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Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA.

Stiller M, Sucker A, Griewank K, Aust D, Baretton GB, Schadendorf D, Horn S.

Oncotarget. 2016 Sep 13;7(37):59115-59128. doi: 10.18632/oncotarget.10827.


Detecting hybridization using ancient DNA.

Schaefer NK, Shapiro B, Green RE.

Mol Ecol. 2016 Jun;25(11):2398-412. doi: 10.1111/mec.13556. Epub 2016 Mar 23. Review.


Gourds and squashes (Cucurbita spp.) adapted to megafaunal extinction and ecological anachronism through domestication.

Kistler L, Newsom LA, Ryan TM, Clarke AC, Smith BD, Perry GH.

Proc Natl Acad Sci U S A. 2015 Dec 8;112(49):15107-12. doi: 10.1073/pnas.1516109112. Epub 2015 Nov 16.


Molecular analysis of ancient caries.

Simón M, Montiel R, Smerling A, Solórzano E, Díaz N, Álvarez-Sandoval BA, Jiménez-Marín AR, Malgosa A.

Proc Biol Sci. 2014 Sep 7;281(1790). pii: 20140586. doi: 10.1098/rspb.2014.0586.


Genotyping of ancient Mycobacterium tuberculosis strains reveals historic genetic diversity.

Müller R, Roberts CA, Brown TA.

Proc Biol Sci. 2014 Feb 26;281(1781):20133236. doi: 10.1098/rspb.2013.3236. Print 2014 Apr 22.


Ancient DNA damage.

Dabney J, Meyer M, Pääbo S.

Cold Spring Harb Perspect Biol. 2013 Jul 1;5(7). pii: a012567. doi: 10.1101/cshperspect.a012567. Review.


Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM.

Retrovirology. 2013 Feb 13;10:18. doi: 10.1186/1742-4690-10-18.


PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data.

Weissbrodt DG, Shani N, Sinclair L, Lefebvre G, Rossi P, Maillard J, Rougemont J, Holliger C.

BMC Microbiol. 2012 Dec 27;12:306. doi: 10.1186/1471-2180-12-306.


High potential for using DNA from ancient herring bones to inform modern fisheries management and conservation.

Speller CF, Hauser L, Lepofsky D, Moore J, Rodrigues AT, Moss ML, McKechnie I, Yang DY.

PLoS One. 2012;7(11):e51122. doi: 10.1371/journal.pone.0051122. Epub 2012 Nov 30. Erratum in: PLoS One. 2013;8(6). doi: 10.1371/annotation/cd8623ff-b708-4972-8d59-803e56e77005.


Reconstructing the history of a fragmented and heavily exploited red deer population using ancient and contemporary DNA.

Rosvold J, Røed KH, Hufthammer AK, Andersen R, Stenøien HK.

BMC Evol Biol. 2012 Sep 26;12:191. doi: 10.1186/1471-2148-12-191.


Heat degradation of eukaryotic and bacterial DNA: an experimental model for paleomicrobiology.

Nguyen-Hieu T, Aboudharam G, Drancourt M.

BMC Res Notes. 2012 Sep 25;5:528. doi: 10.1186/1756-0500-5-528.


Earliest Mexican Turkeys (Meleagris gallopavo) in the Maya Region: implications for pre-Hispanic animal trade and the timing of turkey domestication.

Thornton EK, Emery KF, Steadman DW, Speller C, Matheny R, Yang D.

PLoS One. 2012;7(8):e42630. doi: 10.1371/journal.pone.0042630. Epub 2012 Aug 8.


Improving ancient DNA read mapping against modern reference genomes.

Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KA, Willerslev E, Krogh A, Orlando L.

BMC Genomics. 2012 May 10;13:178. doi: 10.1186/1471-2164-13-178.


MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.

Ranwez V, Harispe S, Delsuc F, Douzery EJ.

PLoS One. 2011;6(9):e22594. doi: 10.1371/journal.pone.0022594. Epub 2011 Sep 16.


True single-molecule DNA sequencing of a pleistocene horse bone.

Orlando L, Ginolhac A, Raghavan M, Vilstrup J, Rasmussen M, Magnussen K, Steinmann KE, Kapranov P, Thompson JF, Zazula G, Froese D, Moltke I, Shapiro B, Hofreiter M, Al-Rasheid KA, Gilbert MT, Willerslev E.

Genome Res. 2011 Oct;21(10):1705-19. doi: 10.1101/gr.122747.111. Epub 2011 Jul 29.


Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects.

Thèves C, Senescau A, Vanin S, Keyser C, Ricaut FX, Alekseev AN, Dabernat H, Ludes B, Fabre R, Crubézy E.

PLoS One. 2011;6(7):e21733. doi: 10.1371/journal.pone.0021733. Epub 2011 Jul 13.


To clone or not to clone: method analysis for retrieving consensus sequences in ancient DNA samples.

Winters M, Barta JL, Monroe C, Kemp BM.

PLoS One. 2011;6(6):e21247. doi: 10.1371/journal.pone.0021247. Epub 2011 Jun 27.


Ancient DNA suggests dwarf and 'giant' emu are conspecific.

Heupink TH, Huynen L, Lambert DM.

PLoS One. 2011 Apr 11;6(4):e18728. doi: 10.1371/journal.pone.0018728.


Accurate determination of phenotypic information from historic thoroughbred horses by single base extension.

Campana MG, Whitten CM, Edwards CJ, Stock F, Murphy AM, Binns MM, Barker GW, Bower MA.

PLoS One. 2010 Dec 2;5(12):e15172. doi: 10.1371/journal.pone.0015172.


The microcephalin ancestral allele in a Neanderthal individual.

Lari M, Rizzi E, Milani L, Corti G, Balsamo C, Vai S, Catalano G, Pilli E, Longo L, Condemi S, Giunti P, Hänni C, De Bellis G, Orlando L, Barbujani G, Caramelli D.

PLoS One. 2010 May 14;5(5):e10648. doi: 10.1371/journal.pone.0010648.

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