<commit_before>.. _pyani-citations:

================
Citing ``pyani``
================

We would be grateful if you could please cite the following manuscript in your work if you have found ``pyani`` useful:

    Pritchard *et al.* (2016) "Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens" *Anal. Methods*, 2016, **8**, 12-24 DOI: 10.1039/C5AY02550H

.. code-block:: latex

    @Article{C5AY02550H,
    author ="<NAME>, <NAME>. and <NAME> <NAME>.",
    title  ="Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens",
    journal  ="Anal. Methods",
    year  ="2016",
    volume  ="8",
    issue  ="1",
    pages  ="12-24",
    publisher  ="The Royal Society of Chemistry",
    doi  ="10.1039/C5AY02550H",
    url  ="http://dx.doi.org/10.1039/C5AY02550H",
    abstract  ="Soft rot Enterobacteriaceae (SRE) are bacterial plant pathogens that cause blackleg{,} wilt and soft rot
    diseases on a broad range of important crop and ornamental plants worldwide. These organisms (spanning the genera Erwinia{,}
    Pectobacterium{,} Dickeya{,} and Pantoea) cause significant economic and yield losses in the field{,} and in storage. They
    are transmissible through surface water{,} by trade and other movement of plant material and soil{,} and in some cases are
    subject to international legislative and quarantine restrictions. Effective detection and diagnosis in support of food
    security legislation and epidemiology is dependent on the ability to classify pathogenic isolates precisely. Diagnostics and
    classification are made more difficult by the influence of horizontal gene transfer on phenotype{,} and historically complex
    and sometimes inaccurate nomenclatural and taxonomic assignments that persist in strain collections and online sequence
    databases. Here{,} we briefly discuss the relationship between taxonomy{,} genotype and phenotype in the SRE{,} and their
    implications for diagnostic testing and legislation. We present novel whole-genome classifications of the SRE{,}
    illustrating inconsistencies between the established taxonomies and evidence from completely sequenced isolates. We conclude
    with a perspective on the future impact of widespread whole-genome sequencing and classification methods on detection and
    identification of bacterial plant pathogens in support of legislative and policy efforts in food security."}


.. TIP::
    When citing ``pyani`` in your text, please consider quoting the precise release version (if you are using a specific release), or the specific commit hash (if you are using the 'bleeding-edge' development verison), e.g.

    ``"...using PYANI (v0.3.0)..."``

    or

    ``"...using PYANI (commit bb1cb5c)..."``

    This will enable precise reproduction of this part of your work by others.

-----------------------------
Publications citing ``pyani``
-----------------------------

If you are using ``pyani``, you are in good company. These authors and manuscripts have employed ``pyani`` to help with their whole-genome classification:

(If I've missed out your paper, please do put in a pull request on ``GitHub`` or get in touch and I'll be happy to add it!)

^^^^
2020
^^^^

* Albert *et al.* (2020) "Comparative Pangenomics of the Mammalian Gut Commensal *Bifidobacterium longum*" *Microorganisms* `doi:10.3390/microorganisms8010007 <https://doi.org/10.3390/microorganisms8010007>`_
* Bisanz *et al.* (2020) "A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria" *Cell Host & Microbe* `doi:10.1016/j.chom.2020.04.006 <https://doi.org/10.1016/j.chom.2020.04.006>`_
* Bridel *et al.* (2020) "Genetic diversity and population structure of *Tenacibaculum maritimum*, a serious bacterial pathogen of marine fish: from genome comparisons to high throughput MALDI-TOF typing" *Vet. Res.* `doi:10.1186/s13567-020-00782-0 <https://doi.org/10.1186/s13567-020-00782-0>`_
* Brock *et al.* (2020) "Endosymbiotic adaptations in three new bacterial species associated with *Dictyostelium discoideum*: *Paraburkholderia agricolaris* sp. nov., *Paraburkholderia hayleyella* sp. nov., and *Paraburkholderia bonniea* sp. nov" *PeerJ* `doi:10.7717/peerj.9151 <https://doi.org/10.7717/peerj.9151>`_
* Chibani *et al.* (2020) "Genomic variation among closely related *Vibrio alginolyticus* strains is located on mobile genetic elements" *BMC Genomics* `doi:10.1186/s12864-020-6735-5 <https://doi.org/10.1186/s12864-020-6735-5>`_
* Christman *et al.* (2020) "Novel clostridial lineages recovered from metagenomes of a hot oil reservoir" *Sci. Rep.* `doi:10.1038/s41598-020-64904-6 <https://doi.org/10.1038/s41598-020-64904-6>`_
* Cunningham-Oakes *et al.* (2020) "Genome Sequence of *Pluralibacter gergoviae* ECO77, a Multireplicon Isolate of Industrial Origin" *Microbiol. Res. Ann.* `doi:10.1128/MRA.01561-19 <https://doi.org/0.1128/MRA.01561-19>`_
* Dangel *et al.* (2020) "*Corynebacterium silvaticum* sp. nov., a unique group of NTTB corynebacteria in wild boar and roe deer" *Int. J. Syst. Evol. Microb.* `doi:10.1099/ijsem.0.004195 <https://doi.org/10.1099/ijsem.0.004195>`_
* Déraspe *et al.* (2020) "Genome Sequence of a *Klebsiella pneumoniae* NDM-1 Producer Isolated in Quebec City" *Microbiol. Resour. Announc.* `doi:10.1128/MRA.00829-19 <https://doi.org/10.1128/MRA.00829-19>`_
* France *et al.* (2020) "Complete Genome Sequences of Six *Lactobacillus iners* Strains Isolated from the Human Vagina" *Microbiol. Res. Ann.* `doi:10.1128/MRA.00234-20 <https://doi.org/10.1128/MRA.00234-20>`_
* Furrer *et al.* (2020) "Phage vB_BveM-Goe7 represents a new genus in the subfamily *Bastillevirinae*" *Arch. Virol.* `doi:10.1007/s00705-020-04546-1 <https://doi.org/10.1007/s00705-020-04546-1>`_
* Hempel *et al.* (2020) "Complete Genome Sequence of *Bacillus velezensis* Strain S4, Isolated from Biochar-Treated Soil" *Microbiol. Res. Ann.* `doi:10.1128/MRA.00352-20 <https://doi.org/10.1128/MRA.00352-20>`_
* Hinger *et al.* (2020) "Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus *Pseudovibrio* Suggest Distinct Evolutionary Trajectories and a Novel Genus, *Polycladidibacter* gen. nov." *Appl. Env. Microbiol.* `doi:10.1128/AEM.02395-19 <https://doi.org/10.1128/AEM.02395-19>`_
* Hollensteiner *et al.* (2020) "Genome Sequence of *Komagataeibacter saccharivorans* Strain JH1, Isolated from Fruit Flies" *Microbiol. Res. Announc.* `doi:10.1128/MRA.00098-20 <https://doi.org/10.1128/MRA.00098-20>`_
* Hulin *et al.* (2020) "Cherry picking by pseudomonads: after a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits" *Plant Pathology* `doi:10.1111/ppa.13189 <https://doi.org/10.1111/ppa.13189>`_
* <NAME> *et al.* (2020) "Genome comparison and transcriptome analysis of the invasive brown root rot pathogen, *Phellinus noxius*, from different geographic regions reveals potential enzymes associated with degradation of different wood substrates" *Fungal Biology* `doi:10.1016/j.funbio.2019.12.007 <https://doi.org/10.1016/j.funbio.2019.12.007>`_
* Inderbitzin *et al.* (2020) "Species identification in plant-associated prokaryotes and fungi using DNA" *Phytobiomes J.* `doi:10.1094/PBIOMES-12-19-0067-RVW <https://doi.org/10.1094/PBIOMES-12-19-0067-RVW">`_
* Joglekar *et al.* (2020) "Polyphasic analysis reveals correlation between phenotypic and genotypic analysis in soybean bradyrhizobia (*Bradyrhizobium* spp.)" *Syst. Appl. Microb.* `doi:10.1016/j.syapm.2020.126073 <https://doi.org/10.1016/j.syapm.2020.126073>`_
* Julian *et al.* (2020) "A simple, rapid typing method for *Streptococcus agalactiae* based on ribosomal subunit proteins by MALDI-TOF MS" *Sci. Reports* `doi:10.1038/s41598-020-65707-5 <https://doi.org/10.1038/s41598-020-65707-5>`_
* Jung *et al.* (2020) "Genome Analysis of *Enterococcus mundtii* Pe103, a Human Gut-Originated Pectinolytic Bacterium" *Curr. Microbiol.* `doi:10.1007/s00284-020-01932-5 <https://doi.org/10.1007/s00284-020-01932-5>`_
* Kim *et al.* (2020) "Genome analysis of *Lactobacillus plantarum* subsp. *plantarum* KCCP11226 reveals a well-conserved C30 carotenoid biosynthetic pathway" *3 Biotech.* `doi:10.1007/s13205-020-2149-y <https://doi.org/10.1007/s13205-020-2149-y>`_
* Kim *et al.* (2020) "Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in *Streptomyces venezuelae* Strains" *Biomolecules* `doi:10.3390/biom10060864 <https://doi.org/10.3390/biom10060864>`_
* Kuleshov *et al.* (2020) "Whole genome sequencing of *Borrelia miyamotoi* isolate Izh-4: reference for a complex bacterial genome" *BMC Genomics* `doi:10.1186/s12864-019-6388-4 <https://doi.org/10.1186/s12864-019-6388-4>`_
* Kumar *et al.* (2020) "Phylogenetic Relationship Among Brackishwater *Vibrio* Species" *Evol. Bioinf.* `doi:10.1177/1176934320903288 <https://doi.org/10.1177/1176934320903288>`_
* La China *et al.* (2020) "Genome sequencing and phylogenetic analysis of K1G4: a new *Komagataeibacter* strain producing bacterial cellulose from different carbon sources" *Biotech. Lett.* `doi:10.1007/s10529-020-02811-6 <https://doi.org/10.1007/s10529-020-02811-6>`_
* Lacault *et al.* (2020) "Zucchini vein clearing disease is caused by several lineages within *Pseudomonas syringae* species complex." *Phytopathology* `doi:10.1094/PHYTO-07-19-0266-R <https://doi.org/10.1094/PHYTO-07-19-0266-R>`_
* Liu *et al.* (2020) "Whole genome sequence and comparative genome analyses of multi-resistant *Staphylococcus warneri* GD01 isolated from a diseased pig in China" *PLoS One* `doi:10.1371/journal.pone.0233363 <https://doi.org/10.1371/journal.pone.0233363>`_
* Miyoshi *et al.* (2020) "Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis" *bioRxiv* `doi:10.1101/2020.03.11.987412 <https://doi.org/10.1101/2020.03.11.987412>`_
* Mu *et al.* (2020) "*Bradymonabacteria*, a novel bacterial predator with versatile survival strategies in saline environments" *Microbiome* `doi:10.21203/rs.2.20535/v1 <https://doi.org/10.21203/rs.2.20535/v1>`_
* Nilsson *et al.* (2020) "Diversity and Host Interactions Among Virulent and Temperate Baltic Sea *Flavobacterium* Phages" *Viruses* `doi:10.3390/v12020158 <https://doi.org/10.3390/v12020158>`_
* Norris *et al.* (2020) "*Acidithiobacillus ferrianus* sp. nov.: an ancestral extremely acidophilic and facultatively anaerobic chemolithoautotroph" *Extremophiles* `doi:0.1007/s00792-020-01157-1 <https://doi.org/0.1007/s00792-020-01157-1>`_
* Oshkin *et al.* (2020) "Pan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus" *Microorganisms* `doi:10.3390/microorganisms8050768 <https://doi.org/10.3390/microorganisms8050768>`_
* Pang *et al.* (2020) "The Genomic Context for the Evolution and Transmission of Community-Associated *Staphylococcus aureus* ST59 Through the Food Chain" *Front. Microbiol.* `doi:10.3389/fmicb.2020.00422 <https://doi.org/10.3389/fmicb.2020.00422>`_
* Pasanen *et al.* (2020) "*Pectobacterium parvum* sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence" *Int. J. Syst. Evol. Microb.* `doi:10.1099/ijsem.0.004057 <https://doi.org/10.1099/ijsem.0.004057>`_
* Rackaityte (2020) "Viable bacterial colonization is highly limited in the human intestine in utero" *Nature Medicine* `doi:10.1038/s41591-020-0761-3 <https://doi.org/10.1038/s41591-020-0761-3>`_
* Rothen *et al.* (2020) "A simple, rapid typing method for *Streptococcus agalactiae* based on ribosomal subunit proteins by MALDI-TOF MS" *Sci. Reports* `doi:10.1038/s41598-020-65707-5 <https://doi.org/10.1038/s41598-020-65707-5>`_
* Salgar-Chaparro *et al.* (2020) "Complete Genome Sequence of *Pseudomonas balearica* Strain EC28, an Iron-Oxidizing Bacterium Isolated from Corroded Steel" *Microbiol. Res. Ann.* `doi:10.1128/MRA.00275-20 <https://doi.org/10.1128/MRA.00275-20>`_
* Strang (2020) "Genomic Insights and Ecological Adaptations of Deep-Subsurface and Near Subsurface *Thermococcus* Isolates and Near Subsurface *Thermococcus* Isolates" *WWU Graduate School Collection* `https://cedar.wwu.edu/wwuet/926 <https://cedar.wwu.edu/wwuet/926>`_
* Thapa *et al.* (2020) "Genome‐wide analyses of Liberibacter species provides insights into evolution, phylogenetic relationships, and virulence factors" *Mol. Plant Path.* `doi:10.1111/mpp.12925  <https://doi.org/10.1111/mpp.12925>`_
* Tian *et al.* (2020) "LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa" *Nuc. Acids Res.* `doi:10.1093/nar/gkaa190 <https://doi.org/10.1093/nar/gkaa190>`_
* Tsukimi *et al.* (2020) "Draft Genome Sequences of *Bifidobacterium animalis* Consecutively Isolated from Healthy Japanese Individuals" *J. Genomics* `doi:10.7150/jgen.38516 <https://doi.org/10.7150/jgen.38516>`_
* Vijayan *et al.* (2020) "Bacteria known to induce settlement of larvae of *Hydroides elegans* are rare in natural inductive biofilm" *Aquatic Microb. Ecol.* `doi:10.3354/ame01925 <https://doi.org/10.3354/ame01925>`_
* Waleron *et al.* (2020) "*Arthrospiribacter ruber* gen. nov., sp. nov., a novel bacterium isolated from *Arthrospira* cultures" *Syst. Appl. Microbiol.* `doi:10.1016/j.syapm.2020.126072 <https://doi.org/10.1016/j.syapm.2020.126072>`_
* Wang *et al.* (2020) "Comparative Genomics Analysis of *Lactobacillus ruminis* from Different Niches" *Genes* `doi:10.3390/genes11010070 <https://doi.org/10.3390/genes11010070>`_<commit_msg>add five citations to docs<commit_after>.. _pyani-citations:

================
Citing ``pyani``
================

We would be grateful if you could please cite the following manuscript in your work if you have found ``pyani`` useful:

    Pritchard *et al.* (2016) "Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens" *Anal. Methods*, 2016, **8**, 12-24 DOI: 10.1039/C5AY02550H

.. code-block:: latex

    @Article{C5AY02550H,
    author ="<NAME> Glover, <NAME>. and Humphris, <NAME> Elphinstone, <NAME>. and Toth, <NAME>.",
    title  ="Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens",
    journal  ="Anal. Methods",
    year  ="2016",
    volume  ="8",
    issue  ="1",
    pages  ="12-24",
    publisher  ="The Royal Society of Chemistry",
    doi  ="10.1039/C5AY02550H",
    url  ="http://dx.doi.org/10.1039/C5AY02550H",
    abstract  ="Soft rot Enterobacteriaceae (SRE) are bacterial plant pathogens that cause blackleg{,} wilt and soft rot
    diseases on a broad range of important crop and ornamental plants worldwide. These organisms (spanning the genera Erwinia{,}
    Pectobacterium{,} Dickeya{,} and Pantoea) cause significant economic and yield losses in the field{,} and in storage. They
    are transmissible through surface water{,} by trade and other movement of plant material and soil{,} and in some cases are
    subject to international legislative and quarantine restrictions. Effective detection and diagnosis in support of food
    security legislation and epidemiology is dependent on the ability to classify pathogenic isolates precisely. Diagnostics and
    classification are made more difficult by the influence of horizontal gene transfer on phenotype{,} and historically complex
    and sometimes inaccurate nomenclatural and taxonomic assignments that persist in strain collections and online sequence
    databases. Here{,} we briefly discuss the relationship between taxonomy{,} genotype and phenotype in the SRE{,} and their
    implications for diagnostic testing and legislation. We present novel whole-genome classifications of the SRE{,}
    illustrating inconsistencies between the established taxonomies and evidence from completely sequenced isolates. We conclude
    with a perspective on the future impact of widespread whole-genome sequencing and classification methods on detection and
    identification of bacterial plant pathogens in support of legislative and policy efforts in food security."}


.. TIP::
    When citing ``pyani`` in your text, please consider quoting the precise release version (if you are using a specific release), or the specific commit hash (if you are using the 'bleeding-edge' development verison), e.g.

    ``"...using PYANI (v0.3.0)..."``

    or

    ``"...using PYANI (commit bb1cb5c)..."``

    This will enable precise reproduction of this part of your work by others.

-----------------------------
Publications citing ``pyani``
-----------------------------

If you are using ``pyani``, you are in good company. These authors and manuscripts have employed ``pyani`` to help with their whole-genome classification:

(If I've missed out your paper, please do put in a pull request on ``GitHub`` or get in touch and I'll be happy to add it!)

^^^^
2020
^^^^

* Albert *et al.* (2020) "Comparative Pangenomics of the Mammalian Gut Commensal *Bifidobacterium longum*" *Microorganisms* `doi:10.3390/microorganisms8010007 <https://doi.org/10.3390/microorganisms8010007>`_
* Bisanz *et al.* (2020) "A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria" *Cell Host & Microbe* `doi:10.1016/j.chom.2020.04.006 <https://doi.org/10.1016/j.chom.2020.04.006>`_
* Bridel *et al.* (2020) "Genetic diversity and population structure of *Tenacibaculum maritimum*, a serious bacterial pathogen of marine fish: from genome comparisons to high throughput MALDI-TOF typing" *Vet. Res.* `doi:10.1186/s13567-020-00782-0 <https://doi.org/10.1186/s13567-020-00782-0>`_
* Brock *et al.* (2020) "Endosymbiotic adaptations in three new bacterial species associated with *Dictyostelium discoideum*: *Paraburkholderia agricolaris* sp. nov., *Paraburkholderia hayleyella* sp. nov., and *Paraburkholderia bonniea* sp. nov" *PeerJ* `doi:10.7717/peerj.9151 <https://doi.org/10.7717/peerj.9151>`_
* Chibani *et al.* (2020) "Genomic variation among closely related *Vibrio alginolyticus* strains is located on mobile genetic elements" *BMC Genomics* `doi:10.1186/s12864-020-6735-5 <https://doi.org/10.1186/s12864-020-6735-5>`_
* Christman *et al.* (2020) "Novel clostridial lineages recovered from metagenomes of a hot oil reservoir" *Sci. Rep.* `doi:10.1038/s41598-020-64904-6 <https://doi.org/10.1038/s41598-020-64904-6>`_
* Cunningham-Oakes *et al.* (2020) "Genome Sequence of *Pluralibacter gergoviae* ECO77, a Multireplicon Isolate of Industrial Origin" *Microbiol. Res. Ann.* `doi:10.1128/MRA.01561-19 <https://doi.org/0.1128/MRA.01561-19>`_
* Damnjanovich *et al.* (2020) "Bacteriophage genotyping using BOXA repetitive-PCR" *BMC Microbiol.* `doi:10.1186/s12866-020-01770-2 <https://doi.org/10.1186/s12866-020-01770-2>`_
* Dangel *et al.* (2020) "*Corynebacterium silvaticum* sp. nov., a unique group of NTTB corynebacteria in wild boar and roe deer" *Int. J. Syst. Evol. Microb.* `doi:10.1099/ijsem.0.004195 <https://doi.org/10.1099/ijsem.0.004195>`_
* Déraspe *et al.* (2020) "Genome Sequence of a *Klebsiella pneumoniae* NDM-1 Producer Isolated in Quebec City" *Microbiol. Resour. Announc.* `doi:10.1128/MRA.00829-19 <https://doi.org/10.1128/MRA.00829-19>`_
* France *et al.* (2020) "Complete Genome Sequences of Six *Lactobacillus iners* Strains Isolated from the Human Vagina" *Microbiol. Res. Ann.* `doi:10.1128/MRA.00234-20 <https://doi.org/10.1128/MRA.00234-20>`_
* Furrer *et al.* (2020) "Phage vB_BveM-Goe7 represents a new genus in the subfamily *Bastillevirinae*" *Arch. Virol.* `doi:10.1007/s00705-020-04546-1 <https://doi.org/10.1007/s00705-020-04546-1>`_
* Hempel *et al.* (2020) "Complete Genome Sequence of *Bacillus velezensis* Strain S4, Isolated from Biochar-Treated Soil" *Microbiol. Res. Ann.* `doi:10.1128/MRA.00352-20 <https://doi.org/10.1128/MRA.00352-20>`_
* Hinger *et al.* (2020) "Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus *Pseudovibrio* Suggest Distinct Evolutionary Trajectories and a Novel Genus, *Polycladidibacter* gen. nov." *Appl. Env. Microbiol.* `doi:10.1128/AEM.02395-19 <https://doi.org/10.1128/AEM.02395-19>`_
* Hollensteiner *et al.* (2020) "Genome Sequence of *Komagataeibacter saccharivorans* Strain JH1, Isolated from Fruit Flies" *Microbiol. Res. Announc.* `doi:10.1128/MRA.00098-20 <https://doi.org/10.1128/MRA.00098-20>`_
* Hulin *et al.* (2020) "Cherry picking by pseudomonads: after a century of research on canker, genomics provides insights into the evolution of pathogenicity towards stone fruits" *Plant Pathology* `doi:10.1111/ppa.13189 <https://doi.org/10.1111/ppa.13189>`_
* <NAME> *et al.* (2020) "Genome comparison and transcriptome analysis of the invasive brown root rot pathogen, *Phellinus noxius*, from different geographic regions reveals potential enzymes associated with degradation of different wood substrates" *Fungal Biology* `doi:10.1016/j.funbio.2019.12.007 <https://doi.org/10.1016/j.funbio.2019.12.007>`_
* Inderbitzin *et al.* (2020) "Species identification in plant-associated prokaryotes and fungi using DNA" *Phytobiomes J.* `doi:10.1094/PBIOMES-12-19-0067-RVW <https://doi.org/10.1094/PBIOMES-12-19-0067-RVW">`_
* Joglekar *et al.* (2020) "Polyphasic analysis reveals correlation between phenotypic and genotypic analysis in soybean bradyrhizobia (*Bradyrhizobium* spp.)" *Syst. Appl. Microb.* `doi:10.1016/j.syapm.2020.126073 <https://doi.org/10.1016/j.syapm.2020.126073>`_
* Julian *et al.* (2020) "A simple, rapid typing method for *Streptococcus agalactiae* based on ribosomal subunit proteins by MALDI-TOF MS" *Sci. Reports* `doi:10.1038/s41598-020-65707-5 <https://doi.org/10.1038/s41598-020-65707-5>`_
* Jung *et al.* (2020) "Genome Analysis of *Enterococcus mundtii* Pe103, a Human Gut-Originated Pectinolytic Bacterium" *Curr. Microbiol.* `doi:10.1007/s00284-020-01932-5 <https://doi.org/10.1007/s00284-020-01932-5>`_
* Kim *et al.* (2020) "Genome analysis of *Lactobacillus plantarum* subsp. *plantarum* KCCP11226 reveals a well-conserved C30 carotenoid biosynthetic pathway" *3 Biotech.* `doi:10.1007/s13205-020-2149-y <https://doi.org/10.1007/s13205-020-2149-y>`_
* Kim *et al.* (2020) "Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in *Streptomyces venezuelae* Strains" *Biomolecules* `doi:10.3390/biom10060864 <https://doi.org/10.3390/biom10060864>`_
* Kuleshov *et al.* (2020) "Whole genome sequencing of *Borrelia miyamotoi* isolate Izh-4: reference for a complex bacterial genome" *BMC Genomics* `doi:10.1186/s12864-019-6388-4 <https://doi.org/10.1186/s12864-019-6388-4>`_
* Kumar *et al.* (2020) "Phylogenetic Relationship Among Brackishwater *Vibrio* Species" *Evol. Bioinf.* `doi:10.1177/1176934320903288 <https://doi.org/10.1177/1176934320903288>`_
* La China *et al.* (2020) "Genome sequencing and phylogenetic analysis of K1G4: a new *Komagataeibacter* strain producing bacterial cellulose from different carbon sources" *Biotech. Lett.* `doi:10.1007/s10529-020-02811-6 <https://doi.org/10.1007/s10529-020-02811-6>`_
* Lacault *et al.* (2020) "Zucchini vein clearing disease is caused by several lineages within *Pseudomonas syringae* species complex." *Phytopathology* `doi:10.1094/PHYTO-07-19-0266-R <https://doi.org/10.1094/PHYTO-07-19-0266-R>`_
* Liu *et al.* (2020) "Whole genome sequence and comparative genome analyses of multi-resistant *Staphylococcus warneri* GD01 isolated from a diseased pig in China" *PLoS One* `doi:10.1371/journal.pone.0233363 <https://doi.org/10.1371/journal.pone.0233363>`_
* Machado *et al.* (2020) "Molecular relationships of *Campomanesia xanthocarpa* within Myrtaceae based on the complete plastome sequence and on the plastid ycf2 gene" *Genet. Mol. Biol.* `doi:10.1590/1678-4685-gmb-2018-0377  <https://doi.org/10.1590/1678-4685-gmb-2018-0377>`_
* Miyoshi *et al.* (2020) "Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis" *bioRxiv* `doi:10.1101/2020.03.11.987412 <https://doi.org/10.1101/2020.03.11.987412>`_
* Mu *et al.* (2020) "*Bradymonabacteria*, a novel bacterial predator with versatile survival strategies in saline environments" *Microbiome* `doi:10.21203/rs.2.20535/v1 <https://doi.org/10.21203/rs.2.20535/v1>`_
* Nilsson *et al.* (2020) "Diversity and Host Interactions Among Virulent and Temperate Baltic Sea *Flavobacterium* Phages" *Viruses* `doi:10.3390/v12020158 <https://doi.org/10.3390/v12020158>`_
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