@PubMLST

Public databases for molecular typing and microbial genome diversity. Follow us now on https://nitter.cf/t.co/0eiWNkW7wY.

 Oxford, UK
pubmlst.org/
Joined June 2020
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  • Following182
  • Followers437
9Media
BIGSdb v1.47.0 has been released and is now live on @PubMLST. This introduces an embargo system for isolate submissions. If enabled, submitters will now see an option to request an embargo when they submit isolates.
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1st year PhD student @emPriyanshu with Sam Sheppard attended The 2nd IOI Oxbridge Cohort conference at Selwyn College, Cambridge @Cambridge_Uni @emPriyanshu talked about exploring Ribosomal protein as a plausible drug target. @IneosOxford @UniofOxford @OxfordBiology – at Cambridge, England
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Our 2018 paper describing PubMLST, the BIGSdb platform, and their applications has just reached 2000 citations on Google Scholar. ncbi.nlm.nih.gov/pmc/article…

Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their...

The PubMLST.org website hosts a collection of open-access, curated databases that integrate population sequence data with provenance and phenotype information for over 100 different microbial species...

pmc.ncbi.nlm.nih.gov
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Please note that PubMLST will be unavailable from Thursday 21 - Monday 25 March due to essential data centre maintenance. Normal service should resume on Tuesday 26 March.
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My first PhD paper is out - exploring mosaicism in the 𝑁𝑒𝑖𝑠𝑠𝑒𝑟𝑖𝑎 𝑝𝑒𝑛𝐴 gene at the population level! Very excited to share this work. Thanks are in order to @OdileHarrison and Martin Maiden @MaidenLab for their excellent supervision. microbiologyresearch.org/con…

Characterizing the diversity and commensal origins of penA mosaicism in the genus Neisseria

microbiologyresearch.org
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Yesterdays viva celebrations after completing my PhD with no corrections! #PhDone
Group of people sat round a table in a restaurant smiling

ALT Group of people sat round a table in a restaurant smiling

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BIGSdb v.1.42.6 has been released. This version expands list query functionality to every table in the database – previously it was only possible to use lists to search by attribute values for isolates, profiles and alleles for single loci.
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Come and do a PhD with me and Tim. It'll be fun, I promise! @Overtonlab @ChemEngBham @IMIBirmingham
Tim Overton@Overtonlab
3 Nov 2023
Fully-funded PhD position now recruiting as part of @MIBTP1 with me & @JessicaMABlair: efflux pumps are used by bacteria to confer antibiotic resistance, but can they be used to pump out organic chemicals and so improve industrial processes? @ChemEngBham warwick.ac.uk/fac/cross_fac/…
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We have had to implement rate-limiting on the PubMLST API. We have always requested that API calls are limited to no more than 4 concurrent connections. This is now enforced due to abuse and additional connections will automatically be rejected. pubmlst.org/api

PubMLST

Public databases for molecular typing and microbial genome diversity

pubmlst.org
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BIGSdb v1.42.5 has been released. This introduces a new plugin that provides a wrapper for ReporTree (pubmed.ncbi.nlm.nih.gov/3732…) – a tool for the automated identification of genetic clusters. BIGSdb powers all the databases on @PubMLST. github.com/kjolley/BIGSdb.
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I’d like to think PubMLST as a hub for data AND bioinformatic tools integration. This is one of the many examples. For my thesis, I found hicap very useful for Hinf serotype identification, and asked Keith’s help to do his magic so other users can easily access the tool ✨
Keith Jolley@keithajolley
10 Oct 2023
PubMLST now incorporates serotype identification using results from hicap (@stephen_watts & @DrKatHolt) in H. influenzae genome records. Example at pubmlst.org/bigsdb?page=info…. Overseen by @made__krisna.
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PubMLST now incorporates serotype identification using results from hicap (@stephen_watts & @DrKatHolt) in H. influenzae genome records. Example at pubmlst.org/bigsdb?page=info…. Overseen by @made__krisna.
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Short-term opportunity to work with me and amazing people in our Gastro Bioinfo Team at @UKHSA. Come join us for sequencing bacterial pathogens and diving into the world of gastro illness investigation. tinyurl.com/BioinfoGastro
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Had an amazing session at EduCon 2023 which was all about diversity and inclusivity in teaching. Had the honour to deliver a bioinformatics worship for beginners for implementation in undergraduate courses. #educon2023 #ASM2023
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Come and see the latest visual analytic developments on the PubMLST website at the #ABPHM23 bioinformatics showcase. youtu.be/mC22A4WYmhA
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Presenting one of my DPhil projects at @MaidenLab group: Development and Validation of Haemophilus influenzae core genome MLST scheme at @MicrobioSoc Annual Conference today as a Society Conference Grants recipient. P.S. The scheme has been implemented at @PubMLST too 😉
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pubmlst.org/organisms/bacter… 👇

PubMLST

Public databases for molecular typing and microbial genome diversity

pubmlst.org
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BIGSdb v1.41.2 has been released. This introduces a choice of 26 colour palettes for use on front-end and query dashboards that can be selected by users. BIGSdb powers all the databases on @PubMLST. github.com/kjolley/BIGSdb.
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A new database has been set up for Lactococcus garvieae to support the MLST scheme described in pubmed.ncbi.nlm.nih.gov/2439…. The database is curated by Guilherme Campos, Universidade Federal de Minas Gerais, Brazil. pubmlst.org/organisms/lactoc…
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New scheme available on PubMLST. 👇
Chrispin Chaguza@ChrispinChaguza
14 Dec 2022
Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis @AKalizangoma @B_KwambanaAdams @StephenBentley5 @johnlees6 @keithajolley @RHeyderman journals.asm.org/eprint/7SSY…
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