Skip to content

Update introduction-to-edna.bib #108

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Sep 10, 2024
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
219 changes: 188 additions & 31 deletions assets/references/introduction-to-edna.bib
Original file line number Diff line number Diff line change
@@ -1,33 +1,3 @@
@article{Unknown2024-lw,
title = {Using {DNA} archived in lake sediments to reconstruct past
ecosystems},
publisher = {Elsevier},
abstract = {Ecosystems are continuously responding to both natural and
anthropogenic environmental change. Lake sediments preserve local
and global evidence of th…},
month = jan,
year = 2024,
url = {http://dx.doi.org/10.1016/B978-0-323-99931-1.00171-9},
doi = {10.1016/B978-0-323-99931-1.00171-9}
}

@article{Unknown2020-ht,
title = {Geochemical identification of potential {DNA}-hotspots and
{DNA}-infrared fingerprints in lake sediments},
journal = {Applied Geochemistry},
publisher = {Pergamon},
volume = 122,
pages = 104728,
abstract = {DNA preserved in sedimentary materials can be used to study past
ecosystem changes, such as species' colonization and extinction.
It is believed that …},
month = nov,
year = 2020,
url = {http://dx.doi.org/10.1016/j.apgeochem.2020.104728},
doi = {10.1016/j.apgeochem.2020.104728},
issn = {0883-2927}
}

@article{Jia2022-vv,
title = {Preservation of sedimentary plant {DNA} is related to lake water
chemistry},
Expand Down Expand Up @@ -785,4 +755,191 @@ @article{Jenkins2012-ac
pmid = 22798611,
issn = {0036-8075,1095-9203}
}

@article{Pedersen2015,
title={Ancient and modern environmental DNA},
author={Pedersen, Mikkel Winther and Overballe-Petersen, S{\o}ren and Ermini, Luca and Sarkissian, Clio Der and Haile, James and Hellstrom, Micaela and Spens, Johan and Thomsen, Philip Francis and Bohmann, Kristine and Cappellini, Enrico and others},
journal={Philosophical Transactions of the Royal Society B: Biological Sciences},
volume={370},
number={1660},
pages={20130383},
year={2015},
publisher={The Royal Society}
}
@article{Orlando2021,
title={Ancient DNA analysis},
author={Orlando, Ludovic and Allaby, Robin and Skoglund, Pontus and Der Sarkissian, Clio and Stockhammer, Philipp W and {\'A}vila-Arcos, Mar{\'\i}a C and Fu, Qiaomei and Krause, Johannes and Willerslev, Eske and Stone, Anne C and others},
journal={Nature reviews methods primers},
volume={1},
number={1},
pages={14},
year={2021},
publisher={Nature Publishing Group UK London}
}
@incollection{Murchie2023,
title={Terrestrial Fauna and Hominin DNA from Sedimentary Archives},
author={Murchie, Tyler J and Giguet-Covex, Charline and Heintzman, Peter D and Slon, Viviane and Wang, Yucheng},
booktitle={Tracking Environmental Change Using Lake Sediments: Volume 6: Sedimentary DNA},
pages={299--378},
year={2023},
publisher={Springer}
}
@article{Capo2021,
title={Lake sedimentary DNA research on past terrestrial and aquatic biodiversity: Overview and recommendations},
author={Capo, Eric and Giguet-Covex, Charline and Rouillard, Alexandra and Nota, Kevin and Heintzman, Peter D and Vuillemin, Aur{\`e}le and Ariztegui, Daniel and Arnaud, Fabien and Belle, Simon and Bertilsson, Stefan and others},
journal={Quaternary},
volume={4},
number={1},
pages={6},
year={2021},
publisher={MDPI}
}
@article{Sand2024,
title={Importance of eDNA taphonomy and sediment provenance for robust ecological inference: Insights from interfacial geochemistry},
author={Sand, KK and Jelavi{\'c}, S and Kj{\ae}r, KH and Prohaska, A},
journal={Environmental DNA},
volume={6},
number={2},
pages={e519},
year={2024},
publisher={Wiley Online Library}
}
@incollection{Garces2023,
title={Terrestrial plant DNA from lake sediments},
author={Garc{\'e}s-Pastor, Sandra and Nota, Kevin and Rijal, Dilli P and Liu, Sisi and Jia, Weihan and Leunda, Maria and Schw{\"o}rer, Christoph and Crump, Sarah E and Parducci, Laura and Alsos, Inger G},
booktitle={Tracking Environmental Change Using Lake Sediments: Volume 6: Sedimentary DNA},
pages={275--298},
year={2023},
publisher={Springer}
}
@article{Torti2015,
title={Origin, dynamics, and implications of extracellular DNA pools in marine sediments},
author={Torti, Andrea and Lever, Mark Alexander and J{\o}rgensen, Bo Barker},
journal={Marine genomics},
volume={24},
pages={185--196},
year={2015},
publisher={Elsevier}
}
@article{Stotzky2000,
title={Persistence and biological activity in soil of insecticidal proteins from Bacillus thuringiensis and of bacterial DNA bound on clays and humic acids},
author={Stotzky, G},
journal={Journal of Environmental Quality},
volume={29},
number={3},
pages={691--705},
year={2000},
publisher={Wiley Online Library}
}
@article{Lorenz1987,
title={Adsorption of DNA to sand and variable degradation rates of adsorbed DNA},
author={Lorenz, MICHAEL G and Wackernagel, WILFRIED},
journal={Applied and environmental microbiology},
volume={53},
number={12},
pages={2948--2952},
year={1987},
publisher={Am Soc Microbiol}
}
@article{Lorenz1981,
title={Interaction of marine sediment with DNA and DNA availability to nucleases},
author={Lorenz, MG and Aardema, BW and Krumbein, WE},
journal={Marine Biology},
volume={64},
pages={225--230},
year={1981},
publisher={Springer}
}
@article{Beall2009,
title={Analysis of oligonucleotide DNA binding and sedimentation properties of montmorillonite clay using ultraviolet light spectroscopy},
author={Beall, Gary W and Sowersby, Drew S and Roberts, Rachel D and Robson, Michael H and Lewis, L Kevin},
journal={Biomacromolecules},
volume={10},
number={1},
pages={105--112},
year={2009},
publisher={ACS Publications}
}
@article{Armbrecht2020,
title={An optimized method for the extraction of ancient eukaryote DNA from marine sediments},
author={Armbrecht, Linda and Herrando-P{\'e}rez, Salvador and Eisenhofer, Raphael and Hallegraeff, Gustaaf M and Bolch, Christopher JS and Cooper, Alan},
journal={Molecular Ecology Resources},
volume={20},
number={4},
pages={906--919},
year={2020},
publisher={Wiley Online Library}
}
@article{Perez2022,
title={A case study for the recovery of authentic microbial ancient DNA from soil samples},
author={P{\'e}rez, Vilma and Liu, Yichen and Hengst, Martha B and Weyrich, Laura S},
journal={Microorganisms},
volume={10},
number={8},
pages={1623},
year={2022},
publisher={MDPI}
}
@incollection{Heintzman2023,
title={The sedimentary ancient DNA workflow},
author={Heintzman, Peter D and Nota, Kevin and Rouillard, Alexandra and Lammers, Youri and Murchie, Tyler J and Armbrecht, Linda and Garc{\'e}s-Pastor, Sandra and Vernot, Benjamin},
booktitle={Tracking Environmental Change Using Lake Sediments: Volume 6: Sedimentary DNA},
pages={53--84},
year={2023},
publisher={Springer}
}
@article{Murchie2021,
title={Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set},
author={Murchie, Tyler J and Kuch, Melanie and Duggan, Ana T and Ledger, Marissa L and Roche, Kevin and Klunk, Jennifer and Karpinski, Emil and Hackenberger, Dirk and Sadoway, Tara and MacPhee, Ross and others},
journal={Quaternary Research},
volume={99},
pages={305--328},
year={2021},
publisher={Cambridge University Press}
}
@article{Slon2017,
title={Neandertal and Denisovan DNA from Pleistocene sediments},
author={Slon, Viviane and Hopfe, Charlotte and Wei{\ss}, Clemens L and Mafessoni, Fabrizio and De La Rasilla, Marco and Lalueza-Fox, Carles and Rosas, Antonio and Soressi, Marie and Knul, Monika V and Miller, Rebecca and others},
journal={Science},
volume={356},
number={6338},
pages={605--608},
year={2017},
publisher={American Association for the Advancement of Science}
}
@article{Crump2021,
title={Sedimentary ancient DNA as a tool in paleoecology},
author={Crump, Sarah E},
journal={Nature Reviews Earth \& Environment},
volume={2},
number={4},
pages={229--229},
year={2021},
publisher={Nature Publishing Group UK London}
}
@article{Cribdon2020,
title={PIA: more accurate taxonomic assignment of metagenomic data demonstrated on sedaDNA from the North Sea},
author={Cribdon, Becky and Ware, Roselyn and Smith, Oliver and Gaffney, Vincent and Allaby, Robin G},
journal={Frontiers in Ecology and Evolution},
volume={8},
pages={84},
year={2020},
publisher={Frontiers Media SA}
}
@incollection{Vuillemin2023,
title={Bacterial and archaeal DNA from lake sediments},
author={Vuillemin, Aur{\`e}le and Coolen, Marco JL and Kallmeyer, Jens and Liebner, Susanne and Bertilsson, Stefan},
booktitle={Tracking Environmental Change Using Lake Sediments: Volume 6: Sedimentary DNA},
pages={85--151},
year={2023},
publisher={Springer}
}
@article{Schulte2021,
title={Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest},
author={Schulte, Luise and Bernhardt, Nadine and Stoof-Leichsenring, Kathleen and Zimmermann, Heike H and Pestryakova, Luidmila A and Epp, Laura S and Herzschuh, Ulrike},
journal={Molecular Ecology Resources},
volume={21},
number={3},
pages={801--815},
year={2021},
publisher={Wiley Online Library}
}