Literature DB >> 23729639

Ancient DNA damage.

Jesse Dabney1, Matthias Meyer, Svante Pääbo.   

Abstract

Under favorable conditions DNA can survive for thousands of years in the remains of dead organisms. The DNA extracted from such remains is invariably degraded to a small average size by processes that at least partly involve depurination. It also contains large amounts of deaminated cytosine residues that are accumulated toward the ends of the molecules, as well as several other lesions that are less well characterized.

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Year:  2013        PMID: 23729639      PMCID: PMC3685887          DOI: 10.1101/cshperspect.a012567

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  32 in total

1.  Statistical evidence for miscoding lesions in ancient DNA templates.

Authors:  A Hansen; E Willerslev; C Wiuf; T Mourier; P Arctander
Journal:  Mol Biol Evol       Date:  2001-02       Impact factor: 16.240

2.  Distribution patterns of postmortem damage in human mitochondrial DNA.

Authors:  M Thomas P Gilbert; Eske Willerslev; Anders J Hansen; Ian Barnes; Lars Rudbeck; Niels Lynnerup; Alan Cooper
Journal:  Am J Hum Genet       Date:  2002-12-12       Impact factor: 11.025

3.  Miocene DNA sequences - a dream come true?

Authors:  S Pääbo; A C Wilson
Journal:  Curr Biol       Date:  1991-02       Impact factor: 10.834

Review 4.  Genetic analyses from ancient DNA.

Authors:  Svante Pääbo; Hendrik Poinar; David Serre; Viviane Jaenicke-Despres; Juliane Hebler; Nadin Rohland; Melanie Kuch; Johannes Krause; Linda Vigilant; Michael Hofreiter
Journal:  Annu Rev Genet       Date:  2004       Impact factor: 16.830

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

Authors:  Ludovic Orlando; Aurelien Ginolhac; Maanasa Raghavan; Julia Vilstrup; Morten Rasmussen; Kim Magnussen; Kathleen E Steinmann; Philipp Kapranov; John F Thompson; Grant Zazula; Duane Froese; Ida Moltke; Beth Shapiro; Michael Hofreiter; Khaled A S Al-Rasheid; M Thomas P Gilbert; Eske Willerslev
Journal:  Genome Res       Date:  2011-07-29       Impact factor: 9.043

6.  Chloroplast DNA sequence from a miocene Magnolia species.

Authors:  E M Golenberg; D E Giannasi; M T Clegg; C J Smiley; M Durbin; D Henderson; G Zurawski
Journal:  Nature       Date:  1990-04-12       Impact factor: 49.962

7.  Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid.

Authors:  T Lindahl; A Andersson
Journal:  Biochemistry       Date:  1972-09-12       Impact factor: 3.162

Review 8.  The potential and challenges of nanopore sequencing.

Authors:  Daniel Branton; David W Deamer; Andre Marziali; Hagan Bayley; Steven A Benner; Thomas Butler; Massimiliano Di Ventra; Slaven Garaj; Andrew Hibbs; Xiaohua Huang; Stevan B Jovanovich; Predrag S Krstic; Stuart Lindsay; Xinsheng Sean Ling; Carlos H Mastrangelo; Amit Meller; John S Oliver; Yuriy V Pershin; J Michael Ramsey; Robert Riehn; Gautam V Soni; Vincent Tabard-Cossa; Meni Wanunu; Matthew Wiggin; Jeffery A Schloss
Journal:  Nat Biotechnol       Date:  2008-10       Impact factor: 54.908

9.  DNA damage and DNA sequence retrieval from ancient tissues.

Authors:  M Höss; P Jaruga; T H Zastawny; M Dizdaroglu; S Pääbo
Journal:  Nucleic Acids Res       Date:  1996-04-01       Impact factor: 16.971

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

Authors:  M Thomas P Gilbert; Jonas Binladen; Webb Miller; Carsten Wiuf; Eske Willerslev; Hendrik Poinar; John E Carlson; James H Leebens-Mack; Stephan C Schuster
Journal:  Nucleic Acids Res       Date:  2006-08-18       Impact factor: 16.971

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  93 in total

1.  Ancient mtDNA sequences from the First Australians revisited.

Authors:  Tim H Heupink; Sankar Subramanian; Joanne L Wright; Phillip Endicott; Michael Carrington Westaway; Leon Huynen; Walther Parson; Craig D Millar; Eske Willerslev; David M Lambert
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-06       Impact factor: 11.205

2.  Himalayan 'yeti' DNA: polar bear or DNA degradation? A comment on 'Genetic analysis of hair samples attributed to yeti' by Sykes et al. (2014).

Authors:  C J Edwards; R Barnett
Journal:  Proc Biol Sci       Date:  2015-02-07       Impact factor: 5.349

3.  Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA.

Authors:  Laura Parducci; Minna Väliranta; J Sakari Salonen; Tiina Ronkainen; Irina Matetovici; Sonia L Fontana; Tiina Eskola; Pertti Sarala; Yoshihisa Suyama
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2015-01-19       Impact factor: 6.237

4.  Screening ancient tuberculosis with qPCR: challenges and opportunities.

Authors:  Kelly M Harkins; Jane E Buikstra; Tessa Campbell; Kirsten I Bos; Eric D Johnson; Johannes Krause; Anne C Stone
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2015-01-19       Impact factor: 6.237

5.  Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids.

Authors:  Clio Der Sarkissian; Julia T Vilstrup; Mikkel Schubert; Andaine Seguin-Orlando; David Eme; Jacobo Weinstock; Maria Teresa Alberdi; Fabiana Martin; Patricio M Lopez; Jose L Prado; Alfredo Prieto; Christophe J Douady; Tom W Stafford; Eske Willerslev; Ludovic Orlando
Journal:  Biol Lett       Date:  2015-03       Impact factor: 3.703

Review 6.  Inference of population history using coalescent HMMs: review and outlook.

Authors:  Jeffrey P Spence; Matthias Steinrücken; Jonathan Terhorst; Yun S Song
Journal:  Curr Opin Genet Dev       Date:  2018-07-26       Impact factor: 5.578

7.  Dynamics of Escherichia coli type I-E CRISPR spacers over 42 000 years.

Authors:  Ekaterina Savitskaya; Anna Lopatina; Sofia Medvedeva; Mikhail Kapustin; Sergey Shmakov; Alexey Tikhonov; Irena I Artamonova; Maria Logacheva; Konstantin Severinov
Journal:  Mol Ecol       Date:  2017-01-17       Impact factor: 6.185

8.  Fossil and genomic evidence constrains the timing of bison arrival in North America.

Authors:  Duane Froese; Mathias Stiller; Peter D Heintzman; Alberto V Reyes; Grant D Zazula; André E R Soares; Matthias Meyer; Elizabeth Hall; Britta J L Jensen; Lee J Arnold; Ross D E MacPhee; Beth Shapiro
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-13       Impact factor: 11.205

9.  Efficiently inferring the demographic history of many populations with allele count data.

Authors:  Jack Kamm; Jonathan Terhorst; Richard Durbin; Yun S Song
Journal:  J Am Stat Assoc       Date:  2019-07-22       Impact factor: 5.033

10.  Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year-old slides from the Ebro Delta in Spain.

Authors:  Pere Gelabert; Marcela Sandoval-Velasco; Iñigo Olalde; Rosa Fregel; Adrien Rieux; Raül Escosa; Carles Aranda; Krijn Paaijmans; Ivo Mueller; M Thomas P Gilbert; Carles Lalueza-Fox
Journal:  Proc Natl Acad Sci U S A       Date:  2016-09-26       Impact factor: 11.205

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