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1
ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes
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ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

Antimicrobial Agents and Chemotherapy, 2014-01, Vol.58 (1), p.212-220 [Peer Reviewed Journal]

2015 INIST-CNRS ;Copyright © 2014, American Society for Microbiology. All Rights Reserved. ;Distributed under a Creative Commons Attribution 4.0 International License ;Copyright © 2014, American Society for Microbiology. All Rights Reserved. 2014 American Society for Microbiology ;ISSN: 0066-4804 ;EISSN: 1098-6596 ;DOI: 10.1128/aac.01310-13 ;PMID: 24145532 ;CODEN: AACHAX

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2
Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations
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Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

Nature reviews. Microbiology, 2018-10, Vol.16 (10), p.629-645 [Peer Reviewed Journal]

COPYRIGHT 2018 Nature Publishing Group ;Copyright Nature Publishing Group Oct 2018 ;ISSN: 1740-1526 ;EISSN: 1740-1534 ;DOI: 10.1038/s41579-018-0076-2 ;PMID: 30181663

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3
Integrated evolutionary analysis reveals antimicrobial peptides with limited resistance
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Integrated evolutionary analysis reveals antimicrobial peptides with limited resistance

Nature communications, 2019-10, Vol.10 (1), p.4538-13, Article 4538 [Peer Reviewed Journal]

2019. 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. ;The Author(s) 2019 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-019-12364-6 ;PMID: 31586049

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4
Bacterial phylogeny structures soil resistomes across habitats
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Bacterial phylogeny structures soil resistomes across habitats

Nature (London), 2014-05, Vol.509 (7502), p.612-616 [Peer Reviewed Journal]

COPYRIGHT 2014 Nature Publishing Group ;COPYRIGHT 2014 Nature Publishing Group ;Copyright Nature Publishing Group May 29, 2014 ;ISSN: 0028-0836 ;EISSN: 1476-4687 ;DOI: 10.1038/nature13377 ;PMID: 24847883 ;CODEN: NATUAS

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5
Proksee: in-depth characterization and visualization of bacterial genomes
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Proksee: in-depth characterization and visualization of bacterial genomes

Nucleic acids research, 2023-07, Vol.51 (W1), p.W484-W492 [Peer Reviewed Journal]

The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. 2023 ;The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkad326 ;PMID: 37140037

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6
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
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antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Nucleic acids research, 2019-07, Vol.47 (W1), p.W81-W87 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 ;Wageningen University & Research ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkz310 ;PMID: 31032519

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7
The distinction of CPR bacteria from other bacteria based on protein family content
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The distinction of CPR bacteria from other bacteria based on protein family content

Nature communications, 2019-09, Vol.10 (1), p.4173-12, Article 4173 [Peer Reviewed Journal]

2019. 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 U.S.; foreign copyright protection may apply 2019 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-019-12171-z ;PMID: 31519891

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8
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Nucleic acids research, 2015-02, Vol.43 (3), p.e15-e15 [Peer Reviewed Journal]

The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. 2015 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gku1196 ;PMID: 25414349

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9
VFDB 2019: a comparative pathogenomic platform with an interactive web interface
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VFDB 2019: a comparative pathogenomic platform with an interactive web interface

Nucleic acids research, 2019-01, Vol.47 (D1), p.D687-D692 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gky1080 ;PMID: 30395255

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10
Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome
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Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome

Molecular cell, 2019-05, Vol.74 (3), p.481-493.e6 [Peer Reviewed Journal]

2019 Elsevier Inc. ;Copyright © 2019 Elsevier Inc. All rights reserved. ;ISSN: 1097-2765 ;ISSN: 1097-4164 ;EISSN: 1097-4164 ;DOI: 10.1016/j.molcel.2019.02.017 ;PMID: 30904393

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11
metaSPAdes: a new versatile metagenomic assembler
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metaSPAdes: a new versatile metagenomic assembler

Genome research, 2017-05, Vol.27 (5), p.824-834 [Peer Reviewed Journal]

2017 Nurk et al.; Published by Cold Spring Harbor Laboratory Press. ;2017 ;ISSN: 1088-9051 ;EISSN: 1549-5469 ;DOI: 10.1101/gr.213959.116 ;PMID: 28298430

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12
GenBank
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GenBank

Nucleic acids research, 2017-01, Vol.45 (D1), p.D37-D42 [Peer Reviewed Journal]

Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. ;Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. 2017 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkw1070 ;PMID: 27899564

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13
NCBI prokaryotic genome annotation pipeline
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NCBI prokaryotic genome annotation pipeline

Nucleic acids research, 2016-08, Vol.44 (14), p.6614-6624 [Peer Reviewed Journal]

Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. ;Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. 2016 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkw569 ;PMID: 27342282

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14
MIBiG 2.0: a repository for biosynthetic gene clusters of known function
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MIBiG 2.0: a repository for biosynthetic gene clusters of known function

Nucleic acids research, 2020-01, Vol.48 (D1), p.D454-D458 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 ;The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkz882 ;PMID: 31612915

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15
A human gut microbial gene catalogue established by metagenomic sequencing
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A human gut microbial gene catalogue established by metagenomic sequencing

Nature (London), 2010-03, Vol.464 (7285), p.59-65 [Peer Reviewed Journal]

2015 INIST-CNRS ;COPYRIGHT 2010 Nature Publishing Group ;COPYRIGHT 2010 Nature Publishing Group ;Copyright Nature Publishing Group Mar 4, 2010 ;Attribution - NonCommercial - ShareAlike ;Wageningen University & Research ;ISSN: 0028-0836 ;EISSN: 1476-4687 ;DOI: 10.1038/nature08821 ;PMID: 20203603 ;CODEN: NATUAS

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16
Genealogical inference and more flexible sequence clustering using iterative-PopPUNK
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Genealogical inference and more flexible sequence clustering using iterative-PopPUNK

Genome research, 2023-06, Vol.33 (6), p.988-998 [Peer Reviewed Journal]

2023 Zhao et al.; Published by Cold Spring Harbor Laboratory Press. ;2023 ;ISSN: 1088-9051 ;EISSN: 1549-5469 ;DOI: 10.1101/gr.277395.122 ;PMID: 37253539

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17
Horizontal gene transfer and adaptive evolution in bacteria
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Horizontal gene transfer and adaptive evolution in bacteria

Nature reviews. Microbiology, 2022-04, Vol.20 (4), p.206-218 [Peer Reviewed Journal]

2021. Springer Nature Limited. ;Springer Nature Limited 2021. ;ISSN: 1740-1526 ;EISSN: 1740-1534 ;DOI: 10.1038/s41579-021-00650-4 ;PMID: 34773098

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18
Synthetic bacterial genome upgraded for viral defence and biocontainment
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Synthetic bacterial genome upgraded for viral defence and biocontainment

Nature (London), 2023-03, Vol.615 (7953), p.592-594 [Peer Reviewed Journal]

ISSN: 0028-0836 ;EISSN: 1476-4687 ;DOI: 10.1038/d41586-023-00702-0 ;PMID: 36922657

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19
Diversity and evolution of class 2 CRISPR-Cas systems
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Diversity and evolution of class 2 CRISPR-Cas systems

Nature reviews. Microbiology, 2017-03, Vol.15 (3), p.169-182 [Peer Reviewed Journal]

COPYRIGHT 2017 Nature Publishing Group ;Copyright Nature Publishing Group Mar 2017 ;ISSN: 1740-1526 ;EISSN: 1740-1534 ;DOI: 10.1038/nrmicro.2016.184 ;PMID: 28111461

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20
Database Resources of the National Center for Biotechnology Information
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Database Resources of the National Center for Biotechnology Information

Nucleic acids research, 2017-01, Vol.45 (D1), p.D12-D17 [Peer Reviewed Journal]

Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. ;Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US. 2017 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkw1071 ;PMID: 27899561

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