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1
The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
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The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

Genome research, 2020-01, Vol.30 (1), p.138-152 [Peer Reviewed Journal]

2020 Zhou et al.; Published by Cold Spring Harbor Laboratory Press. ;Copyright Cold Spring Harbor Laboratory Press Jan 2020 ;Attribution ;2020 ;ISSN: 1088-9051 ;EISSN: 1549-5469 ;DOI: 10.1101/gr.251678.119 ;PMID: 31809257

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2
Critical Assessment of Metagenome Interpretation: the second round of challenges
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Critical Assessment of Metagenome Interpretation: the second round of challenges

Nature methods, 2022-04, Vol.19 (4), p.429-440 [Peer Reviewed Journal]

2022. The Author(s). ;The Author(s) 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;info:eu-repo/semantics/openAccess ;Attribution ;The Author(s) 2022 ;ISSN: 1548-7091 ;ISSN: 1548-7105 ;EISSN: 1548-7105 ;DOI: 10.1038/s41592-022-01431-4 ;PMID: 35396482

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3
Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics
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Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

Nature communications, 2021-05, Vol.12 (1), p.3209-3209, Article 3209 [Peer Reviewed Journal]

This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Distributed under a Creative Commons Attribution 4.0 International License ;This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-021-23553-7 ;PMID: 34050180

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4
Quality control of microbiota metagenomics by k-mer analysis
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Quality control of microbiota metagenomics by k-mer analysis

BMC genomics, 2015-03, Vol.16 (1), p.183-183, Article 183 [Peer Reviewed Journal]

COPYRIGHT 2015 BioMed Central Ltd. ;COPYRIGHT 2015 BioMed Central Ltd. ;Attribution ;Plaza Onate et al.; licensee BioMed Central. 2015 ;ISSN: 1471-2164 ;EISSN: 1471-2164 ;DOI: 10.1186/s12864-015-1406-7 ;PMID: 25887914

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5
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
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Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

Environmental microbiology, 2014-09, Vol.16 (9), p.2659-2671 [Peer Reviewed Journal]

2013 Society for Applied Microbiology and John Wiley & Sons Ltd ;2013 Society for Applied Microbiology and John Wiley & Sons Ltd. ;Copyright © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd ;Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 1462-2912 ;EISSN: 1462-2920 ;DOI: 10.1111/1462-2920.12250 ;PMID: 24102695

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6
STRONG: metagenomics strain resolution on assembly graphs
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STRONG: metagenomics strain resolution on assembly graphs

Genome Biology, 2021-07, Vol.22 (1), p.214-214, Article 214 [Peer Reviewed Journal]

2021. The Author(s). ;2021. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Distributed under a Creative Commons Attribution 4.0 International License ;The Author(s) 2021 ;ISSN: 1474-760X ;ISSN: 1474-7596 ;ISSN: 1465-6906 ;EISSN: 1474-760X ;DOI: 10.1186/s13059-021-02419-7 ;PMID: 34311761

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7
Storage conditions of intestinal microbiota matter in metagenomic analysis
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Storage conditions of intestinal microbiota matter in metagenomic analysis

BMC microbiology, 2012-07, Vol.12 (1), p.158-158, Article 158 [Peer Reviewed Journal]

COPYRIGHT 2012 BioMed Central Ltd. ;COPYRIGHT 2012 BioMed Central Ltd. ;2012 Cardona et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. ;Distributed under a Creative Commons Attribution 4.0 International License ;Copyright ©2012 Cardona et al.; licensee BioMed Central Ltd. 2012 Cardona et al.; licensee BioMed Central Ltd. ;ISSN: 1471-2180 ;EISSN: 1471-2180 ;DOI: 10.1186/1471-2180-12-158 ;PMID: 22846661

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8
Viruses of archaea: Structural, functional, environmental and evolutionary genomics
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Viruses of archaea: Structural, functional, environmental and evolutionary genomics

Virus research, 2018-01, Vol.244, p.181-193 [Peer Reviewed Journal]

Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 0168-1702 ;EISSN: 1872-7492 ;DOI: 10.1016/j.virusres.2017.11.025 ;PMID: 29175107

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9
Exploring the Archaeal Virosphere by Metagenomics
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Exploring the Archaeal Virosphere by Metagenomics

Viral Metagenomics, 2024, Vol.2732, p.1-22

Attribution - NonCommercial ;ISBN: 9781071635148 ;ISBN: 107163514X ;DOI: 10.1007/978-1-0716-3515-5_1 ;PMID: 38060114

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10
In-depth resistome analysis by targeted metagenomics
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In-depth resistome analysis by targeted metagenomics

Microbiome, 2018-01, Vol.6 (1), p.11-11, Article 11 [Peer Reviewed Journal]

COPYRIGHT 2018 BioMed Central Ltd. ;Attribution ;The Author(s). 2018 ;ISSN: 2049-2618 ;EISSN: 2049-2618 ;DOI: 10.1186/s40168-017-0387-y ;PMID: 29335005

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11
Reproducible protocols for metagenomic analysis of human faecal phageomes
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Article
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Reproducible protocols for metagenomic analysis of human faecal phageomes

Microbiome, 2018-04, Vol.6 (1), p.68-68, Article 68 [Peer Reviewed Journal]

COPYRIGHT 2018 BioMed Central Ltd. ;Attribution ;The Author(s). 2018 ;ISSN: 2049-2618 ;EISSN: 2049-2618 ;DOI: 10.1186/s40168-018-0446-z ;PMID: 29631623

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12
Strainberry: automated strain separation in low-complexity metagenomes using long reads
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Strainberry: automated strain separation in low-complexity metagenomes using long reads

Nature communications, 2021-07, Vol.12 (1), p.4485-4485, Article 4485 [Peer Reviewed Journal]

2021. The Author(s). ;The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Attribution ;The Author(s) 2021 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-021-24515-9 ;PMID: 34301928

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13
Messages from the third International Conference on Clinical Metagenomics (ICCMg3)
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Article
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Messages from the third International Conference on Clinical Metagenomics (ICCMg3)

Microbes and infection, 2019-08, Vol.21, p.273-277 [Peer Reviewed Journal]

Attribution - NonCommercial ;ISSN: 1286-4579 ;EISSN: 1769-714X ;DOI: 10.1016/j.micinf.2019.02.004 ;PMID: 30836173

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14
Marine DNA Viral Macro- and Microdiversity from Pole to Pole
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Article
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Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Cell, 2019-05, Vol.177 (5), p.1109-1123.e14 [Peer Reviewed Journal]

2019 Elsevier Inc. ;Copyright © 2019 Elsevier Inc. All rights reserved. ;Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 0092-8674 ;EISSN: 1097-4172 ;DOI: 10.1016/j.cell.2019.03.040 ;PMID: 31031001

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15
Megataxonomy and global ecology of the virosphere
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Article
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Megataxonomy and global ecology of the virosphere

The ISME Journal, 2024-01, Vol.18 (1) [Peer Reviewed Journal]

Attribution ;ISSN: 1751-7362 ;EISSN: 1751-7370 ;DOI: 10.1093/ismejo/wrad042

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16
MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics
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MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics

Molecular ecology resources, 2020-07, Vol.20, p.892-905 [Peer Reviewed Journal]

Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 1755-098X ;EISSN: 1755-0998 ;DOI: 10.1111/1755-0998.13160

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17
MINTIA: a metagenomic INserT integrated assembly and annotation tool
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MINTIA: a metagenomic INserT integrated assembly and annotation tool

PeerJ (San Francisco, CA), 2021-09, Vol.9, p.e11885-e11885, Article e11885 [Peer Reviewed Journal]

2021 Bardou et al. ;COPYRIGHT 2021 PeerJ. Ltd. ;2021 Bardou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Attribution ;2021 Bardou et al. 2021 Bardou et al. ;ISSN: 2167-8359 ;EISSN: 2167-8359 ;DOI: 10.7717/peerj.11885 ;PMID: 34692239

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18
Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing
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Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing

Viruses, 2023-01, Vol.15 (1), p.76 [Peer Reviewed Journal]

2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Distributed under a Creative Commons Attribution 4.0 International License ;2022 by the authors. 2022 ;ISSN: 1999-4915 ;EISSN: 1999-4915 ;DOI: 10.3390/v15010076 ;PMID: 36680116

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19
Marine Synechococcus picocyanobacteria: Light utilization across latitudes
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Article
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Marine Synechococcus picocyanobacteria: Light utilization across latitudes

Proceedings of the National Academy of Sciences - PNAS, 2021-09, Vol.118 (38) [Peer Reviewed Journal]

Copyright National Academy of Sciences Sep 21, 2021 ;Distributed under a Creative Commons Attribution 4.0 International License ;2021 ;ISSN: 0027-8424 ;EISSN: 1091-6490 ;DOI: 10.1073/pnas.2111300118 ;PMID: 34518213

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20
Characterisation of the Viral Community Associated with the Alfalfa Weevil ( Hypera postica ) and Its Host Plant, Alfalfa ( Medicago sativa )
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Article
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Characterisation of the Viral Community Associated with the Alfalfa Weevil ( Hypera postica ) and Its Host Plant, Alfalfa ( Medicago sativa )

Viruses, 2021-04, Vol.13 (5), p.791 [Peer Reviewed Journal]

2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;Attribution ;2021 by the authors. 2021 ;ISSN: 1999-4915 ;EISSN: 1999-4915 ;DOI: 10.3390/v13050791 ;PMID: 33925168

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