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all_papers.bib
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@article{dal:alt::gon:des:13,
author = {Dalquen, Daniel A. AND Altenhoff, Adrian M. AND
Gonnet, Gaston H. AND Dessimoz, Christophe},
journal = {PLOS ONE},
publisher = {Public Library of Science},
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Lateral Gene Transfer and Sequencing Error on Orthology
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year = {2013},
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}
@article{kuc:19,
author = {Kucherov, Gregory},
title = "{Evolution of biosequence search algorithms: a brief survey}",
year = {2019},
journal = "Bioinformatics",
volume = {btz272},
}
@article {zie:gir:ber:19,
author = {Zielezinski, Andrzej and Girgis, Hani Z and Bernard, Guillaume
and Leimeister, Chris-Andre and Tang, Kujin and Dencker, Thomas and Lau,
Anna Katharina and R{\"o}hling, Sophie and Choi, JaeJin and Waterman,
Michael S and
Comin, Matteo and Kim, Sung-Hou and Vinga, Susana and Almeida, Jonas S
and Chan, Cheong Xin and James, Benjamin and Sun, Fengzhu and Morgenstern, Burkhard and Karlowski, Wojciech M},
title = {Benchmarking of alignment-free sequence comparison methods},
year = {2019},
volume = {10.1101/611137},
doi = {10.1101/611137},
journal = {bioRxiv}
}
@Article{ski:rag:11,
author={Skippington, Elizabeth and Ragan, Mark A.},
title={{Within-species lateral genetic transfer and the evolution
of transcription al regulation in Escherichia coli and Shigella}},
journal={BMC Genomics},
year={2011},
volume={12},
pages={532},
}
@article{dar:mik:rag:08,
author = {Darling, Aaron E. AND Mikl{\'o}s, Istv{\'a}n AND Ragan, Mark A.},
journal = {PLOS Genetics},
publisher = {Public Library of Science},
title = {Dynamics of Genome Rearrangement in Bacterial Populations},
year = {2008},
volume = {4},
number = {7},
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@Article{chi:mil:19,
author={Chiu, Charles Y. and Miller, Steven A.},
title={Clinical metagenomics},
journal={Nature Reviews Genetics},
year={2019},
doi={10.1038/s41576-019-0113-7},
url={https://doi.org/10.1038/s41576-019-0113-7}
}
@Article{fis:kob:gue:14,
author={Fischer, Christoph
and Koblm{\"u}ller, Stephan
and G{\"u}lly, Christian
and Schl{\"o}tterer, Christian
and Sturmbauer, Christian
and Thallinger, Gerhard G.},
title={{Complete mitochondrial DNA sequences of the threadfin cichlid (Petrochromis trewavasae)
and the blunthead cichlid (Tropheus moorii) and patterns of mitochondrial genome evolution in cichlid fishes}},
journal={PLoS One},
year={2013},
publisher={Public Library of Science},
volume={8},
number={6},
pages={e67048-e67048},
}
@article{AFproject,
title = "http://150.254.120.147:7000/",
}
@INPROCEEDINGS{ klo:hau:18 ,
author = {Kl{\"o}tzl, Fabian and Haubold, Bernhard},
title = "Fast and Accurate Distance Computation from Unaligned Genomes",
booktitle = "Proceedings German Conference on Bioinformatics GCB'18,
Poster Abstracts",
year = "2018",
pages= ""}
@article{lu:tan:ren:17,
author = {Lu, Yang Young and Tang, Kujin and Ren, Jie and Fuhrman, Jed A.
and Waterman, Michael S. and Sun, Fengzhu},
title = "{CAFE: aCcelerated Alignment-FrEe sequence analysis}",
journal = {Nucleic Acids Research},
volume = {45},
pages = {W554-W559},
year = {2017},
}
@Article{cha:duf:edw:gir:05,
author="Chapus, Charles and Dufraigne, Christine and Edwards, Scott
and Giron, Alain and Fertil, Bernard and Deschavanne, Patrick",
title="Exploration of phylogenetic data using
a global sequence analysis method",
journal="BMC Evolutionary Biology",
year="2005",
volume="5",
pages="63",
}
@article{sch:pac:pim:bra:mel:17,
author = {Schaeffer, L and Pachter, L and Pimentel, H and Bray, N and Melsted, P},
title = "{Pseudoalignment for metagenomic read assignment}",
journal = {Bioinformatics},
volume = {33},
pages = {2082-2088},
year = {2017},
}
:q
@article{mch:gre:dro:14,
author = {McHardy, A. C. and Gregor, I. and Dr{\"o}ge, J.},
title = "{Taxator-tk: precise taxonomic assignment of metagenomes by fast ap
proximation of evolutionary neighborhoods}",
journal = {Bioinformatics},
volume = {31},
pages = {817-824},
year = {2014},
}
@article{dod:15,
title = "Genome skimming for next-generation biodiversity analysis",
journal = "Trends in Plant Science",
volume = "20",
pages = "525 - 527",
year = "2015",
author = "Steven Dodsworth",
}
@article{sch:ric:ble:15,
author = {Richter, Sandy and Schwarz, Francine and Hering, Lars and
B{\"o}ggemann, Markus and Bleidorn, Christoph},
title = "The Utility of Genome Skimming for Phylogenomic Analyses
as Demonstrated for Glycerid Relationships ({Annelida, Glyceridae})",
journal = {Genome Biology and Evolution},
volume = {7},
pages = {3443-3462},
year = {2015},
}
@article {mey:bre:bel:18,
author = {Meyer, Fernando and Bremges, Andreas and Belmann, Peter and Janssen, Stefan and McHardy, Alice Carolyn and Koslicki, David},
title = {Assessing taxonomic metagenome profilers with {OPAL}},
year = {2018},
volume = {10.1101/372680},
journal = {bioRxiv}
}
@Article{sar:boh:gil:19,
author="Sarmashghi, Shahab and Bohmann, Kristine and P. Gilbert, M. Thomas
and Bafna, Vineet and Mirarab, Siavash",
title="Skmer: assembly-free and alignment-free sample identification using genome skims",
journal="Genome Biology",
year="2019",
volume="20",
pages="34",
}
@article {wem:tay:dan:18,
author = {Wemheuer, Franziska and Taylor, Jessica A and Daniel, Rolf and Johnston, Emma and Meinicke, Peter and Thomas, Torsten and Wemheuer, Bernd},
title = {{Tax4Fun2}: a {R}-based tool for the rapid prediction of
habitat-specific functional profiles and functional redundancy
based on {16S rRNA} gene marker gene sequences},
year = {2018},
volume = {doi:10.1101/490037},
journal = {bioRxiv}
}
@article {bak:lan:19,
author = {Baker, Daniel N and Langmead, Ben},
title = {Dashing: Fast and Accurate Genomic Distances
with {HyperLogLog}},
volume = {doi:10.1101/501726},
year = {2019},
journal = {bioRxiv}
}
@article{erp:ste:sch:19,
author = {Erpenbeck, Dirk and Steiner, Markus and Schuster, Astrid and
Genner, Martin J. and Manconi, Renata and Pronzato, Roberto and
Ruthensteiner, Bernhard and van den Spiegel, Didier and van Soest, Rob W.M.
and W{\"o}rheide, Gert},
title = {Minimalist barcodes for sponges: a case study classifying
{A}frican freshwater {S}pongillida},
journal = {Genome},
volume = {62},
pages = {1-10},
year = {2019},
}
@article{li:yan:hen:15,
author = {Li, Xiwen and Yang, Yang and Henry, Robert J. and Rossetto,
Maurizio and Wang, Yitao and Chen, Shilin},
title = {Plant {DNA} barcoding: from gene to genome},
journal = {Biological Reviews},
volume = {90},
pages = {157-166},
year = {2015}
}
@article{lau:lei:mor:19,
author = {Anna Katharina Lau and Chris-Andr{\'e} Leimeister and Burkhard Morgenstern},
title = {{\em Read-SpaM}: assembly-free and alignment-free comparison
of bacterial genomes},
volume = {doi:10.1101/550632},
year = {2019},
journal = {bioRxiv},
}
@Article{kan:yan:lin:ye:19,
AUTHOR = {Kang, Yongyong and Yang, Xiaofei and Lin, Jiadong and Ye, Kai},
TITLE = {{PVTree}: A Sequential Pattern Mining Method for Alignment Independent Phylogeny Reconstruction},
JOURNAL = {Genes},
VOLUME = {10},
PAGES = 73,
YEAR = {2019},
}
@article{roe:den:mor:19,
author = {Sophie R{\"o}hling and Thomas Dencker and Burkhard Morgenstern},
title = {The number of $k$-mer matches between two {DNA} sequences
as a function of $k$},
volume = {doi:10.1101/527515},
year = {2019},
journal = {bioRxiv},
}
@article{roe:mor:19,
author = {Sophie R{\"o}hling and Thomas Dencker and Burkhard Morgenstern},
title = {The number of $k$-mer matches between two {DNA} sequences
as a function of $k$},
volume = {doi:10.1101/527515},
year = {2019},
journal = {bioRxiv},
}
@inproceedings{bro:00,
author = {Broder, Andrei Z.},
title = {Identifying and Filtering Near-Duplicate Documents},
booktitle = {Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching},
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year = {2000},
pages = {1--10},
publisher = {Springer-Verlag},
address = {Berlin, Heidelberg},
}
@Article{afl:sev:san:etal:15,
author="Aflitos, Saulo Alves and Severing, Edouard and Sanchez-Perez, Gabino
and Peters, Sander and de Jong, Hans and de Ridder, Dick",
title="Cnidaria: fast, reference-free clustering of raw and assembled
genome and transcriptome {NGS} data",
journal="BMC Bioinformatics",
year="2015",
volume="16",
pages="352",
}
@article{ahl:ren:lu:etal:17,
author = {Ahlgren, Nathan A. and Ren, Jie and Lu, Yang Young and Fuhrman,
Jed A. and Sun, Fengzhu},
title = {Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity
measure improves prediction of hosts from metagenomically-derived
viral sequences},
journal = {Nucleic Acids Research},
volume = {45},
pages = {39-53},
year = {2017},
}
@article {lin:swe:par:18,
author = {Linard, Benjamin and Swenson, Krister and Pardi, Fabio},
title = {Rapid alignment-free phylogenetic identification of
metagenomic sequences},
year = {2018},
doi = {10.1101/328740},
journal = {bioRxiv}
}
@article {lin:swe:par:19,
author = {Linard, Benjamin and Swenson, Krister and Pardi, Fabio},
title = {Rapid alignment-free phylogenetic identification of
metagenomic sequences},
year = {2019},
journal = {Bioinformatics},
volume = {btz068},
volume = {35},
}
@Article{zha:jun:leu:etal:17,
author={Zhang, Qian and Jun, Se-Ran and Leuze, Michael and Ussery, David
and Nookaew, Intawat},
title={Viral Phylogenomics Using an Alignment-Free Method: A Three-Step
Approach to Determine Optimal Length of $k$-mer},
journal={Scientific Reports},
year={2017},
volume={7},
pages={40712},
}
@article{kal:arg:qui:etal:18,
author = {Kalvari, Ioanna and Argasinska, Joanna and Quinones-Olvera,
Natalia and Nawrocki, Eric P and Rivas, Elena and Eddy,
Sean R and Bateman, Alex and Finn, Robert D and Petrov, Anton I},
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{RNA} families},
journal = {Nucleic Acids Research},
volume = {46},
pages = {D335-D342},
year = {2018},
}
@article{egi:man:14,
title = "Design and analysis of periodic multiple seeds",
journal = "Theoretical Computer Science",
volume = "522",
pages = "62 - 76",
year = "2014",
author = "Lavinia Egidi and Giovanni Manzini",
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@article {sar:boh:gil:etal:19,
author = {Sarmashghi, Shahab and Bohmann, Kristine and Gilbert, M. Thomas P. and Bafna, Vineet and Mirarab, Siavash},
title = {Assembly-free and alignment-free sample identification using genome skims},
year = {2019},
volume = {},
journal = {Genome Biology}
}
@article {sar:boh:gil:etal:17,
author = {Sarmashghi, Shahab and Bohmann, Kristine and Gilbert, M. Thomas P. and Bafna, Vineet and Mirarab, Siavash},
title = {Assembly-free and alignment-free sample identification using genome skims},
year = {2017},
volume = {10.1101/230409},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2017/12/08/230409},
journal = {bioRxiv}
}
@Article{den:bro:how:etal:16,
author={Denver, Dee R. and Brown, Amanda M. V. and Howe, Dana K.
and Peetz, Amy B. and Zasada, Inga A.},
title={{Genome Skimming}: A Rapid Approach to Gaining Diverse
Biological Insights into Multicellular Pathogens},
journal={PLoS Pathogens},
year={2016},
volume={12},
number={8},
pages={e1005713},
}
@manual{illumina,
url={https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet-hiseq-2500.pdf}
}
@article{benoit2016multiple,
title={Multiple comparative metagenomics using multiset k-mer counting},
author={Benoit, Ga{\"e}tan and Peterlongo, Pierre and Mariadassou, Mahendra and Drezen, Erwan and Schbath, Sophie and Lavenier, Dominique and Lemaitre, Claire},
journal={PeerJ Computer Science},
volume={2},
pages={e94},
year={2016},
publisher={PeerJ Inc.}
}
@article{ondov2016mash,
title={Mash: fast genome and metagenome distance estimation using MinHash},
author={Ondov, Brian D and Treangen, Todd J and Melsted, P{\'a}ll and Mallonee, Adam B and Bergman, Nicholas H and Koren, Sergey and Phillippy, Adam M},
journal={Genome Biology},
volume={17},
pages={132},
year={2016},
publisher={BioMed Central}
}
@article{huang2011art,
title={{ART}: a next-generation sequencing read simulator},
author={Huang, Weichun and Li, Leping and Myers, Jason R and Marth, Gabor T},
journal={Bioinformatics},
volume={28},
pages={593--594},
year={2011},
publisher={Oxford University Press}
}
@article{pfe:gro:bla:18,
title={Systematic evaluation of error rates and causes in short samples in next-generation sequencing},
author={Pfeiffer, Franziska and Gr{\"o}ber, Carsten and Blank, Michael and H{\"a}ndler, Kristian and Beyer, Marc and Schultze, Joachim L and Mayer, G{\"u}nter},
journal={Scientific Reports},
volume={8},
pages={10950},
year={2018},
publisher={Nature Publishing Group}
}
@article{gir:com:piz:18,
author="Girotto, Samuele and Comin, Matteo and Pizzi, Cinzia",
title="Efficient computation of spaced seed hashing with block indexing",
journal="BMC Bioinformatics",
year="2018",
volume="19",
number="Suppl 15",
pages="441",
}
@article{che:xu:lei:16,
author = {Cheng, Tao and Xu, Chao and Lei, Li and Li, Changhao and Zhang, Yu and Zhou, Shiliang},
title = {Barcoding the kingdom Plantae: new {PCR} primers for {ITS} regions of plants with improved universality and specificity},
journal = {Molecular Ecology Resources},
volume = {16},
year = {2016},
pages = {138-149},
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