterization of genetic miscoding lesions caused by postmortem damage.

Gilbert MT, Hansen AJ, Willerslev E, Rudbeck L, Barnes I, Lynnerup N, Cooper A.

Am J Hum Genet. 2003 Jan;72(1):48-61. Epub 2002 Dec 13.

6.

Bayesian estimation of sequence damage in ancient DNA.

Ho SY, Heupink TH, Rambaut A, Shapiro B.

Mol Biol Evol. 2007 Jun;24(6):1416-22. Epub 2007 Mar 29. Erratum in: Mol Biol Evol. 2007 Jul;24(7):1576.

PMID:
17395598
7.

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.

8.

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.

9.

Characterization of nucleotide misincorporation patterns in the iceman's mitochondrial DNA.

Olivieri C, Ermini L, Rizzi E, Corti G, Bonnal R, Luciani S, Marota I, De Bellis G, Rollo F.

PLoS One. 2010 Jan 8;5(1):e8629. doi: 10.1371/journal.pone.0008629.

10.
11.

PCR amplification, cloning, and sequencing of ancient DNA.

Fulton TL, Stiller M.

Methods Mol Biol. 2012;840:111-9. doi: 10.1007/978-1-61779-516-9_15.

PMID:
22237529
12.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E.

PLoS One. 2007 Feb 14;2(2):e197.

13.

Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.

Poinar HN, Schwarz C, Qi J, Shapiro B, Macphee RD, Buigues B, Tikhonov A, Huson DH, Tomsho LP, Auch A, Rampp M, Miller W, Schuster SC.

Science. 2006 Jan 20;311(5759):392-4. Epub 2005 Dec 20.

14.

A statistical approach to identify ancient template DNA.

Helgason A, Pálsson S, Lalueza-Fox C, Ghosh S, Sigurdardóttir S, Baker A, Hrafnkelsson B, Arnadóttir L, Thorsteinsdóttir U, Stefánsson K.

J Mol Evol. 2007 Jul;65(1):92-102. Epub 2007 Jun 25.

PMID:
17593420
15.

New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains.

Schwarz C, Debruyne R, Kuch M, McNally E, Schwarcz H, Aubrey AD, Bada J, Poinar H.

Nucleic Acids Res. 2009 Jun;37(10):3215-29. doi: 10.1093/nar/gkp159. Epub 2009 Mar 24.

16.

DNA damage in plant herbarium tissue.

Staats M, Cuenca A, Richardson JE, Vrielink-van Ginkel R, Petersen G, Seberg O, Bakker FT.

PLoS One. 2011;6(12):e28448. doi: 10.1371/journal.pone.0028448. Epub 2011 Dec 5.

17.

Statistical evidence for miscoding lesions in ancient DNA templates.

Hansen A, Willerslev E, Wiuf C, Mourier T, Arctander P.

Mol Biol Evol. 2001 Feb;18(2):262-5. No abstract available.

PMID:
11158385
18.

Analysis of high-throughput ancient DNA sequencing data.

Kircher M.

Methods Mol Biol. 2012;840:197-228. doi: 10.1007/978-1-61779-516-9_23.

PMID:
22237537
19.

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.

Jónsson H, Ginolhac A, Schubert M, Johnson PL, Orlando L.

Bioinformatics. 2013 Jul 1;29(13):1682-4. doi: 10.1093/bioinformatics/btt193. Epub 2013 Apr 23.

20.

Evolution of endogenous retrovirus-like elements of the woolly mammoth (Mammuthus primigenius) and its relatives.

Greenwood AD, Lee F, Capelli C, DeSalle R, Tikhonov A, Marx PA, MacPhee RD.

Mol Biol Evol. 2001 May;18(5):840-7.

PMID:
11319267

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